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Q72498

- Q72498_9HIV1

UniProt

Q72498 - Q72498_9HIV1

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Protein
Submitted name:

POL polyprotein

Gene

pol

Organism
Human immunodeficiency virus 1
Status
Unreviewed - Annotation score: 2 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic activityi

3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.SAAS annotation
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).SAAS annotation
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 annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi780 – 7801Cadmium 1Imported
Metal bindingi780 – 7801Cadmium 2Imported
Metal bindingi782 – 7821Cadmium 1; via tele nitrogenImported
Metal bindingi807 – 8071Cadmium 1Imported
Metal bindingi807 – 8071Cadmium 2Imported
Binding sitei818 – 8181SucroseImported
Metal bindingi831 – 8311Cadmium 2Imported
Binding sitei888 – 8881SucroseImported

GO - Molecular functioni

  1. aspartic-type endopeptidase activity Source: UniProtKB-KW
  2. DNA binding Source: UniProtKB-KW
  3. RNA-directed DNA polymerase activity Source: UniProtKB-KW
  4. RNA-DNA hybrid ribonuclease activity Source: InterPro
  5. zinc ion binding Source: InterPro

GO - Biological processi

  1. DNA integration Source: UniProtKB-KW
  2. DNA recombination Source: UniProtKB-KW
  3. establishment of integrated proviral latency Source: UniProtKB-KW
  4. viral entry into host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Aspartyl proteaseSAAS annotation, EndonucleaseSAAS annotation, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymeraseSAAS annotation, Transferase

Keywords - Biological processi

DNA integration, DNA recombinationSAAS annotation, Viral genome integrationSAAS annotation, Virus entry into host cell

Keywords - Ligandi

DNA-bindingSAAS annotation, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Submitted name:
POL polyproteinImported
Gene namesi
Name:polImported
OrganismiHuman immunodeficiency virus 1Imported
Taxonomic identifieri11676 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiHomo sapiens (Human) [TaxID: 9606]

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3AO1X-ray1.90A/B765-927[»]
3AO3X-ray1.90A/B765-927[»]
3AO4X-ray1.95A/B765-927[»]
3AO5X-ray1.80A/B765-927[»]
3L3UX-ray1.40A/B765-927[»]
3L3VX-ray2.00A/B765-927[»]
3OVNX-ray1.95A/B765-927[»]
3VQ4X-ray1.90A/B770-927[»]
3VQ5X-ray1.70A/B771-927[»]
3VQ6X-ray1.80A/B770-927[»]
3VQ7X-ray1.63A/B770-927[»]
3VQ8X-ray1.60A/B771-927[»]
3VQ9X-ray1.90A/B/C765-925[»]
3VQAX-ray1.90A/B770-927[»]
3VQBX-ray2.10A/B770-927[»]
3VQCX-ray2.30A/B770-927[»]
3VQDX-ray2.00A/B770-927[»]
3VQEX-ray1.70A/B771-927[»]
3VQPX-ray2.10A/B770-927[»]
3VQQX-ray2.00A/B770-927[»]
ProteinModelPortaliQ72498.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ72498.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni802 – 8032Sucrose bindingImported
Regioni811 – 8144Sucrose bindingImported

Sequence similaritiesi

Belongs to the retroviral Pol polyprotein family.UniRule annotation
Contains RNase H domain.SAAS annotation
Contains integrase catalytic domain.SAAS annotation
Contains integrase-type DNA-binding domain.SAAS annotation
Contains integrase-type zinc finger.SAAS annotation
Contains peptidase A2 domain.SAAS annotation
Contains peptidase Adomain.SAAS annotation
Contains reverse transcriptase domain.SAAS annotation

Keywords - Domaini

Zinc-fingerSAAS annotation

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
InterProiIPR001969. Aspartic_peptidase_AS.
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_dom.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view]
PfamiPF00552. 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]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
PROSITEiPS50175. 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]

Sequencei

Sequence statusi: Fragment.

Q72498-1 [UniParc]FASTAAdd to Basket

« Hide

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

DED
Length:1,003
Mass (Da):113,720
Last modified:November 1, 1996 - v1
Checksum:i4E67C747EED795C7
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Non-terminal residuei1 – 11Imported

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U26942 Genomic DNA. Translation: AAB60572.1.
PIRiA47330.
B47330.
C47330.
D47330.
E47330.
F47330.
S32132.
S32140.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U26942 Genomic DNA. Translation: AAB60572.1 .
PIRi A47330.
B47330.
C47330.
D47330.
E47330.
F47330.
S32132.
S32140.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
3L3U X-ray 1.40 A/B 765-927 [» ]
3L3V X-ray 2.00 A/B 765-927 [» ]
3OVN X-ray 1.95 A/B 765-927 [» ]
3VQ4 X-ray 1.90 A/B 770-927 [» ]
3VQ5 X-ray 1.70 A/B 771-927 [» ]
3VQ6 X-ray 1.80 A/B 770-927 [» ]
3VQ7 X-ray 1.63 A/B 770-927 [» ]
3VQ8 X-ray 1.60 A/B 771-927 [» ]
3VQ9 X-ray 1.90 A/B/C 765-925 [» ]
3VQA X-ray 1.90 A/B 770-927 [» ]
3VQB X-ray 2.10 A/B 770-927 [» ]
3VQC X-ray 2.30 A/B 770-927 [» ]
3VQD X-ray 2.00 A/B 770-927 [» ]
3VQE X-ray 1.70 A/B 771-927 [» ]
3VQP X-ray 2.10 A/B 770-927 [» ]
3VQQ X-ray 2.00 A/B 770-927 [» ]
ProteinModelPortali Q72498.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei Q72498.

Family and domain databases

Gene3Di 1.10.10.200. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
InterProi IPR001969. Aspartic_peptidase_AS.
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_dom.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view ]
Pfami 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 ]
SUPFAMi SSF46919. SSF46919. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
PROSITEi 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 ]
ProtoNeti Search...

Publicationsi

  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: NL4-3Imported.
  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: NL4-3Imported.
  3. Salminen M.S.
    Submitted (MAY-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: NL4-3Imported.
  4. "Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site."
    Wielens J., Headey S.J., Jeevarajah D., Rhodes D.I., Deadman J., Chalmers D.K., Scanlon M.J., Parker M.W.
    FEBS Lett. 584:1455-1462(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF 765-927.
  5. "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.
  6. "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 771-927.

Entry informationi

Entry nameiQ72498_9HIV1
AccessioniPrimary (citable) accession number: Q72498
Entry historyi
Integrated into UniProtKB/TrEMBL: November 1, 1996
Last sequence update: November 1, 1996
Last modified: October 29, 2014
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureImported, Multifunctional enzymeSAAS annotation

External Data

Dasty 3