Pol polyprotein - Maedi visna virus (strain KV1772) (MVV)

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P35956 (POL_VILVK) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 105. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Pol polyprotein

Cleaved into the following 4 chains:

Protease
EC=3.4.23.-
Alternative name(s):
Retropepsin
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
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Short name=dUTPase
EC=3.6.1.23
Integrase
Short name=IN

Gene names

Name:

pol

Organism

Maedi visna virus (strain KV1772) (MVV) (Visna lentivirus)

Taxonomic identifier

36374 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Lentivirus › Ovine/caprine lentivirus group ›

Virus host

Ovis aries (Sheep) [TaxID: 9940]

Protein attributes

Sequence length	1101 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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 process	DNA integration DNA recombination Nucleotide metabolism Viral genome integration Virus entry into host cell
Domain	Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Aspartyl protease Endonuclease Hydrolase Nuclease Nucleotidyltransferase Protease RNA-directed DNA polymerase Transferase
Technical term	3D-structure Multifunctional enzyme
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 dUTP metabolic process 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 dUTP diphosphatase activity Inferred from electronic annotation. Source: EC exoribonuclease H activity Inferred from electronic annotation. Source: EC 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

Molecule processing

Chain

1 – 135

135

Protease By similarity

PRO_0000038869

Chain

136 – 686

551

Reverse transcriptase/ribonuclease H By similarity

PRO_0000038870

Chain

687 – 820

134

Deoxyuridine 5'-triphosphate nucleotidohydrolase By similarity

PRO_0000038871

Chain

821 – 1101

281

Integrase By similarity

PRO_0000038872

Regions

Domain

54 – 125

Peptidase A2

Domain

182 – 371

190

Reverse transcriptase

Domain

566 – 688

123

RNase H

Domain

865 – 1025

161

Integrase catalytic

Zinc finger

823 – 864

Integrase-type

DNA binding

1042 – 1094

Integrase-type

Sites

Active site

By similarity

Secondary structure

1101

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P35956 [UniParc].

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

FASTA

1,101

126,178

        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.

RefSeq

NP_040840.1. NC_001452.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3HPG	X-ray	3.28	A/B/C/D/E/F	823-1039	[»]
3HPH	X-ray	2.64	A/B/C/D	823-1039	[»]

ProteinModelPortal

P35956.

ModBase

Search...

Protein family/group databases

MEROPS

A02.006.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1490013.

Family and domain databases

Gene3D

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

InterPro

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.
IPR001969. Peptidase_aspartic_AS.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RVT.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view]

Pfam

PF00692. 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]

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

Search...

Other

EvolutionaryTrace

P35956.

Entry information

Entry name

POL_VILVK

Accession

Primary (citable) accession number: P35956

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	June 1, 1994
Last modified:	April 3, 2013
This is version 105 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program

Relevant documents

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Cleaved into the following 4 chains:

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein family/group databases

Protocols and materials databases

Genome annotation databases

Family and domain databases

Other

Entry information

Relevant documents