Imperfect DNA mirror repeats in the gag gene of HIV-1 (HXB2) identify key functional domains and coincide with protein structural elements in each of the mature proteins

Lang, Dorothy M

doi:10.1186/1743-422X-4-113

Virology Journal

Table 8 mIMRs and rdIMRs that are ≥66% symmetric

From: Imperfect DNA mirror repeats in the gag gene of HIV-1 (HXB2) identify key functional domains and coincide with protein structural elements in each of the mature proteins

	mIMR DNA		mIMR AA		Protein function	rdIMR AA
len	begin	end	begin	end		begin	end
37	1158	1194	386	398	1st cys-his box
37	1314	1350	438	450	p1-p6 cleavage site F449..L450	440	445
36	1087	1122	362	374	p2 helix, most of p2 A364..M377	364	373
36	1349	1384	450	461	L domain P455..P459	448	456
30	74	103	25	34	residues essential to binding to cell membrane	25	36
28	1302	1329	434	443	most of p1 F433..F448	436	442
27	17	43	6	14	myristoylation	8	13
26	562	587	187	196	bridges CA H3 and CA H4 helices	189	195
25	322	346	107	115	part of MA H5 helix T97..A120	107	113
25	478	502	159	167	bridges CA H1 and CA H2 helices
25	734	758	245	253	bridges CA H6 helix and downstream B-sheet
25	930	954	310	318	CA H9 helix, endocytosis signal T311..Q324	310	318
25	1022	1046	341	349	CA H11 helix L343..C350	343	351
25	1404	1428	468	476	T471A mutation leads to incomplete separation from host cell membrane
24	356	379	119	126	labile structure at end of MA	123	128
24	838	861	279	287	required for dimer interface	278	284
24	1146	1169	382	390	g helix, near start p7
23	772	794	257	265	CA H7, potential NEC cleavage site	256	268
23	1189	1211	396	404	1st cys-his box
22	1253	1274	418	425	2cd cys-his box	416	427
21	1	21	0	7	minimum signal required for myristoylation	0	7
21	268	288	89	96	loop with highly variable charge btwn MA H4-H5	90	100
21	361	381	120	127	near end of MA	123	128
21	1238	1258	413	419	2cd cys-his box C412..H421	406	421
21	1274	1294	425	431	ends at p7-p1 cleavage site N432..F433	426	433
20	990	1009	330	336	CA H10 helix, endocytosis signal P328..L337	426	433
19	63	81	21	27	basic residues essential to binding P23..H33	23	33
19	159	177	53	59	MA H3 helix, mutations affect virus assembly	51	57
19	192	210	64	70	MA H3 helix, mutations affect virus assembly	62	71
19	305	323	102	108	part of MA H5 helix, potential PDZ domain binding
19	956	974	319	325	CA H9 helix, endocytosis signal Q311..Q324	316	323
19	1060	1078	353	359	G-rich segment at end CA
19	1427	1445	476	482	end of Gag-PolTF	476	481
18	468	485	156	162	CA H1 helix
18	541	558	180	186	CA H3 helix, D184 essential to mature capsid
18	886	903	295	301	MHR	299	306
18	919	936	306	312	deletion causes major defect in particle formation	304	310
18	956	973	319	324	CA H9 helix, endocytosis signal T311..Q324	316	323
18	1389	1406	463	469	ubiquitin-gag conjugates found L449..Q500	460	470
18	1461	1478	487	493	vpr packaging L489..F493	487	493

Increased stringency for symmetry results in substantial overlap of mIMRs and rdIMRs. Many of the mIMRs listed in this table are relatively short and therefore do not appear in Tables 3, 4 or 5.

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ISSN: 1743-422X

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