Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives
© Mueser et al; licensee BioMed Central Ltd. 2010
Received: 8 October 2010
Accepted: 3 December 2010
Published: 3 December 2010
The bacteriophage T4 encodes 10 proteins, known collectively as the replisome, that are responsible for the replication of the phage genome. The replisomal proteins can be subdivided into three activities; the replicase, responsible for duplicating DNA, the primosomal proteins, responsible for unwinding and Okazaki fragment initiation, and the Okazaki repair proteins. The replicase includes the gp43 DNA polymerase, the gp45 processivity clamp, the gp44/62 clamp loader complex, and the gp32 single-stranded DNA binding protein. The primosomal proteins include the gp41 hexameric helicase, the gp61 primase, and the gp59 helicase loading protein. The RNaseH, a 5' to 3' exonuclease and T4 DNA ligase comprise the activities necessary for Okazaki repair. The T4 provides a model system for DNA replication. As a consequence, significant effort has been put forth to solve the crystallographic structures of these replisomal proteins. In this review, we discuss the structures that are available and provide comparison to related proteins when the T4 structures are unavailable. Three of the ten full-length T4 replisomal proteins have been determined; the gp59 helicase loading protein, the RNase H, and the gp45 processivity clamp. The core of T4 gp32 and two proteins from the T4 related phage RB69, the gp43 polymerase and the gp45 clamp are also solved. The T4 gp44/62 clamp loader has not been crystallized but a comparison to the E. coli gamma complex is provided. The structures of T4 gp41 helicase, gp61 primase, and T4 DNA ligase are unknown, structures from bacteriophage T7 proteins are discussed instead. To better understand the functionality of T4 DNA replication, in depth structural analysis will require complexes between proteins and DNA substrates. A DNA primer template bound by gp43 polymerase, a fork DNA substrate bound by RNase H, gp43 polymerase bound to gp32 protein, and RNase H bound to gp32 have been crystallographically determined. The preparation and crystallization of complexes is a significant challenge. We discuss alternate approaches, such as small angle X-ray and neutron scattering to generate molecular envelopes for modeling macromolecular assemblies.
Bacteriophage T4 DNA Replication
The semi-conservative, semi-discontinuous process of DNA replication is conserved in all life forms. The parental anti-parallel DNA strands are separated and copied following hydrogen bonding rules for the keto form of each base as proposed by Watson and Crick . Progeny cells therefore inherit one parental strand and one newly synthesized strand comprising a new duplex DNA genome. Protection of the integrity of genomic DNA is vital to the survival of all organisms. In a masterful dichotomy, the genome encodes proteins that are also the caretakers of the genome. RNA can be viewed as the evolutionary center of this juxtaposition of DNA and protein. Viruses have also played an intriguing role in the evolutionary process, perhaps from the inception of DNA in primordial times to modern day lateral gene transfer. Simply defined, viruses are encapsulated genomic information. Possibly an ancient encapsulated virus became the nucleus of an ancient prokaryote, a symbiotic relationship comparable to mitochondria, as some have recently proposed [2–4]. This early relationship has evolved into highly complex eukaryotic cellular processes of replication, recombination and repair requiring multiple signaling pathways to coordinate activities required for the processing of complex genomes. Throughout evolution, these processes have become increasing complicated with protein architecture becoming larger and more complex. Our interest, as structural biologists, is to visualize these proteins as they orchestrate their functions, posing them in sequential steps to examine functional mechanisms. Efforts to crystallize proteins and protein:DNA complexes are hampered for multiple reasons, from limited solubility and sample heterogeneity to the fundamental lack of crystallizability due to the absence of complimentary surface contacts required to form an ordered lattice. For crystallographers, the simpler organisms provide smaller proteins with greater order which have a greater propensity to crystallize. Since the early days of structural biology, viral and prokaryotic proteins were successfully utilized as model systems for visualizing biological processes. In this review, we discuss our current progress to complete a structural view of DNA replication using the viral proteins encoded by bacteriophage T4 or its relatives.
DNA Replication Proteins Encoded by Bacteriophage T4
gp43 DNA polymerase
DNA directed 5' to 3' DNA polymerase
Polymerase clamp enhances processivity of gp43 polymerase and RNase H
clamp loader utilizes ATP to open and load the gp45 clamp
cooperative single stranded DNA binding protein assists in unwinding duplex
processive 5' to 3' replicative helicase
DNA dependent RNA polymerase generates lagging strand RNA pentamer primers in concert with gp41 helicase
helicase assembly protein required for loading the gp41 helicase in the presence of gp32 protein
Lagging strand repair
5' to 3' exonuclease cleaves Okazaki RNA primers
gp30 DNA ligase
ATP-dependent ligation of nicks after lagging strand gap repair
The bacteriophage T4 replisome can be subdivided into two components, the DNA replicase and the primosome. The DNA replicase is composed of the gene 43-encoded DNA polymerase (gp43), the gene 45 sliding clamp (gp45), the gene 44 and 62 encoded ATP-dependent clamp loader complex (gp44/62), and the gene 32 encoded single-stranded DNA binding protein (gp32) . The gp45 protein is a trimeric, circular molecular clamp that is equivalent to the eukaryotic processivity factor, proliferating cell nuclear antigen (PCNA) . The gp44/62 protein is an accessory protein required for gp45 loading onto DNA . The gp32 protein assists in the unwinding of DNA and the gp43 DNA polymerase extends the invading strand primer into the next genome, likely co-opting the E. coli gyrase (topo II) to reduced positive supercoiling ahead of the polymerase . The early stages of elongation involves replication of the leading strand template in which gp43 DNA polymerase can continuously synthesize a daughter strand in a 5' to 3' direction. The lagging strand requires segmental synthesis of Okazaki fragments which are initiated by the second component of the replication complex, the primosome. This T4 replicative complex is composed of the gp41 helicase and the gp61 primase, a DNA directed RNA polymerase . The gp41 helicase is a homohexameric protein that encompasses the lagging strand and traverses in the 5' to 3' direction, hydrolyzing ATP as it unwinds the duplex in front of the replisome . Yonesaki and Alberts demonstrated that gp41 helicase cannot load onto replication forks protected by the gp32 protein single-stranded DNA binding protein [13, 14]. The T4 gp59 protein is a helicase loading protein comparable to E. coli DnaC and is required for the loading of gp41 helicase if DNA is preincubated with the gp32 single-stranded DNA binding protein . We have shown that the gp59 protein preferentially recognizes branched DNA and Holliday junction architectures and can recruit gp32 single-strand DNA binding protein to the 5' arm of a short fork of DNA [16, 17]. The gp59 helicase loading protein also delays progression of the leading strand polymerase, allowing for the assembly and coordination of lagging strand synthesis. Once gp41 helicase is assembled onto the replication fork by gp59 protein, the gp61 primase synthesizes an RNA pentaprimer to initiate lagging strand Okazaki fragment synthesis. It is unlikely that the short RNA primer, in an A-form hybrid duplex with template DNA, would remain annealed in the absence of protein, so a hand-off from primase to either gp32 protein or gp43 polymerase is probably necessary .
Crystal Structures of the T4 DNA Replication Proteins
Proteins of the DNA Replication Fork and Protein Database (pdb) reference numbers.
T4 and Related Phage
Replicative DNA polymerase
gp43 polymerase (pdb 1ig9, 1clq, 1noy, 1ih7)
Gene 5 Polymerase (pdb 1t7p, 1skr, 1t8e, 1x9m)
Pol III (αεθ) (pdb 2hnh, 1ido)
Pol δ (subunits p125, p50, p66, p12) (pdb 3e0j)
gp45 protein (pdb 1czd, 1b8h)
E. coli Thioredoxin (pdb 1t7p, 1skr)
β (pdb 2pol)
PCNA (pdb 1plr, 1axc, 1ul1)
γ complex (γδδ'ψχ) (pdb 1jr3, 1jqj, 3glf)
RF-C (subunits p140, p40, p38, p37, p36) (pdb 1sxj)
ssDNA binding protein
gp32 protein (pdb 1gpc)
Gene 2.5 protein (pdb 1je5)
SSB (pdb 1qvc)
RP-A (subunits p14, p32, p70) (pdb 1fgu, 2b29, 1jmc, 1l1o, 2pi2)
Gene 4 helicase (pdb 1e0j, 1e0k, 1q57)
DnaB (pdb 1b79, 2r6a)
MCM (pdb 3f9v, 1ltl)
helicase assembly protein
gp59 protein (pdb 1c1k)
DnaC, PriA (pdb 3ec2)
Gene 4 primase (pdb 1nui, 1q57)
DnaG (pdb 1dd9, 3b39, 2r6c)
Pol α/primase (pdb 3flo)
5' to 3' Exonuclease
RNase H (pdb 1tfr, 2ihn)
Pol I N-domain
FEN-1, RNase H1 (pdb 1ul1, 2qk9)
DNA ligase 1
T4 ligase (gp30)
T7 ligase (pdb 1a0i)
DNA ligase (pdb 2owo)
DNA ligase I
Gene 43 DNA Polymerase
E. coli Pol I, the first DNA polymerase discovered by Kornberg, has three domains, an N-terminal 5' to 3' exonuclease (cleaved to create the Klenow fragment), a 3' to 5' editing exonuclease domain, and a C-terminal polymerase domain . The structure of the E. coli Pol I Klenow fragment was described through anthropomorphic terminology of fingers, palm, and thumb domains [39, 40]. The RB69 gp43 DNA polymerase has two active sites, the 3' to 5' exonuclease (residues 103 - 339) and the polymerase domain (residues 381 - 903), comparable to Klenow fragment domains . The gp43 DNA polymerase also has an N-terminal domain (residues 1 - 102 and 340 - 380) and a C-terminal tail containing a PCNA interacting peptide (PIP box) motif (residues 883 - 903) that interacts with the 45 sliding clamp protein. The polymerase domain contains a fingers subunit (residues 472 - 571) involved in template display (Ser 565, Lys 560, amd Leu 561) and NTP binding (Asn 564) and a palm domain (residues 381 - 471 and 572 - 699) which contains the active site, a cluster of aspartate residues (Asp 411, 621, 622, 684, and 686) that coordinates the two divalent active site metals (Figure 3B). The T4 gp43 DNA polymerase appears to be active in a monomeric form, however it has been suggested that polymerase dimerization is necessary to coordinate leading and lagging strand synthesis [6, 20].
Gene 45 Clamp
The gp45 related PCNA clamp proteins participate in many protein/DNA interactions including DNA replication, repair, and repair signaling proteins. A multitude of different proteins have been identified that contain a PCNA interaction protein box (PIP box) motif Qxxhxxaa where x is any residue, h is L, I or M, and a is aromatic . In T4, PIP box sequences have been identified in the C-terminal domain of gp43 DNA polymerase, mentioned above, and in the N-terminal domain of RNase H, discussed below. The C-terminal PIP box peptide from RB69 gp43 DNA polymerase has been co-crystallized with RB69 gp45 clamp protein (PDB 1b8h, Figures 3A and 3C) and allows modeling of the gp45 clamp and gp43 DNA polymerase complex (Figure 3A) . The gp45 clamp trails behind the 43 DNA polymerase, coupled through the gp43 C-terminal PIP box bound to a pocket on the outer surface of the gp45 clamp protein. Within RB69 gp45 clamp protein, the binding pocket is primarily hydrophobic (residues Tyr 39, Ile 107, Phe 109, Trp 199, and Val 217) with two basic residues (Arg 32 and Lys 204) interacting with the acidic groups in the PIP box motif. The rate of DNA synthesis, in the presence and absence of gp45 clamp protein, is approximately 400 nucleotides per second, indicating that the accessory gp45 clamp protein does not affect the enzymatic activity of the gp43 DNA polymerase . More discussion about the interactions between T4 gp43 polymerase and T4 gp45 clamp can be found in Geiduschek and Kassavetis, this series. While the gp45 clamp is considered to be a processivity factor, this function may be most prevalent when misincorporation occurs. When a mismatch is introduced, the template strand releases, activating the 3' to 5' exonuclease activity of the gp43 DNA polymerase. During the switch, gp45 clamp maintains the interaction between the replicase and DNA.
Gene 44/62 Clamp Loader
The mechanism for loading of the ring shaped PCNA clamps onto duplex DNA is a conundrum; imagine a magician's linking rings taken apart and reassembled without an obvious point for opening. The clamp loaders, the magicians opening the PCNA rings, belong to the AAA + ATPase family which include the E. coli gamma (γ) complex and eukaryotic replication factor C (RF-C) [44, 45]. The clamp loaders bind to the sliding clamps, open the rings through ATP hydrolysis, and then close the sliding clamps around DNA, delivering these ring proteins to initiating replisomes or to sites of DNA repair. The gp44 clamp loader protein (gi:5354262, NP_049665) is a 319 residue, two-domain, homotetrameric protein. The N-domain of gp44 clamp loader protein has a Walker A p-loop motif (residues 45-52, G TR GVGKT) . The gp62 clamp loader protein (gi:5354306, NP_049664) at 187 residues, is half the size of gp44 clamp loader protein and must be co-expressed with gp44 protein to form an active recombinant complex .
The T4 gp44/62 clamp loader complex is analogous to the E. coli heteropentameric γ complex (γ3δ'δ) and yeast RF-C despite an almost complete lack of sequence homology with these clamp loaders . The yeast p36, p37, and p40 subunits of RF-C are equivalent to the E. coli γ, yeast p38 subunit is equivalent to δ', and yeast p140 subunit is equivalent to δ. The T4 homotetrameric gp44 clamp loader protein is equivalent to the E. coli γ3δ' and T4 gp62 clamp loader is equivalent to the E. coli δ. The first architectural view of clamp loaders came from the collaborative efforts of John Kuriyan and Mike O'Donnell who have completed crystal structures of several components of the E. coli Pol III holoenzyme including the ψ-χ complex (PDB 1em8), the β-δ complex (PDB 1jqj) and the full γ complex γ3δ'δ (PDB 1jr3, Figure 4B) [48–50]. More recently, the yeast RF-C complex has been solved (PDB 1sxj) . Mechanisms of all clamp loaders are likely very similar, therefore comparison of T4 gp44/62 clamp loader protein with the E. coli model system is most appropriate. The E. coli γ3δ', referred to as the motor/stator (equivalent to T4 gp44 clamp loader protein), binds and hydrolyzes ATP, while the δ subunit, known as the wrench (equivalent to T4 gp62 clamp loader protein), binds to the β clamp (T4 gp45 clamp protein). The E. coli γ complex is comparable in size to the E. coli β clamp and the two proteins interact face to face, with one side of the β clamp dimer interface bound to the δ (wrench) subunit, and the other positioned against the δ' (stator). Upon hydrolysis of ATP, the γ (motor) domains rotate, the δ subunit pulls on one side of a β clamp interface as the δ' subunit pushes against the other side of the β clamp, resulting in ring opening. For the T4 system, interaction with DNA and the presence of the gp43 DNA polymerase releases the gp45 clamp from the gp44/62 clamp loader. In the absence of gp43 DNA polymerase, the gp44/62 clamp loader complex becomes a clamp unloader. Current models of the E. coli Pol III holoenzyme have leading and lagging strand synthesis coordinated with a single clamp loader coupled to two DNA polymerases through the τ subunit and to single-stranded DNA binding protein through the χ subunit . There are no T4 encoded proteins that are comparable to E. coli τ or χ.
Gene 32 Single-Stranded DNA Binding Protein
Single-stranded DNA binding proteins have an oligonucleotide-oligosaccharide binding fold (OB fold), an open curved antiparallel β-sheet [52, 53]. The aromatic residues within the OB fold stack with bases, thereby reducing the rate of spontaneous deamination of single-stranded DNA . The OB fold is typically lined with basic residues for interaction with the phosphate backbone to increase stability of the interaction. Cooperative binding of ssb proteins assists in unwinding the DNA duplex at replication forks, recombination intermediates, and origins of replication. The T4 gp32 single-stranded DNA binding protein (gi:5354247, NP_049854) is a 301 residue protein consisting of three domain. The N-terminal basic B-domain (residues 1 - 21) is involved in cooperative interactions, likely through two conformations. In the absence of DNA, the unstructured N-terminal domain interferes with the protein multimerization. In the presence of DNA, the lysine residues within the N-terminal peptide presumably interact with the phosphate backbone of DNA. Organization of the gp32 N-terminus by DNA creates the cooperative binding site for assembly of gp32 ssb filaments.
Gene 41 Helicase
The replicative helicase family of enzymes, which includes bacteriophages T4 gp41 helicase and T7 gene 4 helicase, E. coli DnaB, and the eukaryotic MCM proteins, are responsible for the unwinding of duplex DNA in front of the leading strand replisome . The T4 gp41 protein (gi:9632635, NP_049654) is the 475 residue helicase subunit of the primase(gp61)-helicase(gp41) complex and a member of the p-loop NTPase family of proteins . Similar to other replicative helicases, the gp41 helicase assembles by surrounding the lagging strand and excluding the leading strand of DNA. ATP hydrolysis translocates the enzyme 5' to 3' along the lagging DNA strand, thereby unwinding the DNA duplex approximately one base pair per hydrolyzed ATP molecule. Efforts to crystallize full length or truncated gp41 helicase individually, in complex with nucleotide analogs, or in complex with other T4 replication proteins have not been successful in part due to the limited solubility of this protein. In addition, the protein is a heterogeneous mixture of dimers, trimers and hexamers, according to dynamic light scattering measurements. The solubility of T4 41 helicase can be improved to greater than 40 mg/ml of homogenous hexamers by eliminating salt and using buffer alone (10 mM TAPS pH 8.5) . However, the low ionic strength crystal screen does not produce crystals . To understand the T4 gp41 helicase, we must therefore look to related model systems.
Like T4 41 helicase, efforts to crystallize E. coli DnaB have met with minimal success. Thus far only a fragment of the non-hexameric N-terminal domain (PDB 1b79) has been crystallized successfully for structural determinations . More recently, thermal stable eubacteria (Bacillus and Geobacillus stearothermophilis) have been utilized by the Steitz lab to yield more complete structures of the helicase-primase complex (PDB 2r6c and 2r6a, respectively) . A large central opening in the hexamer appears to be the appropriate size for enveloping single-stranded DNA, as it is too small for duplex DNA. Collaborative efforts between the Wigley and Ellenberger groups revealed the hexameric structure of T7 gene 4 helicase domain alone (residues 261 - 549, PDB 1eOk) and in complex with a non-hydrolyzable ATP analog (PDB 1e0h) . Interestingly, the central opening in the T7 gene 4 helicase hexamer is smaller than other comparable helicase, suggesting that a fairly large rearrangement is necessary to accomplish DNA binding. A more complete structure from the Ellenberger lab of T7 gene 4 helicase that includes a large segment of the N-terminal primase domain (residues 64 - 566) reveals a heptameric complex with a larger central opening (Figure 5B) . Both the eubacterial and bacteriophage helicase have similar α/β folds. The C-terminal Rec A like domain follows 6-fold symmetry and has nucleotide binding sites at each interface. In the eubacterial structures, the helical N-domains alternate orientation and follow a three-fold symmetry with domain swapping. The T4 gp41 helicase is a hexameric two-domain protein with Walker A p-loop motif (residues 197 - 204, G VNVGKS) located at the beginning of the conserved NTPase domain (residues 170 - 380), likely near the protein:protein interfaces, similar to the T7 helicase structure.
Gene 59 Helicase Assembly Protein
The progression of the DNA replisome is restricted in the absence of either gp32 ssb protein or the gp41 helicase . In the presence of gp32 ssb protein, loading of the gp41 helicase is inhibited. In the absence of gp32 ssb protein, the addition of gp41 helicase improves the rate of DNA synthesis but displays a significant lag prior to reaching maximal DNA synthesis . The gp59 helicase loading protein (gi:5354296, NP_049856) is a 217 residue protein that alleviates the lag phase of gp41 helicase [13, 14]. In the presence gp32 ssb protein, the loading of gp41 helicase requires gp59 helicase loading protein. This activity is similar to the E. coli DnaC loading of DnaB helicase [70, 71]. Initially, 59 helicase loading protein was thought to be a single-stranded DNA binding protein that competes with 32 ssb protein on the lagging strand [13, 72]. In that model, the presence of gp59 protein within the gp32 filament presumably created a docking site for gp41 helicase. However, the gp59 helicase loading protein is currently known to have more specific binding affinity for branched and Holliday junctions [16, 17]. This activity is comparable to the E. coli replication rescue protein, PriA, which was first described as the PAS recognition protein (n' protein) in φX174 phage replication . Using short pseudo-Y junction DNA substrates, gp59 helicase loading protein has been shown to recruit gp32 ssb protein to the 5' (lagging strand) arm, a scenario relevant to replication fork assembly .
The high-resolution crystal structure of 59 helicase loading protein reveals a two-domain, α-helical structure that has no obvious cleft for DNA binding . The E. coli helicase loader, DnaC, is also a two domain protein. However, the C-terminal domain of DnaC is an AAA + ATPase related to DnaA, as revealed by the structure of a truncated DnaC from Aquifex aeolicus (pdb 3ec2) . The DnaC N-domain interacts with the hexameric DnaB in a one-to-one ratio forming a second hexameric ring. Sequence alignments of gp59 helicase loading protein reveal an "ORFaned" (orphaned open reading frame) protein; a protein that is unique to the T-even and other related bacteriophages [4, 17]. Interestingly, searches for structural alignments of the gp59 protein, using both Dali  and combinatorial extension , have revealed partial homology with the eukaryotic high mobility group 1A (HMG1A) protein, a nuclear protein involved in chromatin remodeling . Using the HMG1A:DNA structure as a guide, we have successfully modeled gp59 helicase assembly protein bound to a branched DNA substrate which suggests a possible mode of cooperative interaction with 32 ssb protein (Figure 5C) . Attempts to co-crystallize gp59 protein with DNA, or with gp41 helicase, or with gp32 ssb constructs have all been unsuccessful. The 59 helicase assembly protein combined with 32(-B) ssb protein yields a homogenous solution of heterodimers, amenable for small angle X-ray scattering analysis (Hinerman, unpublished data).
Gene 61 Primase
The gp61 DNA dependent RNA polymerase (gi:5354295, NP_049648) is a 348 residue enzyme that is responsible for the synthesis of short RNA primers used to initiate lagging strand DNA synthesis. In the absence of gp41 helicase and gp32 ssb proteins, the gp61 primase synthesizes ppp(Pu)pC dimers that are not recognized by DNA polymerase [79, 80]. A monomer of gp61 primase and a hexamer of gp41 helicase are essential components of the initiating primosome [63, 81]. Each subunit of the hexameric gp41 helicase has the ability to bind a gp61 primase. Higher occupancies of association have been reported but physiological relevance is unclear [82, 83]. When associated with gp41 helicase, the gp61 primase synthesizes pentaprimers that begin with 5'-pppApC onto template 3'-TG; a very short primer that does not remain annealed in the absence of protein . An interaction between gp32 ssb protein and gp61 primase likely coordinates the handoff of the RNA primer to the gp43 DNA polymerase, establishing a synergy between leading strand progression and lagging strand synthesis . The gp32 ssb protein will bind to single-stranded DNA unwound by gp41 helicase. This activity inhibits the majority of 3'-TG template sites for gp61 primase and therefore increases the size of Okazaki fragments . Activity of gp61 primase is obligate to the activity of the gp41 helicase. The polymerase accessory proteins, gp45 clamp and gp44/62 clamp loader, are essential for primer synthesis when DNA is covered by gp32 ssb protein . Truncation of 20 amino acids from the C-terminus of gp41 helicase protein retains interaction with gp61 primase but eliminates gp45 clamp and gp44/62 clamp loader stimulation of primase activity .
The gp61 primase contains an N-terminal zinc finger DNA binding domain (residues cys 37, 40, 65, and 68) and a central toprim catalytic core domain (residues 179 - 208) [87, 88]. Crystallization trials of full length gp61 primase and complexes with gp41 helicase have been unsuccessful. Publication of a preliminary crystallization report of gp61 primase C-terminal domain (residues 192 - 342) was limited in resolution, and a crystal structure has not yet been published . A structure of the toprim core fragment of E. coli DnaG primase (residues 110 to 433 of 582) has been solved, concurrently by the Berger and Kuriyan labs (PDB 1dd9, ) (PDB 1eqn, ). To accomplish this, the N-terminal Zn finger and the C-terminal DnaB interacting domain were removed. More recently, this same DnaG fragment has been resolved in complex with single-stranded DNA revealing a binding track adjacent to the toprim domain (PDB 3b39, ). Other known primase structures include the Stearothermophilis enzymes solved in complex with helicase (discussed above) and the primase domain of T7 gene 4 primase (PDB 1nui) (Figure 5D) . The primase domain of T7 gene 4 is comprised of the N-terminal Zn finger (residues 1 - 62) and toprim domain (residues 63 - 255). This structure is actually a primase-helicase fusion protein.
Okazaki Repair Proteins
RNase H, 5' to 3' exonuclease
The processivity of RNase H exonuclease activity is enhanced by the gp32 ssb protein. Protein interactions can be abrogated by mutations in the C-terminal domain of RNase H  and within the core domain of gp32 ssb protein (Mueser, unpublished data). Full length gp32 ssb protein and RNase H do not interact in the absence of DNA substrate. Removal of the N-terminal peptide of gp32 ssb protein (gp32(-B)), responsible for gp32 ssb cooperativity, yields a protein that has high affinity for RNase H. It is likely that the reorganization of gp32 B-domain when bound to DNA reveals a binding site for RNase H and therefore helps to coordinate 5'-3' primer removal after extension by the DNA polymerase. This is compatible with the model proposed for the cooperative self assembly of gp32 protein. The structure of RNase H in complex with gp32(-B) has been solved using X-ray crystallography and small angle X-ray scattering (Mueser, unpublished data) (Figure 6C). The gp45 clamp protein enhances the processivity of RNase H on nicked and flap DNA substrates . Removal of the N-terminal peptide of RNase H eliminates the interaction between RNase H and gp45 clamp protein and decreases processivity of RNase H. The structure of the N-terminal peptide of RNase H in complex with gp45 clamp protein reveals that binding occurs within the gp45 clamp PIP-box motif of RNase H (Devos, unpublished data).
Sequence alignment of T4 RNase H reveals membership to a highly conserved family of nucleases that includes yeast rad27, rad2, human FEN-1, and xeroderma pigmentosa group G (XPG) proteins. The domain structure of both FEN-1 and XPG proteins is designated N, I, and C . The yeast rad2 and human XPG proteins are much larger than the yeast rad27 and human FEN-1 proteins. This is due to a large insertion in the middle of rad2 and XPG proteins between the N and I domains. The N and I domains are not separable in the T4 RNase H protein as the N-domain forms part of the α/β structure responsible for fork binding and half of the active site. The I domain is connected to the N-domain by a bridge region above the active site which is unstructured in the presence of active site metals and DNA substrate. It is this region that corresponds with the position of the large insertions of rad2 and XPG. Curiously, this bridge region of T4 RNase H becomes a highly ordered a-helical structure in the absence of metals. Arg and Lys residues are interdigitated between the active site Asp groups within the highly ordered structure (Mueser, unpublished data). The I domain encompasses the remainder of the larger α/β subdomain and the α-helical H3TH motif responsible for duplex binding. The C-domain is truncated at the helical cap that interacts with gp32 ssb and the PIP motif is located in the N-terminus of T4 RNase H. In the FEN-1 family of proteins, the C-domain, located opposite the H3TH domain, contains a helical cap and an unstructured C-terminal PIP-box motif for interaction with a PCNA clamp.
Gene 30 DNA Ligase
The T4 gp30 protein (gi: 5354233, NP_049813) is best known as T4 DNA ligase, a 487 residue ATP-dependent ligase. DNA ligases repair nicks in double-stranded DNA containing 3' OH and 5' phosphate ends. Ligases are activated by the covalent modification of a conserved lysine with AMP donated by NADH or ATP. The conserved lysine and the nucleotide binding site reside in the adenylation domain (NTPase domain) of ligases. Sequence alignment of the DNA ligase family Motif 1 (K XDGXR) within the adenylation domain identifies Lys 159 in T4 DNA ligase (159 K ADGAR 164) as the moiety for covalent modification . The bacterial ligases are NADH-dependent, while all eukaryotic enzymes are ATP-dependent . Curiously, T4 phage, whose existence is confined within a prokaryote, encodes an ATP-dependent ligase. During repair, the AMP group from the activated ligase is transferred to the 5' phosphate of the DNA nick. This activates the position for condensation with the 3' OH, releasing AMP in the reaction. The T4 ligase has been cloned, expressed, and purified but attempts to crystallize T4 ligase, with and without cofactor, have not been successful. The structure of the bacteriophage T7 ATP-dependent ligase has been solved (PDB 1a0i, Figure 6C) [98, 99], which has a similar fold to T4 DNA ligase . The minimal two-domain structure of the 359 residue T7 ligase has a large central cleft, with the larger N-terminal adenylation domain containing the cofactor binding site and a C-terminal OB domain. In contrast, the larger 671 residue E. coli DNA ligase has five domains; the N-terminal adenylation and OB fold domains, similar to T7 and T4 ligase, including a Zn finger, HtH and BRCT domains present in the C-terminal half of the protein . Sequence alignment of DNA ligases indicate that the highly conserved ligase signature motifs reside in the central DNA binding cleft, the active site lysine, and the nucleotide binding site . Recently, the structure of NAD-dependent E. coli DNA ligase has been solved in complex with nicked DNA containing an adenylated 5' PO4 (pdb 2owo) . This flexible, multidomain ligase encompasses the duplex DNA with the adenylation domain binding to the nick; a binding mode also found in the human DNA ligase 1 bound to nicked DNA (pdb 1x9n) . T4 DNA ligase is used routinely in molecular cloning for repairing both sticky and blunt ends. The smaller two-domain structure of T4 DNA ligase has lower affinity for DNA than the multidomain ligases. The lack of additional domains to encompass the duplex DNA likely explains the sensitivity of T4 ligase activity to salt concentration.
Conclusion and Future Directions of Structural Analysis
The bacteriophage T4 model system has been an invaluable resource for investigating fundamental aspects of DNA replication. The phage DNA replication system has been reconstituted for both structural and enzymatic studies. For example, the in vitro rates and fidelity of DNA synthesis are equivalent to those measured in vivo. These small, compact proteins define the minimal requirements for enzymatic activity and are the most amenable to structural studies. The T4 DNA replication protein structures reveal the basic molecular requirements for DNA synthesis. These structures, combined with those from other systems, allow us to create a visual image of the complex process of DNA replication.
Macromolecular crystallography is a biophysical technique that is now available to any biochemistry enabled laboratory. Dedicated crystallographers are no longer essential; a consequence of advances in technology. Instead, biologists and biochemists utilize the technique to compliment their primary research. In the past, the bottleneck to determining X-ray structures was data collection and analysis. Over the past two decades, multiple wavelength anomalous dispersion phasing (MAD phasing) has been accompanied by the adaptation of charge-coupled device (CCD) cameras for rapid data collection, and the construction of dedicated, tunable X-ray sources at the National Laboratory facilities such as the National Synchrotron Light Source (NSLS) at Brookhaven National Labs (BNL), the Advanced Light Source (ALS) at Lawrence Berkeley National Labs (LBNL), and the Advanced Photon Source (APS) at Argonne National Labs (ANL). These advances have transformed crystallography to a fairly routine experimental procedure. Today, many of these national facilities provide mail-in service with robotic capability for remote data collection, eliminating the need for expensive in-house equipment. The current bottle neck for protein crystallography has shifted into the realm of molecular cloning and protein purification of macromolecules amenable to crystallization. Even this aspect of crystallography has been commandeered by high throughput methods as structural biology centers attempt to fill "fold space".
A small investment in crystallization tools, by an individual biochemistry research lab, can take advantage of the techniques of macromolecular crystallography. Dedicated suppliers (e.g. Hampton Research) sell crystal screens and other tools for the preparation, handling, and cryogenic preservation of crystals, along with web-based advice. The computational aspects of crystallography are simplified and can operate on laptop computers using open access programs. Data collection and reduction software are typically provided by the beam lines. Suites of programs such as CCP4  and PHENIX [104, 105] provide data processing, phasing, and model refinement. Visualization software has been dominated in recent years by the Python  based programs COOT  for model building and PYMOL, developed by the late Warren DeLano, for the presentation of models for publication. In all, a modest investment in time and resources can convert any biochemistry lab into a structural biology lab.
What should independent structural biology research labs focus on, in the face of competition from high throughput centers? A promising frontier is the visualization of complexes, exemplified by the many protein:DNA complexes with known structures. A multitude of transient interactions occur during DNA replication and repair, a few of these have been visualized in the phage-encoded DNA replication system. The RB69 gp43 polymerase has been crystallized in complex with DNA, and with gp32 ssb as a fusion protein [36, 108]. The gp45 clamp bound with PIP box motif peptides have been used to model the gp43:gp45 interaction . The bacteriophage T4 RNase has been solved in complex with a fork DNA substrate and in complex with gp32 for modeling of the RNaseH:gp32:DNA ternary complex. These few successes required investigation of multiple constructs to obtain a stable, homogeneous complex, therefore indicating that the probability for successful crystallization of protein:DNA constructs can be significantly lower than for solitary protein domains.
Small angle X-ray and Neutron scattering
Thankfully, the inability to crystallize complexes does not preclude structure determination. Multiple angle and dynamic light scattering techniques (MALS and DLS, respectively) use wavelengths of light longer than the particle size. This allows the determination of the size and shape of macromolecular complex. Higher energy light with wavelengths significantly shorter than the particle size provides sufficient information to generate a molecular envelope comparable to those manifested from cryoelectron microscopy image reconstruction. Small angle scattering techniques including X-ray (SAXS) and neutron (SANS) are useful for characterizing proteins and protein complexes in solution. These low-resolution techniques provide information about protein conformation (folded, partially folded and unfolded), aggregation, flexibility, and assembly of higher-ordered protein oligomers and/or complexes . The scattering intensity of biological macromolecules in solution is equivalent to momentum transfer q = [4π sin θ/λ], where 2θ is the scattering angle and λ is the wavelength of the incident X-ray beam. Larger proteins will have a higher scattering intensity (at small angles) compared to smaller proteins or buffer alone. Small angle neutron scattering is useful for contrast variation studies of protein-DNA and protein-RNA complexes (using deuterated components) . The contrast variation method uses the neutron scattering differences between hydrogen isotopes. For specific ratios of D2O to H2O in the solvent, the scattering contribution from DNA, RNA, or perdeuterated protein becomes negligible. This allows for the determination of spatial arrangement of components within the macromolecular complex . There are dedicated SAXS beamlines available at NSLS and LBNL. Neutron studies, almost non-existent in the US in the 1990's, have made a comeback with the recent commissioning of the Spallation Neutron Source (SNS) and the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL) to compliment the existing facility at the National Institute of Standards and Technology (NIST). The bombardment by neutrons is harmless to biological molecules, unlike high energy X-rays that induce significant damage to molecules in solution.
To conduct a scattering experiment, the protein samples should be monodisperse and measurements at different concentrations used to detect concentration-dependent aggregation. The scattering intensity from buffer components is subtracted from the scattering intensity of the protein sample, producing a 1-D scattering curve that is used for data analysis. These corrected scattering curves are evaluated using programs such as GNOM and PRIMUS, components of the ATSAS program suite . Each program allows the determination of the radius of gyration (RG), maximum particle distance, and molecular weight of the species in solution as well as the protein conformation. The 1-D scattering profiles are utilized to generate 3-D models. There are several methods of generating molecular envelopes including ab initio reconstruction (GASBOR, DAMMIN, GA_STRUCT), models based on known atomic structure (SASREF, MASSHA, CRYSOL), and a combination of ab initio/atomic structure models (CREDO, CHADD, GLOOPY). The ab initio programs use simulated annealing and dummy atoms or dummy atom chains to generate molecular envelopes, while structural-based modeling programs, like SASREF, use rigid-body modeling to orient the known X-ray structures into the experimental scattering intensities (verified by comparing experimental scattering curves to theoretical scattering curves). We have used these programs to generate molecular envelopes for the RNaseH:gp32(-B) complex and for the gp59:gp32(-B) complexes. The high resolution crystal structures of the components can be placed into the envelopes to model the complex.
Advanced Light Source
Argonne National Labs
Advanced Photon Source
Brookhaven National Labs
Charge coupled device
Dynamic light scattering
High Flux Isotope Reactor
Lawrence Berkeley National Labs
Multiple wavelength anomalous dispersion
Multiple angle light scattering
National Institute for Standards and Technology
National Synchrotron Light Source
- OB fold:
Oligonucleotide-oligosaccharide binding fold
Oak Ridge National Laboratory
Proliferating cell nuclear antigen
- PIP box:
PCNA interaction protein box
Replication factor - C
Small angle X-ray scattering
Small angle neutron scattering
Spallation Neutron Source
single-stranded DNA binding
The authors wish to thank Dr. Leif Hanson for helpful suggestions. We also wish to dedicate this review to the memory of Dr. Nancy G. Nossal.
- Watson JD, Crick FH: The structure of DNA. Cold Spring Harb Symp Quant Biol 1953, 18: 123-131.PubMed
- Bell PJ: Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus? J Mol Evol 2001, 53: 251-256. 10.1007/s002390010215PubMed
- Bell PJ: The viral eukaryogenesis hypothesis: a key role for viruses in the emergence of eukaryotes from a prokaryotic world environment. Ann N Y Acad Sci 2009, 1178: 91-105. 10.1111/j.1749-6632.2009.04994.xPubMed
- Koonin EV, Senkevich TG, Dolja VV: The ancient Virus World and evolution of cells. Biol Direct 2006, 1: 29. 10.1186/1745-6150-1-29PubMedPubMed Central
- Kornberg A, Baker TA: DNA Replication. Second edition. New York: W.H. Freeman and Company; 1992.
- Nossal NG: The Bacteriophage T4 DNA Replication Fork. Washington, D.C.: American Society for Microbiology; 1994.
- Mosig G: Recombination and recombination-dependent DNA replication in bacteriophage T4. Annu Rev Genet 1998, 32: 379-413. 10.1146/annurev.genet.32.1.379PubMed
- Yao N, Turner J, Kelman Z, Stukenberg PT, Dean F, Shechter D, Pan ZQ, Hurwitz J, O'Donnell M: Clamp loading, unloading and intrinsic stability of the PCNA, beta and gp45 sliding clamps of human, E. coli and T4 replicases. Genes Cells 1996, 1: 101-113. 10.1046/j.1365-2443.1996.07007.xPubMed
- Venkatesan M, Nossal NG: Bacteriophage T4 gene 44/62 and gene 45 polymerase accessory proteins stimulate hydrolysis of duplex DNA by T4 DNA polymerase. J Biol Chem 1982, 257: 12435-12443.PubMed
- Karam JD, Konigsberg WH: DNA polymerase of the T4-related bacteriophages. Prog Nucleic Acid Res Mol Biol 2000, 64: 65-96. full_textPubMed
- Venkatesan M, Silver LL, Nossal NG: Bacteriophage T4 gene 41 protein, required for the synthesis of RNA primers, is also a DNA helicase. J Biol Chem 1982, 257: 12426-12434.PubMed
- Young MC, Schultz DE, Ring D, von Hippel PH: Kinetic parameters of the translocation of bacteriophage T4 gene 41 protein helicase on single-stranded DNA. J Mol Biol 1994, 235: 1447-1458. 10.1006/jmbi.1994.1100PubMed
- Barry J, Alberts B: Purification and characterization of bacteriophage T4 gene 59 protein. A DNA helicase assembly protein involved in DNA replication. J Biol Chem 1994, 269: 33049-33062.PubMed
- Yonesaki T: The purification and characterization of gene 59 protein from bacteriophage T4. J Biol Chem 1994, 269: 1284-1289.PubMed
- Benkovic SJ, Valentine AM, Salinas F: Replisome-mediated DNA replication. Annu Rev Biochem 2001, 70: 181-208. 10.1146/annurev.biochem.70.1.181PubMed
- Jones CE, Mueser TC, Dudas KC, Kreuzer KN, Nossal NG: Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: a versatile couple with roles in replication and recombination. Proc Natl Acad Sci USA 2001, 98: 8312-8318. 10.1073/pnas.121009398PubMedPubMed Central
- Mueser TC, Jones CE, Nossal NG, Hyde CC: Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 A resolution crystal structure reveals a novel alpha-helical two-domain fold. J Mol Biol 2000, 296: 597-612. 10.1006/jmbi.1999.3438PubMed
- Nelson SW, Kumar R, Benkovic SJ: RNA primer handoff in bacteriophage T4 DNA replication: the role of single-stranded DNA-binding protein and polymerase accessory proteins. J Biol Chem 2008, 283: 22838-22846. 10.1074/jbc.M802762200PubMedPubMed Central
- Chastain PD, Makhov AM, Nossal NG, Griffith JD: Analysis of the Okazaki fragment distributions along single long DNAs replicated by the bacteriophage T4 proteins. Mol Cell 2000, 6: 803-814. 10.1016/S1097-2765(05)00093-6PubMed
- Salinas F, Benkovic SJ: Characterization of bacteriophage T4-coordinated leading- and lagging-strand synthesis on a minicircle substrate. Proc Natl Acad Sci USA 2000, 97: 7196-7201. 10.1073/pnas.97.13.7196PubMedPubMed Central
- Sinha NK, Morris CF, Alberts BM: Efficient in vitro replication of double-stranded DNA templates by a purified T4 bacteriophage replication system. J Biol Chem 1980, 255: 4290-4293.PubMed
- Gangisetty O, Jones CE, Bhagwat M, Nossal NG: Maturation of bacteriophage T4 lagging strand fragments depends on interaction of T4 RNase H with T4 32 protein rather than the T4 gene 45 clamp. J Biol Chem 2005, 280: 12876-12887. 10.1074/jbc.M414025200PubMed
- Bhagwat M, Hobbs LJ, Nossal NG: The 5'-exonuclease activity of bacteriophage T4 RNase H is stimulated by the T4 gene 32 single-stranded DNA-binding protein, but its flap endonuclease is inhibited. J Biol Chem 1997, 272: 28523-28530. 10.1074/jbc.272.45.28523PubMed
- Hollingsworth HC, Nossal NG: Bacteriophage T4 encodes an RNase H which removes RNA primers made by the T4 DNA replication system in vitro. J Biol Chem 1991, 266: 1888-1897.PubMed
- Hobbs LJ, Nossal NG: Either bacteriophage T4 RNase H or Escherichia coli DNA polymerase I is essential for phage replication. J Bacteriol 1996, 178: 6772-6777.PubMedPubMed Central
- Weiss B, Richardson CC: Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. Proc Natl Acad Sci USA 1967, 57: 1021-1028. 10.1073/pnas.57.4.1021PubMedPubMed Central
- Nossal NG, Hinton DM, Hobbs LJ, Spacciapoli P: Purification of bacteriophage T4 DNA replication proteins. Methods Enzymol 1995, 262: 560-584. full_textPubMed
- Mueser TC, Nossal NG, Hyde CC: Structure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins. Cell 1996, 85: 1101-1112. 10.1016/S0092-8674(00)81310-0PubMed
- Moarefi I, Jeruzalmi D, Turner J, O'Donnell M, Kuriyan J: Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage. J Mol Biol 2000, 296: 1215-1223. 10.1006/jmbi.1999.3511PubMed
- Nolan JM, Petrov V, Bertrand C, Krisch HM, Karam JD: Genetic diversity among five T4-like bacteriophages. Virol J 2006, 3: 30. 10.1186/1743-422X-3-30PubMedPubMed Central
- Shamoo Y, Steitz TA: Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell 1999, 99: 155-166. 10.1016/S0092-8674(00)81647-5PubMed
- Wang J, Sattar AK, Wang CC, Karam JD, Konigsberg WH, Steitz TA: Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69. Cell 1997, 89: 1087-1099. 10.1016/S0092-8674(00)80296-2PubMed
- Shamoo Y, Friedman AM, Parsons MR, Konigsberg WH, Steitz TA: Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA. Nature 1995, 376: 362-366. 10.1038/376362a0PubMed
- Frey MW, Nossal NG, Capson TL, Benkovic SJ: Construction and characterization of a bacteriophage T4 DNA polymerase deficient in 3'-->5' exonuclease activity. Proc Natl Acad Sci USA 1993, 90: 2579-2583. 10.1073/pnas.90.7.2579PubMedPubMed Central
- Nossal NG: A new look at old mutants of T4 DNA polymerase. Genetics 1998, 148: 1535-1538.PubMedPubMed Central
- Franklin MC, Wang J, Steitz TA: Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 2001, 105: 657-667. 10.1016/S0092-8674(01)00367-1PubMed
- Spicer EK, Rush J, Fung C, Reha-Krantz LJ, Karam JD, Konigsberg WH: Primary structure of T4 DNA polymerase. Evolutionary relatedness to eucaryotic and other procaryotic DNA polymerases. J Biol Chem 1988, 263: 7478-7486.PubMed
- Yeh LS, Hsu T, Karam JD: Divergence of a DNA replication gene cluster in the T4-related bacteriophage RB69. J Bacteriol 1998, 180: 2005-2013.PubMedPubMed Central
- Freemont PS, Friedman JM, Beese LS, Sanderson MR, Steitz TA: Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc Natl Acad Sci USA 1988, 85: 8924-8928. 10.1073/pnas.85.23.8924PubMedPubMed Central
- Steitz TA, Beese L, Freemont PS, Friedman JM, Sanderson MR: Structural studies of Klenow fragment: an enzyme with two active sites. Cold Spring Harb Symp Quant Biol 1987, 52: 465-471.PubMed
- Wang CC, Yeh LS, Karam JD: Modular organization of T4 DNA polymerase. Evidence from phylogenetics. J Biol Chem 1995, 270: 26558-26564. 10.1074/jbc.270.44.26558PubMed
- Tabor S, Huber HE, Richardson CC: Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7. J Biol Chem 1987, 262: 16212-16223.PubMed
- Moldovan GL, Pfander B, Jentsch S: PCNA, the maestro of the replication fork. Cell 2007, 129: 665-679. 10.1016/j.cell.2007.05.003PubMed
- Davey MJ, Jeruzalmi D, Kuriyan J, O'Donnell M: Motors and switches: AAA + machines within the replisome. Nat Rev Mol Cell Biol 2002, 3: 826-835. 10.1038/nrm949PubMed
- Jeruzalmi D, O'Donnell M, Kuriyan J: Clamp loaders and sliding clamps. Curr Opin Struct Biol 2002, 12: 217-224. 10.1016/S0959-440X(02)00313-5PubMed
- Janzen DM, Torgov MY, Reddy MK: In vitro reconstitution of the bacteriophage T4 clamp loader complex (gp44/62). J Biol Chem 1999, 274: 35938-35943. 10.1074/jbc.274.50.35938PubMed
- Bowman GD, O'Donnell M, Kuriyan J: Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Nature 2004, 429: 724-730. 10.1038/nature02585PubMed
- Gulbis JM, Kazmirski SL, Finkelstein J, Kelman Z, O'Donnell M, Kuriyan J: Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex. Eur J Biochem 2004, 271: 439-449. 10.1046/j.1432-1033.2003.03944.xPubMed
- Jeruzalmi D, O'Donnell M, Kuriyan J: Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III. Cell 2001, 106: 429-441. 10.1016/S0092-8674(01)00463-9PubMed
- Jeruzalmi D, Yurieva O, Zhao Y, Young M, Stewart J, Hingorani M, O'Donnell M, Kuriyan J: Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell 2001, 106: 417-428. 10.1016/S0092-8674(01)00462-7PubMed
- O'Donnell M, Jeruzalmi D, Kuriyan J: Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC. Curr Biol 2001, 11: R935-946.PubMed
- Bochkarev A, Bochkareva E: From RPA to BRCA2: lessons from single-stranded DNA binding by the OB-fold. Curr Opin Struct Biol 2004, 14: 36-42. 10.1016/j.sbi.2004.01.001PubMed
- Theobald DL, Mitton-Fry RM, Wuttke DS: Nucleic acid recognition by OB-fold proteins. Annu Rev Biophys Biomol Struct 2003, 32: 115-133. 10.1146/annurev.biophys.32.110601.142506PubMedPubMed Central
- Lindahl T: Instability and decay of the primary structure of DNA. Nature 1993, 362: 709-715. 10.1038/362709a0PubMed
- Villemain JL, Giedroc DP: The N-terminal B-domain of T4 gene 32 protein modulates the lifetime of cooperatively bound Gp32-ss nucleic acid complexes. Biochemistry 1996, 35: 14395-14404. 10.1021/bi961482nPubMed
- Villemain JL, Ma Y, Giedroc DP, Morrical SW: Mutations in the N-terminal cooperativity domain of gene 32 protein alter properties of the T4 DNA replication and recombination systems. J Biol Chem 2000, 275: 31496-31504. 10.1074/jbc.M002902200PubMed
- Krassa KB, Green LS, Gold L: Protein-protein interactions with the acidic COOH terminus of the single-stranded DNA-binding protein of the bacteriophage T4. Proc Natl Acad Sci USA 1991, 88: 4010-4014. 10.1073/pnas.88.9.4010PubMedPubMed Central
- Wold MS: Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu Rev Biochem 1997, 66: 61-92. 10.1146/annurev.biochem.66.1.61PubMed
- Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L: Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 1997, 385: 176-181. 10.1038/385176a0PubMed
- Pfuetzner RA, Bochkarev A, Frappier L, Edwards AM: Replication protein A. Characterization and crystallization of the DNA binding domain. J Biol Chem 1997, 272: 430-434. 10.1074/jbc.272.1.430PubMed
- Savvides SN, Raghunathan S, Futterer K, Kozlov AG, Lohman TM, Waksman G: The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA. Protein Sci 2004, 13: 1942-1947. 10.1110/ps.04661904PubMedPubMed Central
- von Hippel PH, Delagoutte E: A general model for nucleic acid helicases and their "coupling" within macromolecular machines. Cell 2001, 104: 177-190. 10.1016/S0092-8674(01)00203-3PubMed
- Dong F, von Hippel PH: The ATP-activated hexameric helicase of bacteriophage T4 (gp41) forms a stable primosome with a single subunit of T4-coded primase (gp61). J Biol Chem 1996, 271: 19625-19631. 10.1074/jbc.271.32.19625PubMed
- Collins BK, Tomanicek SJ, Lyamicheva N, Kaiser MW, Mueser TC: A preliminary solubility screen used to improve crystallization trials: crystallization and preliminary X-ray structure determination of Aeropyrum pernix flap endonuclease-1. Acta Crystallogr D Biol Crystallogr 2004, 60: 1674-1678. 10.1107/S090744490401844XPubMed
- Izaac A, Schall CA, Mueser TC: Assessment of a preliminary solubility screen to improve crystallization trials: uncoupling crystal condition searches. Acta Crystallogr D Biol Crystallogr 2006, 62: 833-842. 10.1107/S0907444906018385PubMed
- Fass D, Bogden CE, Berger JM: Crystal structure of the N-terminal domain of the DnaB hexameric helicase. Structure 1999, 7: 691-698. 10.1016/S0969-2126(99)80090-2PubMed
- Bailey S, Eliason WK, Steitz TA: Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase. Science 2007, 318: 459-463. 10.1126/science.1147353PubMed
- Singleton MR, Sawaya MR, Ellenberger T, Wigley DB: Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell 2000, 101: 589-600. 10.1016/S0092-8674(00)80871-5PubMed
- Toth EA, Li Y, Sawaya MR, Cheng Y, Ellenberger T: The crystal structure of the bifunctional primase-helicase of bacteriophage T7. Mol Cell 2003, 12: 1113-1123. 10.1016/S1097-2765(03)00442-8PubMed
- Wahle E, Lasken RS, Kornberg A: The dnaB-dnaC replication protein complex of Escherichia coli. II. Role of the complex in mobilizing dnaB functions. J Biol Chem 1989, 264: 2469-2475.PubMed
- Wahle E, Lasken RS, Kornberg A: The dnaB-dnaC replication protein complex of Escherichia coli. I. Formation and properties. J Biol Chem 1989, 264: 2463-2468.PubMed
- Lefebvre SD, Wong ML, Morrical SW: Simultaneous interactions of bacteriophage T4 DNA replication proteins gp59 and gp32 with single-stranded (ss) DNA. Co-modulation of ssDNA binding activities in a DNA helicase assembly intermediate. J Biol Chem 1999, 274: 22830-22838. 10.1074/jbc.274.32.22830PubMed
- Jones JM, Nakai H: PriA and phage T4 gp59: factors that promote DNA replication on forked DNA substrates microreview. Mol Microbiol 2000, 36: 519-527. 10.1046/j.1365-2958.2000.01888.xPubMed
- Jones CE, Mueser TC, Nossal NG: Interaction of the bacteriophage T4 gene 59 helicase loading protein and gene 41 helicase with each other and with fork, flap, and cruciform DNA. J Biol Chem 2000, 275: 27145-27154.PubMed
- Mott ML, Erzberger JP, Coons MM, Berger JM: Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell 2008, 135: 623-634. 10.1016/j.cell.2008.09.058PubMedPubMed Central
- Holm L, Sander C: Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995, 20: 478-480. 10.1016/S0968-0004(00)89105-7PubMed
- Shindyalov IN, Bourne PE: A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res 2001, 29: 228-229. 10.1093/nar/29.1.228PubMedPubMed Central
- Bianchi ME, Agresti A: HMG proteins: dynamic players in gene regulation and differentiation. Curr Opin Genet Dev 2005, 15: 496-506. 10.1016/j.gde.2005.08.007PubMed
- Nossal NG, Hinton DM: Bacteriophage T4 DNA primase-helicase. Characterization of the DNA synthesis primed by T4 61 protein in the absence of T4 41 protein. J Biol Chem 1987, 262: 10879-10885.PubMed
- Hinton DM, Nossal NG: Bacteriophage T4 DNA primase-helicase. Characterization of oligomer synthesis by T4 61 protein alone and in conjunction with T4 41 protein. J Biol Chem 1987, 262: 10873-10878.PubMed
- Jing DH, Dong F, Latham GJ, von Hippel PH: Interactions of bacteriophage T4-coded primase (gp61) with the T4 replication helicase (gp41) and DNA in primosome formation. J Biol Chem 1999, 274: 27287-27298. 10.1074/jbc.274.38.27287PubMed
- Valentine AM, Ishmael FT, Shier VK, Benkovic SJ: A zinc ribbon protein in DNA replication: primer synthesis and macromolecular interactions by the bacteriophage T4 primase. Biochemistry 2001, 40: 15074-15085. 10.1021/bi0108554PubMed
- Norcum MT, Warrington JA, Spiering MM, Ishmael FT, Trakselis MA, Benkovic SJ: Architecture of the bacteriophage T4 primosome: electron microscopy studies of helicase (gp41) and primase (gp61). Proc Natl Acad Sci USA 2005, 102: 3623-3626. 10.1073/pnas.0500713102PubMedPubMed Central
- Cha TA, Alberts BM: Effects of the bacteriophage T4 gene 41 and gene 32 proteins on RNA primer synthesis: coupling of leading- and lagging-strand DNA synthesis at a replication fork. Biochemistry 1990, 29: 1791-1798. 10.1021/bi00459a018PubMed
- Richardson RW, Nossal NG: Characterization of the bacteriophage T4 gene 41 DNA helicase. J Biol Chem 1989, 264: 4725-4731.PubMed
- Richardson RW, Nossal NG: Trypsin cleavage in the COOH terminus of the bacteriophage T4 gene 41 DNA helicase alters the primase-helicase activities of the T4 replication complex in vitro. J Biol Chem 1989, 264: 4732-4739.PubMed
- Aravind L, Leipe DD, Koonin EV: Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res 1998, 26: 4205-4213. 10.1093/nar/26.18.4205PubMedPubMed Central
- Ilyina TV, Gorbalenya AE, Koonin EV: Organization and evolution of bacterial and bacteriophage primase-helicase systems. J Mol Evol 1992, 34: 351-357. 10.1007/BF00160243PubMed
- Korndorfer IP, Salerno J, Jing D, Matthews BW: Crystallization and preliminary X-ray analysis of a bacteriophage T4 primase fragment. Acta Crystallogr D Biol Crystallogr 2000, 56: 95-97. 10.1107/S0907444999014225PubMed
- Keck JL, Roche DD, Lynch AS, Berger JM: Structure of the RNA polymerase domain of E. coli primase. Science 2000, 287: 2482-2486. 10.1126/science.287.5462.2482PubMed
- Podobnik M, McInerney P, O'Donnell M, Kuriyan J: A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases. J Mol Biol 2000, 300: 353-362. 10.1006/jmbi.2000.3844PubMed
- Corn JE, Pelton JG, Berger JM: Identification of a DNA primase template tracking site redefines the geometry of primer synthesis. Nat Struct Mol Biol 2008, 15: 163-169. 10.1038/nsmb.1373PubMed
- Bhagwat M, Meara D, Nossal NG: Identification of residues of T4 RNase H required for catalysis and DNA binding. J Biol Chem 1997, 272: 28531-28538. 10.1074/jbc.272.45.28531PubMed
- Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser TC: Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates. J Biol Chem 2007, 282: 31713-31724. 10.1074/jbc.M703209200PubMed
- Harrington JJ, Lieber MR: Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes Dev 1994, 8: 1344-1355. 10.1101/gad.8.11.1344PubMed
- Lindahl T, Barnes DE: Mammalian DNA ligases. Annu Rev Biochem 1992, 61: 251-281. 10.1146/annurev.bi.61.070192.001343PubMed
- Shuman S: DNA ligases: progress and prospects. J Biol Chem 2009, 284: 17365-17369. 10.1074/jbc.R900017200PubMedPubMed Central
- Subramanya HS, Doherty AJ, Ashford SR, Wigley DB: Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 1996, 85: 607-615. 10.1016/S0092-8674(00)81260-XPubMed
- Doherty AJ, Ashford SR, Subramanya HS, Wigley DB: Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization. J Biol Chem 1996, 271: 11083-11089. 10.1074/jbc.271.52.33242PubMed
- Shuman S, Schwer B: RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases. Mol Microbiol 1995, 17: 405-410. 10.1111/j.1365-2958.1995.mmi_17030405.xPubMed
- Nandakumar J, Nair PA, Shuman S: Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate. Mol Cell 2007, 26: 257-271. 10.1016/j.molcel.2007.02.026PubMed
- Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T: Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 2004, 432: 473-478. 10.1038/nature03082PubMed
- Collaborative Computational Project N: The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994, 50: 760-763. 10.1107/S0907444994003112
- Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, et al.: Automated structure solution with the PHENIX suite. Methods Mol Biol 2008, 426: 419-435. full_textPubMed
- Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC: PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 2002, 58: 1948-1954. 10.1107/S0907444902016657PubMed
- Sanner MF: Python: a programming language for software integration and development. J Mol Graph Model 1999, 17: 57-61.PubMed
- Emsley P, Cowtan K: Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004, 60: 2126-2132. 10.1107/S0907444904019158PubMed
- Sun S, Geng L, Shamoo Y: Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity. Proteins 2006, 65: 231-238. 10.1002/prot.21088PubMed
- Svergun DI, Petoukhov MV, Koch MH: Determination of domain structure of proteins from X-ray solution scattering. Biophys J 2001, 80: 2946-2953. 10.1016/S0006-3495(01)76260-1PubMedPubMed Central
- Niimura N: Neutrons expand the field of structural biology. Curr Opin Struct Biol 1999, 9: 602-608. 10.1016/S0959-440X(99)00012-3PubMed
- Koch MH, Vachette P, Svergun DI: Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev Biophys 2003, 36: 147-227. 10.1017/S0033583503003871PubMed
- Konarev PV, Petoukhov MV, Volkov VV, Svergun DI: ATSAS 2.1, a program package for small-angle scattering data analysis. Journal of Applied Crystallography 2006, 39: 277-286. 10.1107/S0021889806004699
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.