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P16088 (POL_FIVPE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 135. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pol polyprotein

Cleaved into the following 4 chains:

  1. Protease
    Alternative name(s):
    Retropepsin
    EC=3.4.23.-
  2. Reverse transcriptase/ribonuclease H
    Short name=RT
    EC=2.7.7.49
    EC=3.1.26.13
    Alternative name(s):
    Exoribonuclease H
    EC=3.1.13.2
  3. Deoxyuridine 5'-triphosphate nucleotidohydrolase
    Short name=dUTPase
    EC=3.6.1.23
  4. Integrase
    Short name=IN
Gene names
Name:pol
OrganismFeline immunodeficiency virus (isolate Petaluma) (FIV)
Taxonomic identifier11674 [NCBI]
Taxonomic lineageVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusFeline lentivirus group
Virus hostFelidae (cat family) [TaxID: 9681]

Protein attributes

Sequence length1124 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Catalytic activity

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.

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

dUTP + H2O = dUMP + diphosphate.

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

Post-translational modification

Cleavage sites that yield the mature proteins remain to be determined.

Sequence similarities

Belongs to the retroviral Pol polyprotein family.

Contains 1 integrase catalytic domain.

Contains 1 integrase-type DNA-binding domain.

Contains 1 integrase-type zinc finger.

Contains 1 peptidase A2 domain.

Contains 1 reverse transcriptase domain.

Contains 1 RNase H domain.

Ontologies

Keywords
   Biological processDNA integration
DNA recombination
Nucleotide metabolism
Viral genome integration
Virus entry into host cell
   DomainZinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionAspartyl protease
Endonuclease
Hydrolase
Nuclease
Nucleotidyltransferase
Protease
RNA-directed DNA polymerase
Transferase
   Technical term3D-structure
Multifunctional enzyme
Gene Ontology (GO)
   Biological_processDNA integration

Inferred from electronic annotation. Source: UniProtKB-KW

DNA recombination

Inferred from electronic annotation. Source: UniProtKB-KW

dUTP metabolic process

Inferred from electronic annotation. Source: InterPro

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

dUTP diphosphatase activity

Inferred from electronic annotation. Source: UniProtKB-EC

exoribonuclease H activity

Inferred from electronic annotation. Source: UniProtKB-EC

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 154154Protease
PRO_0000038841
Chain155 – 690536Reverse transcriptase/ribonuclease H
PRO_0000038842
Chain691 – 843153Deoxyuridine 5'-triphosphate nucleotidohydrolase
PRO_0000038843
Chain844 – 1124281Integrase
PRO_0000038844

Regions

Domain63 – 14482Peptidase A2
Domain200 – 389190Reverse transcriptase
Domain592 – 712121RNase H
Domain899 – 1049151Integrase catalytic
Zinc finger848 – 88942Integrase-type
DNA binding1067 – 111549Integrase-type

Sites

Active site681For protease activity

Secondary structure

....................................................... 1124
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P16088 [UniParc].

Last modified April 1, 1990. Version 1.
Checksum: EE8214169BE39CF9

FASTA1,124127,494
        10         20         30         40         50         60 
KEFGKLEGGA SCSPSESNAA SSNAICTSNG GETIGFVNYN KVGTTTTLEK RPEILIFVNG 

        70         80         90        100        110        120 
YPIKFLLDTG ADITILNRRD FQVKNSIENG RQNMIGVGGG KRGTNYINVH LEIRDENYKT 

       130        140        150        160        170        180 
QCIFGNVCVL EDNSLIQPLL GRDNMIKFNI RLVMAQISDK IPVVKVKMKD PNKGPQIKQW 

       190        200        210        220        230        240 
PLTNEKIEAL TEIVERLEKE GKVKRADSNN PWNTPVFAIK KKSGKWRMLI DFRELNKLTE 

       250        260        270        280        290        300 
KGAEVQLGLP HPAGLQIKKQ VTVLDIGDAY FTIPLDPDYA PYTAFTLPRK NNAGPGRRFV 

       310        320        330        340        350        360 
WCSLPQGWIL SPLIYQSTLD NIIQPFIRQN PQLDIYQYMD DIYIGSNLSK KEHKEKVEEL 

       370        380        390        400        410        420 
RKLLLWWGFE TPEDKLQEEP PYTWMGYELH PLTWTIQQKQ LDIPEQPTLN ELQKLAGKIN 

       430        440        450        460        470        480 
WASQAIPDLS IKALTNMMRG NQNLNSTRQW TKEARLEVQK AKKAIEEQVQ LGYYDPSKEL 

       490        500        510        520        530        540 
YAKLSLVGPH QISYQVYQKD PEKILWYGKM SRQKKKAENT CDIALRACYK IREESIIRIG 

       550        560        570        580        590        600 
KEPRYEIPTS REAWESNLIN SPYLKAPPPE VEYIHAALNI KRALSMIKDA PIPGAETWYI 

       610        620        630        640        650        660 
DGGRKLGKAA KAAYWTDTGK WRVMDLEGSN QKAEIQALLL ALKAGSEEMN IITDSQYVIN 

       670        680        690        700        710        720 
IILQQPDMME GIWQEVLEEL EKKTAIFIDW VPGHKGIPGN EEVDKLCQTM MIIEGDGILD 

       730        740        750        760        770        780 
KRSEDAGYDL LAAKEIHLLP GEVKVIPTGV KLMLPKGYWG LIIGKSSIGS KGLDVLGGVI 

       790        800        810        820        830        840 
DEGYRGEIGV IMINVSRKSI TLMERQKIAQ LIILPCKHEV LEQGKVVMDS ERGDNGYGST 

       850        860        870        880        890        900 
GVFSSWVDRI EEAEINHEKF HSDPQYLRTE FNLPKMVAEE IRRKCPVCRI IGEQVGGQLK 

       910        920        930        940        950        960 
IGPGIWQMDC THFDGKIILV GIHVESGYIW AQIISQETAD CTVKAVLQLL SAHNVTELQT 

       970        980        990       1000       1010       1020 
DNGPNFKNQK MEGVLNYMGV KHKFGIPGNP QSQALVENVN HTLKVWIQKF LPETTSLDNA 

      1030       1040       1050       1060       1070       1080 
LSLAVHSLNF KRRGRIGGMA PYELLAQQES LRIQDYFSAI PQKLQAQWIY YKDQKDKKWK 

      1090       1100       1110       1120 
GPMRVEYWGQ GSVLLKDEEK GYFLIPRRHI RRVPEPCALP EGDE 

« Hide

References

[1]"Nucleotide sequence and genomic organization of feline immunodeficiency virus."
Talbott R.L., Sparger E.E., Lovelace K.M., Fitch W.M., Pedersen N.C., Luciw P.A., Elder J.H.
Proc. Natl. Acad. Sci. U.S.A. 86:5743-5747(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Strain: Clone 34TF10.
[2]"Nucleotide sequence analysis of feline immunodeficiency virus: genome organization and relationship to other lentiviruses."
Olmsted R.A., Hirsch V.M., Purcell R.H., Johnson P.R.
Proc. Natl. Acad. Sci. U.S.A. 86:8088-8092(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
Strain: Clone FIV-14.
[3]"Identification of proteolytic processing sites within the Gag and Pol polyproteins of feline immunodeficiency virus."
Elder J.H., Schnoelzer M., Hasselkus-Light C.S., Henson M., Lerner D.A., Phillips T.R., Wagaman P.C., Kent S.B.H.
J. Virol. 67:1869-1876(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[4]"Structure of an inhibitor complex of the proteinase from feline immunodeficiency virus."
Wlodawer A., Gustchina A., Reshetnikova L., Lubkowski J., Zdanov J.A., Hui K.Y., Angleton E.L., Farmerie W.G., Goodenow M.M., Bhatt D., Zhang L., Dunn B.M.
Nat. Struct. Biol. 2:480-488(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 42-154.
[5]"Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor."
Laco G.S., Schalk-Hihi C., Lubkowski J., Morris G., Zdanov A., Olson A., Elder J.H., Wlodawer A., Gustchina A.
Biochemistry 36:10696-10708(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 42-154.
[6]"Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus."
Prasad G.S., Stura E.A., McRee D.E., Laco G.S., Hasselkus-Light C., Elder J.H., Stout C.D.
Protein Sci. 5:2429-2437(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 711-827.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M25381 Genomic RNA. Translation: AAB59937.1. Sequence problems.
PIRGNLJFP. B33543.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1B11X-ray1.90A42-154[»]
1DUTX-ray1.90A/B711-843[»]
1F7DX-ray1.40A/B711-846[»]
1F7KX-ray2.20A/B711-846[»]
1F7NX-ray2.20A/B711-846[»]
1F7OX-ray2.20A/B/C711-846[»]
1F7PX-ray2.30A/B/C711-846[»]
1F7QX-ray2.26A/B/C711-846[»]
1F7RX-ray2.50A711-846[»]
1FIVX-ray2.00A42-154[»]
2FIVX-ray2.00A/B39-154[»]
2HAHX-ray1.70A39-154[»]
3FIVX-ray1.85A/B39-154[»]
3OGPX-ray1.70A/B39-154[»]
3OGQX-ray1.80A/B39-154[»]
4FIVX-ray1.80A42-154[»]
5FIVX-ray1.90A42-154[»]
6FIVX-ray1.90A42-154[»]
ProteinModelPortalP16088.
SMRP16088. Positions 42-154, 711-843.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEP16088.

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.
2.70.40.10. 1 hit.
3.30.420.10. 2 hits.
InterProIPR001969. Aspartic_peptidase_AS.
IPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR008181. dUTPase_1.
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]
PfamPF00692. dUTPase. 1 hit.
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]
SUPFAMSSF46919. SSF46919. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF51283. SSF51283. 1 hit.
SSF53098. SSF53098. 2 hits.
TIGRFAMsTIGR00576. dut. 1 hit.
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

EvolutionaryTraceP16088.

Entry information

Entry namePOL_FIVPE
AccessionPrimary (citable) accession number: P16088
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: July 9, 2014
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references