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Q72498 (Q72498_9HIV1) Unreviewed, UniProtKB/TrEMBL

Last modified June 11, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order

Names and origin

Protein names
Gene names
Name:pol EMBL AAB60572.1
OrganismHuman immunodeficiency virus 1 EMBL AAB60572.1
Taxonomic identifier11676 [NCBI]
Taxonomic lineageVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length1003 AA.
Sequence statusFragment.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. SAAS SAAS010659

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). SAAS SAAS010659

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 SAAS010659

Sequence similarities

Belongs to the retroviral Pol polyprotein family. RuleBase RU004064

Contains RNase H domain. SAAS SAAS010659

Contains integrase catalytic domain. SAAS SAAS010659

Contains integrase-type DNA-binding domain. SAAS SAAS010659

Contains integrase-type zinc finger. SAAS SAAS010659

Contains peptidase A2 domain. SAAS SAAS010659

Contains peptidase Adomain. SAAS SAAS010659

Contains reverse transcriptase domain. SAAS SAAS010659

Ontologies

Keywords
   Biological processDNA integration
DNA recombination SAAS SAAS010659
Viral genome integration SAAS SAAS010659
Virus entry into host cell
   DomainZinc-finger SAAS SAAS010659
   LigandCadmium PDB 3L3V PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3AO3 PDB 3AO4 PDB 3AO1 PDB 3AO5 PDB 3OVN
Chloride PDB 3VQ5 PDB 3VQ8 PDB 3VQE PDB 3VQP PDB 3AO3 PDB 3AO4 PDB 3AO5
DNA-binding SAAS SAAS010659
Metal-binding
Zinc
   Molecular functionAspartyl protease SAAS SAAS010659
Endonuclease SAAS SAAS010659
Hydrolase
Nuclease
Nucleotidyltransferase
Protease
RNA-directed DNA polymerase SAAS SAAS010659
Transferase
   Technical term3D-structure PDB 3L3U PDB 3L3V 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 SAAS010659
Gene Ontology (GO)
   Biological_processDNA integration

Inferred from electronic annotation. Source: UniProtKB-KW

DNA recombination

Inferred from electronic annotation. Source: UniProtKB-KW

establishment of integrated proviral latency

Inferred from electronic annotation. Source: UniProtKB-KW

viral entry into host cell

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA binding

Inferred from electronic annotation. Source: InterPro

RNA-DNA hybrid ribonuclease activity

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

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Region781 – 7822Sulfate 1 binding PDB 3L3U PDB 3VQ5 PDB 3VQ8 PDB 3VQE PDB 3AO3 PDB 3AO4 PDB 3AO5
Region781 – 7822Sulfate 3 binding PDB 3AO3 PDB 3AO4
Region784 – 7863Sulfate 5 binding PDB 3L3U PDB 3VQ4 PDB 3VQ5 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3AO4 PDB 3AO5
Region802 – 8032Sucrose binding PDB 3L3V PDB 3VQ7 PDB 3VQA PDB 3VQQ PDB 3AO5 PDB 3OVN
Region811 – 8144Sucrose binding PDB 3L3V PDB 3VQ7 PDB 3VQA PDB 3VQQ PDB 3AO5 PDB 3OVN
Region885 – 8895Sulfate 8 binding PDB 3AO5
Region885 – 8873Sulfate 5 binding PDB 3L3U PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3AO4 PDB 3AO1 PDB 3AO5 PDB 3OVN
Region886 – 8872Sulfate 6 binding PDB 3L3U PDB 3VQ5 PDB 3VQ7 PDB 3VQ8 PDB 3VQD PDB 3VQQ PDB 3AO3 PDB 3AO4 PDB 3AO5 PDB 3OVN
Region886 – 8872Sulfate 9 binding PDB 3L3V PDB 3OVN

Sites

Metal binding7801Cadmium 1 PDB 3L3V PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3OVN
Metal binding7801Cadmium 2 PDB 3L3V PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3OVN
Metal binding7821Cadmium 1; via tele nitrogen PDB 3L3V PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3OVN
Metal binding8071Cadmium 1 PDB 3L3V PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3OVN
Metal binding8071Cadmium 2 PDB 3L3V PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3OVN
Metal binding8311Cadmium 2 PDB 3L3V PDB 3VQ4 PDB 3VQ5 PDB 3VQ6 PDB 3VQ7 PDB 3VQ8 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQE PDB 3VQP PDB 3VQQ PDB 3OVN
Binding site7821Sulfate 2; via amide nitrogen and carbonyl oxygen PDB 3VQP
Binding site7821Sulfate 4; via amide nitrogen and carbonyl oxygen PDB 3AO5
Binding site7861Sulfate 6 PDB 3L3U PDB 3VQ5 PDB 3VQ7 PDB 3VQ8 PDB 3VQQ PDB 3AO3 PDB 3AO5
Binding site8181Sucrose PDB 3L3V PDB 3VQ7 PDB 3VQA PDB 3VQQ PDB 3AO5 PDB 3OVN
Binding site8351Chloride PDB 3VQ5 PDB 3VQ8 PDB 3VQE PDB 3AO4 PDB 3AO5
Binding site8401Sulfate 7 PDB 3VQ5 PDB 3AO3 PDB 3AO5
Binding site8741Sulfate 1 PDB 3L3U PDB 3VQ5 PDB 3VQ8 PDB 3VQE PDB 3AO4
Binding site8741Sulfate 3 PDB 3AO3 PDB 3AO4
Binding site8811Sulfate 5 PDB 3L3U PDB 3VQ4 PDB 3VQ6 PDB 3VQ7 PDB 3VQA PDB 3VQB PDB 3VQC PDB 3VQD PDB 3VQP PDB 3VQQ PDB 3AO1 PDB 3OVN
Binding site8811Sulfate 6 PDB 3L3U PDB 3VQ7 PDB 3VQQ PDB 3OVN
Binding site8881Sucrose PDB 3L3V PDB 3VQ7 PDB 3VQA PDB 3VQQ PDB 3AO5 PDB 3OVN
Binding site9021Sulfate 10 PDB 3L3V
Binding site9021Sulfate 11 PDB 3VQ5

Experimental info

Non-terminal residue11 EMBL AAB60572.1

Sequences

Sequence LengthMass (Da)Tools
Q72498 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 4E67C747EED795C7

FASTA1,003113,720
        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 

« Hide

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]"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 IN COMPLEX WITH CADMIUM; SUCROSE AND SULFATE.
[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 IN COMPLEX WITH CADMIUM; CHLORIDE; SUCROSE AND SULFATE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U26942 Genomic DNA. Translation: AAB60572.1.
PIRA47330.
B47330.
C47330.
D47330.
E47330.
F47330.
S32132.
S32140.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalQ72498.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D1.10.10.200. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
InterProIPR001969. 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]
PfamPF00552. 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]
SUPFAMSSF46919. SSF46919. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
PROSITEPS50175. 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]
ProtoNetSearch...

Other

EvolutionaryTraceQ72498.

Entry information

Entry nameQ72498_9HIV1
AccessionPrimary (citable) accession number: Q72498
Entry history
Integrated into UniProtKB/TrEMBL: November 1, 1996
Last sequence update: November 1, 1996
Last modified: June 11, 2014
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)