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P35956

- POL_VILVK

UniProt

P35956 - POL_VILVK

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
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    • History
      Entry version 113 (01 Oct 2014)
      Sequence version 1 (01 Jun 1994)
      Previous versions | rss
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    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).PROSITE-ProRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei59 – 591PROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri823 – 86442Integrase-typePROSITE-ProRule annotationAdd
    BLAST
    DNA bindingi1042 – 109453Integrase-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

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

    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 – 135135ProteaseBy similarityPRO_0000038869Add
    BLAST
    Chaini136 – 686551Reverse transcriptase/ribonuclease HBy similarityPRO_0000038870Add
    BLAST
    Chaini687 – 820134Deoxyuridine 5'-triphosphate nucleotidohydrolaseBy similarityPRO_0000038871Add
    BLAST
    Chaini821 – 1101281IntegraseBy similarityPRO_0000038872Add
    BLAST

    Post-translational modificationi

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

    Structurei

    Secondary structure

    1
    1101
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP35956.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini54 – 12572Peptidase A2PROSITE-ProRule annotationAdd
    BLAST
    Domaini182 – 371190Reverse transcriptasePROSITE-ProRule annotationAdd
    BLAST
    Domaini566 – 688123RNase HPROSITE-ProRule annotationAdd
    BLAST
    Domaini865 – 1025161Integrase catalyticPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the retroviral Pol polyprotein family.Curated
    Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
    Contains 1 integrase-type DNA-binding domain.PROSITE-ProRule annotation
    Contains 1 integrase-type zinc finger.PROSITE-ProRule annotation
    Contains 1 peptidase A2 domain.PROSITE-ProRule annotation
    Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation
    Contains 1 RNase H domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri823 – 86442Integrase-typePROSITE-ProRule annotationAdd
    BLAST

    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

    « Hide

    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: October 1, 2014
    This is version 113 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