Q72498 (Q72498_9HIV1) Unreviewed, UniProtKB/TrEMBL

Names and origin

Protein names

Submitted name:
POL polyprotein EMBL AAB60572.1

Gene names

Name:

pol EMBL AAB60572.1

Organism

Human immunodeficiency virus 1 EMBL AAB60572.1

Taxonomic identifier

11676 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Lentivirus › Primate lentivirus group

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	1003 AA.
Sequence status	Fragment.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity

3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. SAAS SAAS001584 Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). SAAS SAAS000477 Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus. SAAS SAAS001584

Sequence similarities

Belongs to the retroviral Pol polyprotein family. RuleBase RU004064 Contains 1 RNase H domain. SAAS SAAS001584 Contains 1 integrase catalytic domain. SAAS SAAS000477 Contains 1 integrase-type DNA-binding domain. SAAS SAAS001584 Contains 1 integrase-type zinc finger. SAAS SAAS001584 Contains 1 peptidase A2 domain. SAAS SAAS001584 Contains 1 reverse transcriptase domain. RuleBase RU000322 SAAS SAAS001584

Ontologies

Keywords
Biological process	DNA integration DNA recombination SAAS SAAS000477 Viral genome integration SAAS SAAS001584 Virus entry into host cell
Domain	Zinc-finger SAAS SAAS001584
Ligand	DNA-binding SAAS SAAS001584 Metal-binding Zinc
Molecular function	Aspartyl protease SAAS SAAS001584 Endonuclease SAAS SAAS001584 Hydrolase Nuclease Nucleotidyltransferase Protease RNA-directed DNA polymerase SAAS SAAS000477 Transferase
Technical term	3D-structure PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQ9 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3AO3 PDB 3AO4 PDB 3AO1 PDB 3AO5 PDB 3OVN Multifunctional enzyme SAAS SAAS000477
Gene Ontology (GO)
Biological_process	DNA integration Inferred from electronic annotation. Source: UniProtKB-KW DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW RNA-dependent DNA replication Inferred from electronic annotation. Source: InterPro establishment of integrated proviral latency Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC proteolysis Inferred from electronic annotation. Source: UniProtKB-KW viral entry into host cell Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW aspartic-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease H activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Regions
	Region	802 – 803	2	Sucrose binding PDB 3AO5 PDB 3OVN
	Region	811 – 814	4	Sucrose binding PDB 3AO5 PDB 3OVN
Sites
	Binding site	818	1	Sucrose PDB 3AO5 PDB 3OVN
	Binding site	888	1	Sucrose PDB 3AO5 PDB 3OVN
Experimental info
	Non-terminal residue	1	1	EMBL AAB60572.1

Sequences

	Sequence		Length	Mass (Da)
	Q72498 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 4E67C747EED795C7	FASTA	1,003	113,720
	10 20 30 40 50 60 FFREDLAFPQ GKAREFSSEQ TRANSPTRRE LQVWGRDNNS LSEAGADRQG TVSFSFPQIT 70 80 90 100 110 120 LWQRPLVTIK IGGQLKEALL DTGADDTVLE EMNLPGRWKP KMIGGIGGFI KVRQYDQILI 130 140 150 160 170 180 EICGHKAIGT VLVGPTPVNI IGRNLLTQIG CTLNFPISPI ETVPVKLKPG MDGPKVKQWP 190 200 210 220 230 240 LTEEKIKALV EICTEMEKEG KISKIGPENP YNTPVFAIKK KDSTKWRKLV DFRELNKRTQ 250 260 270 280 290 300 DFWEVQLGIP HPAGLKQKKS VTVLDVGDAY FSVPLDKDFR KYTAFTIPSI NNETPGIRYQ 310 320 330 340 350 360 YNVLPQGWKG SPAIFQCSMT KILEPFRKQN PDVVIYQYMD DLYVGSDLEI GQHRTKIEEL 370 380 390 400 410 420 RQHLLRWGFT TPDKKHQKEP PFLWMGYELH PDKWTVQPIV LPEKDSWTVN DIQKLVGKLN 430 440 450 460 470 480 WASQIYAGIK VRQLCKLLRG TKALTEVVPL TEEAELELAE NREILKEPVH GVYYDPSKDL 490 500 510 520 530 540 IAEIQKQGQG QWTYQIYQEP FRNLKTGKYA RMKGAHTNDV KQLTEAVQKI ATESIVIWGK 550 560 570 580 590 600 TPKFKLPIQK ETWEAWWTEY WQATWIPEWE FVNTPPLVKL WYQLEKEPII GAETFYVDGA 610 620 630 640 650 660 ANRETKLGKA GYVTDRGRQK VVPLTDTTNQ KTELQAIHLA LQDSGLEVNI VTDSQYALGI 670 680 690 700 710 720 IQAQPDKSES ELVSQIIEQL IKKEKVYLAW VPAHKGIGGN EQVDKLVSAG IRKVLFLDGI 730 740 750 760 770 780 DKAQEEHEKY HSNWRAMASD FNLPPVVAKE IVASCDKCQL KGEAMHGQVD CSPGIWQLDC 790 800 810 820 830 840 THLEGKVILV AVHVASGYIE AEVIPAETGQ ETAYFLLKLA GRWPVKTVHT DNGSNFTSTT 850 860 870 880 890 900 VKAACWWAGI KQEFGIPYNP QSQGVIESMN KELKKIIGQV RDQAEHLKTA VQMAVFIHNF 910 920 930 940 950 960 KRKGGIGGYS AGERIVDIIA TDIQTKELQK QITKIQNFRV YYRDSRDPVW KGPAKLLWKG 970 980 990 1000 EGAVVIQDNS DIKVVPRRKA KIIRDYGKQM AGDDCVASRQ DED

References

[1]	"Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone." Adachi A., Gendelman H.E., Koenig S., Folks T., Willey R., Rabson A., Martin M.A. J. Virol. 59:284-291(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE. Strain: NL4-3 EMBL AAB60572.1.
[2]	"Recovery of virtually full-length HIV-1 provirus of diverse subtypes from primary virus cultures using the polymerase chain reaction." Salminen M.O., Koch C., Sanders-Buell E., Ehrenberg P.K., Michael N.L., Carr J.K., Burke D.S., McCutchan F.E. Virology 213:80-86(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE. Strain: NL4-3 EMBL AAB60572.1.
[3]	Salminen M.S. Submitted (MAY-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE. Strain: NL4-3 EMBL AAB60572.1.
[4]	"Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1." Wielens J., Headey S.J., Deadman J.J., Rhodes D.I., Le G.T., Parker M.W., Chalmers D.K., Scanlon M.J. ChemMedChem 6:258-261(2011) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 765-927.
[5]	"Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification?" Wielens J., Headey S.J., Rhodes D.I., Mulder R.J., Dolezal O., Deadman J.J., Newman J., Chalmers D.K., Parker M.W., Peat T.S., Scanlon M.J. J. Biomol. Screen. 18:147-159(2013) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 772-927.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U26942 Genomic DNA. Translation: AAB60572.1.

PIR

A47330.
B47330.
C47330.
D47330.
E47330.
F47330.
S32132.
S32140.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3AO1	X-ray	1.90	A/B	765-927	[»]
3AO3	X-ray	1.90	A/B	765-927	[»]
3AO4	X-ray	1.95	A/B	765-927	[»]
3AO5	X-ray	1.80	A/B	765-927	[»]
3OVN	X-ray	1.95	A/B	765-927	[»]
3VQ4	X-ray	1.90	A/B	772-927	[»]
3VQ5	X-ray	1.70	A/B	772-927	[»]
3VQ6	X-ray	1.80	A/B	772-927	[»]
3VQ7	X-ray	1.63	A/B	772-927	[»]
3VQ8	X-ray	1.60	A/B	772-927	[»]
3VQ9	X-ray	1.90	A/B/C	765-925	[»]
3VQA	X-ray	1.90	A/B	772-927	[»]
3VQB	X-ray	2.10	A/B	772-927	[»]
3VQC	X-ray	2.30	A/B	772-927	[»]
3VQD	X-ray	2.00	A/B	772-927	[»]
3VQE	X-ray	1.70	A/B	772-927	[»]
3VQP	X-ray	2.10	A/B	772-927	[»]
3VQQ	X-ray	2.00	A/B	772-927	[»]

ProteinModelPortal

Q72498.

ModBase

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Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

1.10.10.200. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.

InterPro

IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic.
IPR001969. Peptidase_aspartic_AS.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RVT.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view]

Pfam

PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF06815. RVT_connect. 1 hit.
PF06817. RVT_thumb. 1 hit.
[Graphical view]

SUPFAM

SSF50122. Integrase_C. 1 hit.
SSF46919. Integrase_Zn_N. 1 hit.
SSF50630. Pept_Aspartic. 1 hit.
SSF53098. RNaseH_fold. 2 hits.

PROSITE

PS50175. ASP_PROT_RETROV. 1 hit.
PS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]

ProtoNet

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Other

EvolutionaryTrace

Q72498.

Entry information

Entry name

Q72498_9HIV1

Accession

Primary (citable) accession number: Q72498

Entry history

Integrated into UniProtKB/TrEMBL:	November 1, 1996
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 113 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)