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P35956

- POL_VILVK

UniProt

P35956 - POL_VILVK

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Protein
Pol polyprotein
Gene
pol
Organism
Maedi visna virus (strain KV1772) (MVV) (Visna lentivirus)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 activityi

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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei59 – 591 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri823 – 86442Integrase-type
Add
BLAST
DNA bindingi1042 – 109453Integrase-type
Add
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. RNA binding Source: InterPro
  3. RNA-DNA hybrid ribonuclease activity Source: InterPro
  4. RNA-directed DNA polymerase activity Source: UniProtKB-KW
  5. aspartic-type endopeptidase activity Source: UniProtKB-KW
  6. dUTP diphosphatase activity Source: UniProtKB-EC
  7. exoribonuclease H activity Source: UniProtKB-EC
  8. zinc ion binding Source: InterPro

GO - Biological processi

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

Keywords - Molecular functioni

Aspartyl protease, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

DNA integration, DNA recombination, Nucleotide metabolism, Viral genome integration, Virus entry into host cell

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Protein family/group databases

MEROPSiA02.006.

Names & Taxonomyi

Protein namesi
Recommended name:
Pol polyprotein
Cleaved into the following 4 chains:
Alternative name(s):
Retropepsin
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
Integrase
Short name:
IN
Gene namesi
Name:pol
OrganismiMaedi visna virus (strain KV1772) (MVV) (Visna lentivirus)
Taxonomic identifieri36374 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusOvine/caprine lentivirus group
Virus hostiOvis aries (Sheep) [TaxID: 9940]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 135135Protease By similarity
PRO_0000038869Add
BLAST
Chaini136 – 686551Reverse transcriptase/ribonuclease H By similarity
PRO_0000038870Add
BLAST
Chaini687 – 820134Deoxyuridine 5'-triphosphate nucleotidohydrolase By similarity
PRO_0000038871Add
BLAST
Chaini821 – 1101281Integrase By similarity
PRO_0000038872Add
BLAST

Post-translational modificationi

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

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi825 – 83511
Helixi839 – 8457
Helixi850 – 8578
Helixi861 – 8644
Beta strandi882 – 8909
Beta strandi893 – 9008
Turni901 – 9033
Beta strandi906 – 9127
Helixi916 – 93015
Beta strandi934 – 9374
Helixi941 – 9444
Helixi946 – 95510
Beta strandi958 – 9625
Helixi967 – 98721
Helixi988 – 9903
Helixi994 – 100613
Turni1012 – 10143
Helixi1017 – 103216

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3HPGX-ray3.28A/B/C/D/E/F823-1039[»]
3HPHX-ray2.64A/B/C/D823-1039[»]
ProteinModelPortaliP35956.

Miscellaneous databases

EvolutionaryTraceiP35956.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini54 – 12572Peptidase A2
Add
BLAST
Domaini182 – 371190Reverse transcriptase
Add
BLAST
Domaini566 – 688123RNase H
Add
BLAST
Domaini865 – 1025161Integrase catalytic
Add
BLAST

Sequence similaritiesi

Contains 1 RNase H domain.

Keywords - Domaini

Zinc-finger

Family and domain databases

Gene3Di1.10.10.200. 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.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
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]
PfamiPF00692. 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]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF51283. SSF51283. 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: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P35956-1 [UniParc]FASTAAdd to Basket

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MPSLWKKRTY AKGLPAEETA GKQQEGATCG AVRAPYVVTE APPKIEIKVG     50
TRWKKLLVDT GADKTIVTSH DMSGIPKGRI ILQGIGGIIE GEKWEQVHLQ 100
YKDKIIRGTI VVLATSPVEV LGRDNMRELG IGLIMANLEE KKIPSTRVRL 150
KEGCKGPHIA QWPLTQEKLE GLKEIVDRLE KEGKVGRAPP HWTCNTPIFC 200
IKKKSGKWRM LIDFRELNKQ TEDLAEAQLG LPHPGGLQRK KHVTILDIGD 250
AYFTIPLYEP YRQYTCFTML SPNNLGPCVR YYWKVLPQGW KLSPAVYQFT 300
MQKILRGWIE EHPMIQFGIY MDDIYIGSDL GLEEHRGIVN ELASYIAQYG 350
FMLPEDKRQE GYPAKWLGFE LHPEKWKFQK HTLPEITEGP ITLNKLQKLV 400
GDLVWRQSLI GKSIPNILKL MEGDRALQSE RYIESIHVRE WEACRQKLKE 450
MEGNYYDEEK DIYGQLDWGN KAIEYIVFQE KGKPLWVNVV HSIKNLSQAQ 500
QIIKAAQKLT QEVIIRTGKI PWILLPGREE DWILELQMGN INWMPSFWSC 550
YKGSVRWKKR NVIAEVVPGP TYYTDGGKKN GRGSLGYITS TGEKFRIHEE 600
GTNQQLELRA IEEACKQGPE KMNIVTDSRY AYEFMLRNWD EEVIRNPIQA 650
RIMELVHNKE KIGVHWVPGH KGIPQNEEID RYISEIFLAK EGRGILQKRA 700
EDAGYDLICP QEISIPAGQV KRIAIDLKIN LKKDQWAMIG TKSSFANKGV 750
FVQGGIIDSG YQGTIQVVIY NSNNKEVVIP QGRKFAQLIL MPLIHEELEP 800
WGETRKTERG EQGFGSTGMY WIENIPLAEE EHNKWHQDAV SLHLEFGIPR 850
TAAEDIVQQC DVCQENKMPS TLRGSNKRGI DHWQVDYTHY EDKIILVWVE 900
TNSGLIYAER VKGETGQEFR VQTMKWYAMF APKSLQSDNG PAFVAESTQL 950
LMKYLGIEHT TGIPWNPQSQ ALVERTHQTL KNTLEKLIPM FNAFESALAG 1000
TLITLNIKRK GGLGTSPMDI FIFNKEQQRI QQQSKSKQEK IRFCYYRTRK 1050
RGHPGEWQGP TQVLWGGDGA IVVKDRGTDR YLVIANKDVK FIPPPKEIQK 1100
E 1101
Length:1,101
Mass (Da):126,178
Last modified:June 1, 1994 - v1
Checksum:iAB955654847267CF
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L06906 Genomic RNA. Translation: AAA48359.1.
S55323 Genomic DNA. Translation: AAB25460.1.
RefSeqiNP_040840.1. NC_001452.1.

Genome annotation databases

GeneIDi1490013.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L06906 Genomic RNA. Translation: AAA48359.1 .
S55323 Genomic DNA. Translation: AAB25460.1 .
RefSeqi NP_040840.1. NC_001452.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali P35956.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi A02.006.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 1490013.

Miscellaneous databases

EvolutionaryTracei P35956.

Family and domain databases

Gene3Di 1.10.10.200. 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.
InterProi IPR001969. Aspartic_peptidase_AS.
IPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
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 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 ]
SUPFAMi SSF46919. SSF46919. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF51283. SSF51283. 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. "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].

Entry informationi

Entry nameiPOL_VILVK
AccessioniPrimary (citable) accession number: P35956
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: June 11, 2014
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure, Multifunctional enzyme

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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