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P35956 (POL_VILVK) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 110. 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
    EC=3.4.23.-
    Alternative name(s):
    Retropepsin
  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
OrganismMaedi visna virus (strain KV1772) (MVV) (Visna lentivirus)
Taxonomic identifier36374 [NCBI]
Taxonomic lineageVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusOvine/caprine lentivirus group
Virus hostOvis aries (Sheep) [TaxID: 9940]

Protein attributes

Sequence length1101 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.

Miscellaneous

This protein may be synthesized as a Gag-Pol polyprotein.

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

proteolysis

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 – 135135Protease By similarity
PRO_0000038869
Chain136 – 686551Reverse transcriptase/ribonuclease H By similarity
PRO_0000038870
Chain687 – 820134Deoxyuridine 5'-triphosphate nucleotidohydrolase By similarity
PRO_0000038871
Chain821 – 1101281Integrase By similarity
PRO_0000038872

Regions

Domain54 – 12572Peptidase A2
Domain182 – 371190Reverse transcriptase
Domain566 – 688123RNase H
Domain865 – 1025161Integrase catalytic
Zinc finger823 – 86442Integrase-type
DNA binding1042 – 109453Integrase-type

Sites

Active site591 By similarity

Secondary structure

................................... 1101
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P35956 [UniParc].

Last modified June 1, 1994. Version 1.
Checksum: AB955654847267CF

FASTA1,101126,178
        10         20         30         40         50         60 
MPSLWKKRTY AKGLPAEETA GKQQEGATCG AVRAPYVVTE APPKIEIKVG TRWKKLLVDT 

        70         80         90        100        110        120 
GADKTIVTSH DMSGIPKGRI ILQGIGGIIE GEKWEQVHLQ YKDKIIRGTI VVLATSPVEV 

       130        140        150        160        170        180 
LGRDNMRELG IGLIMANLEE KKIPSTRVRL KEGCKGPHIA QWPLTQEKLE GLKEIVDRLE 

       190        200        210        220        230        240 
KEGKVGRAPP HWTCNTPIFC IKKKSGKWRM LIDFRELNKQ TEDLAEAQLG LPHPGGLQRK 

       250        260        270        280        290        300 
KHVTILDIGD AYFTIPLYEP YRQYTCFTML SPNNLGPCVR YYWKVLPQGW KLSPAVYQFT 

       310        320        330        340        350        360 
MQKILRGWIE EHPMIQFGIY MDDIYIGSDL GLEEHRGIVN ELASYIAQYG FMLPEDKRQE 

       370        380        390        400        410        420 
GYPAKWLGFE LHPEKWKFQK HTLPEITEGP ITLNKLQKLV GDLVWRQSLI GKSIPNILKL 

       430        440        450        460        470        480 
MEGDRALQSE RYIESIHVRE WEACRQKLKE MEGNYYDEEK DIYGQLDWGN KAIEYIVFQE 

       490        500        510        520        530        540 
KGKPLWVNVV HSIKNLSQAQ QIIKAAQKLT QEVIIRTGKI PWILLPGREE DWILELQMGN 

       550        560        570        580        590        600 
INWMPSFWSC YKGSVRWKKR NVIAEVVPGP TYYTDGGKKN GRGSLGYITS TGEKFRIHEE 

       610        620        630        640        650        660 
GTNQQLELRA IEEACKQGPE KMNIVTDSRY AYEFMLRNWD EEVIRNPIQA RIMELVHNKE 

       670        680        690        700        710        720 
KIGVHWVPGH KGIPQNEEID RYISEIFLAK EGRGILQKRA EDAGYDLICP QEISIPAGQV 

       730        740        750        760        770        780 
KRIAIDLKIN LKKDQWAMIG TKSSFANKGV FVQGGIIDSG YQGTIQVVIY NSNNKEVVIP 

       790        800        810        820        830        840 
QGRKFAQLIL MPLIHEELEP WGETRKTERG EQGFGSTGMY WIENIPLAEE EHNKWHQDAV 

       850        860        870        880        890        900 
SLHLEFGIPR TAAEDIVQQC DVCQENKMPS TLRGSNKRGI DHWQVDYTHY EDKIILVWVE 

       910        920        930        940        950        960 
TNSGLIYAER VKGETGQEFR VQTMKWYAMF APKSLQSDNG PAFVAESTQL LMKYLGIEHT 

       970        980        990       1000       1010       1020 
TGIPWNPQSQ ALVERTHQTL KNTLEKLIPM FNAFESALAG TLITLNIKRK GGLGTSPMDI 

      1030       1040       1050       1060       1070       1080 
FIFNKEQQRI QQQSKSKQEK IRFCYYRTRK RGHPGEWQGP TQVLWGGDGA IVVKDRGTDR 

      1090       1100 
YLVIANKDVK FIPPPKEIQK E 

« Hide

References

[1]"Nucleotide sequence and biological properties of a pathogenic proviral molecular clone of neurovirulent visna virus."
Andresson O.S., Elser J.E., Tobin G.J., Greenwood J.D., Gonda M.A., Georgsson G., Andresdottir V., Benediktsdottir E., Carlsdottir H.M., Maentylae E.O., Rafnar B., Palsson P.A., Casey J.W., Petursson G.
Virology 193:89-105(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L06906 Genomic RNA. Translation: AAA48359.1.
S55323 Genomic DNA. Translation: AAB25460.1.
RefSeqNP_040840.1. NC_001452.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3HPGX-ray3.28A/B/C/D/E/F823-1039[»]
3HPHX-ray2.64A/B/C/D823-1039[»]
ProteinModelPortalP35956.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSA02.006.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1490013.

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.
IPR008180. dUTP_pyroPase.
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.
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

EvolutionaryTraceP35956.

Entry information

Entry namePOL_VILVK
AccessionPrimary (citable) accession number: P35956
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: April 16, 2014
This is version 110 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