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B8DN07

- PNP_DESVM

UniProt

B8DN07 - PNP_DESVM

Protein

Polyribonucleotide nucleotidyltransferase

Gene

pnp

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 41 (01 Oct 2014)
      Sequence version 1 (03 Mar 2009)
      Previous versions | rss
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    Functioni

    Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction.UniRule annotation

    Catalytic activityi

    RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.UniRule annotation

    Cofactori

    Magnesium.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi492 – 4921MagnesiumUniRule annotation
    Metal bindingi498 – 4981MagnesiumUniRule annotation

    GO - Molecular functioni

    1. 3'-5'-exoribonuclease activity Source: InterPro
    2. magnesium ion binding Source: UniProtKB-HAMAP
    3. polyribonucleotide nucleotidyltransferase activity Source: UniProtKB-HAMAP
    4. RNA binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. mRNA catabolic process Source: UniProtKB-HAMAP
    2. RNA processing Source: InterPro

    Keywords - Molecular functioni

    Nucleotidyltransferase, Transferase

    Keywords - Ligandi

    Magnesium, Metal-binding, RNA-binding

    Enzyme and pathway databases

    BioCyciDVUL883:GCJ5-2578-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Polyribonucleotide nucleotidyltransferaseUniRule annotation (EC:2.7.7.8UniRule annotation)
    Alternative name(s):
    Polynucleotide phosphorylaseUniRule annotation
    Short name:
    PNPaseUniRule annotation
    Gene namesi
    Name:pnpUniRule annotation
    Ordered Locus Names:DvMF_2508
    OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
    Taxonomic identifieri883 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
    ProteomesiUP000001361: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 756756Polyribonucleotide nucleotidyltransferasePRO_1000147916Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi883.DvMF_2508.

    Structurei

    3D structure databases

    ProteinModelPortaliB8DN07.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini559 – 61860KHUniRule annotationAdd
    BLAST
    Domaini628 – 70275S1 motifUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the polyribonucleotide nucleotidyltransferase family.UniRule annotation
    Contains 1 KH domain.UniRule annotation
    Contains 1 S1 motif domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1185.
    HOGENOMiHOG000218326.
    KOiK00962.
    OMAiHGNFKSN.
    OrthoDBiEOG6WT8CC.

    Family and domain databases

    Gene3Di1.10.10.400. 1 hit.
    2.40.50.140. 1 hit.
    3.30.1370.10. 1 hit.
    3.30.230.70. 2 hits.
    HAMAPiMF_01595. PNPase.
    InterProiIPR001247. ExoRNase_PH_dom1.
    IPR015847. ExoRNase_PH_dom2.
    IPR004087. KH_dom.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    IPR012162. PNPase.
    IPR027408. PNPase/RNase_PH_dom.
    IPR015848. PNPase_PH_RNA-bd_bac/org-type.
    IPR003029. Rbsml_prot_S1_RNA-bd_dom.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR022967. RNA-binding_domain_S1.
    [Graphical view]
    PANTHERiPTHR11252. PTHR11252. 1 hit.
    PfamiPF00013. KH_1. 1 hit.
    PF03726. PNPase. 1 hit.
    PF01138. RNase_PH. 2 hits.
    PF03725. RNase_PH_C. 2 hits.
    PF00575. S1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005499. PNPase. 1 hit.
    SMARTiSM00322. KH. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view]
    SUPFAMiSSF46915. SSF46915. 1 hit.
    SSF50249. SSF50249. 1 hit.
    SSF54211. SSF54211. 2 hits.
    SSF54791. SSF54791. 1 hit.
    SSF55666. SSF55666. 2 hits.
    TIGRFAMsiTIGR03591. polynuc_phos. 1 hit.
    PROSITEiPS50084. KH_TYPE_1. 1 hit.
    PS50126. S1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    B8DN07-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQSVFNATRV SAVVGGKEII LETGRLANQA HGAVWVQCGG TVVLVTACTQ    50
    PLERDMGFFP LTVDYSEKMY AAGRIPGSFF RREIGRPSER ETLVSRLIDR 100
    PVRPLFTKGF RDEVQILANV ISADQENDSD VLAVTGASAA LSISPIPFEG 150
    PVAGARIGRV NGEFVLNPTM KEMEASDLAI VIAASRDSVV MVEGEAHFVP 200
    EDVIVAALEW AHKEIQPLID AQLKLMELVG KAKMAVTPPV ENAELKARVA 250
    ELATTELDAA LRIPEKMARK DARKAVKEKV LEALLADPAL AENANLGREV 300
    GDMLGSLEKV LVRRRILKEG TRIDGRDTKT VRPILIEAGL LPRAHGSALF 350
    SRGETKSLVV ATLGSSTDSQ RMDSLVGDVT KKFMLHYNFP PYSVGEVKMS 400
    RVSRREIGHG ALAEKALKPV LPQDDSFPFT LRVVAETMES NGSSSMAAVC 450
    GGSLSLMDAG VPVTAPVAGV AMGLIKEEGE YLVLTDILGD EDALGDMDFK 500
    IAGTAEGITA VQMDIKITGL PTDVMARAMA QAREARLHIL AEMAKVLEAP 550
    RTELSKYAPQ HAEVFVNPDV IRIIIGPGGK NIKAITAATG ASIDIEDSGK 600
    VSIFAPTYEA MEMAREMVQY YDQRAELGKN YVGKVRKVLE IGAIVEILPN 650
    LEALVHISQL DTNRVEQAGD VARLGEDMTV KVIEINGDRI RASRKAVLLE 700
    EQGVEWNPED TARPSGPPRD RGDRGDRGGR GDRGGDRRGG DRGGRGGDRG 750
    RGGDRR 756
    Length:756
    Mass (Da):81,497
    Last modified:March 3, 2009 - v1
    Checksum:i0BDCD59999A643B2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001197 Genomic DNA. Translation: ACL09447.1.
    RefSeqiWP_015946137.1. NC_011769.1.
    YP_002436915.1. NC_011769.1.

    Genome annotation databases

    EnsemblBacteriaiACL09447; ACL09447; DvMF_2508.
    GeneIDi7174444.
    KEGGidvm:DvMF_2508.
    PATRICi21775438. VBIDesVul86729_2721.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001197 Genomic DNA. Translation: ACL09447.1 .
    RefSeqi WP_015946137.1. NC_011769.1.
    YP_002436915.1. NC_011769.1.

    3D structure databases

    ProteinModelPortali B8DN07.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 883.DvMF_2508.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACL09447 ; ACL09447 ; DvMF_2508 .
    GeneIDi 7174444.
    KEGGi dvm:DvMF_2508.
    PATRICi 21775438. VBIDesVul86729_2721.

    Phylogenomic databases

    eggNOGi COG1185.
    HOGENOMi HOG000218326.
    KOi K00962.
    OMAi HGNFKSN.
    OrthoDBi EOG6WT8CC.

    Enzyme and pathway databases

    BioCyci DVUL883:GCJ5-2578-MONOMER.

    Family and domain databases

    Gene3Di 1.10.10.400. 1 hit.
    2.40.50.140. 1 hit.
    3.30.1370.10. 1 hit.
    3.30.230.70. 2 hits.
    HAMAPi MF_01595. PNPase.
    InterProi IPR001247. ExoRNase_PH_dom1.
    IPR015847. ExoRNase_PH_dom2.
    IPR004087. KH_dom.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    IPR012162. PNPase.
    IPR027408. PNPase/RNase_PH_dom.
    IPR015848. PNPase_PH_RNA-bd_bac/org-type.
    IPR003029. Rbsml_prot_S1_RNA-bd_dom.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR022967. RNA-binding_domain_S1.
    [Graphical view ]
    PANTHERi PTHR11252. PTHR11252. 1 hit.
    Pfami PF00013. KH_1. 1 hit.
    PF03726. PNPase. 1 hit.
    PF01138. RNase_PH. 2 hits.
    PF03725. RNase_PH_C. 2 hits.
    PF00575. S1. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF005499. PNPase. 1 hit.
    SMARTi SM00322. KH. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46915. SSF46915. 1 hit.
    SSF50249. SSF50249. 1 hit.
    SSF54211. SSF54211. 2 hits.
    SSF54791. SSF54791. 1 hit.
    SSF55666. SSF55666. 2 hits.
    TIGRFAMsi TIGR03591. polynuc_phos. 1 hit.
    PROSITEi PS50084. KH_TYPE_1. 1 hit.
    PS50126. S1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
      Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
      Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Miyazaki F / DSM 19637.

    Entry informationi

    Entry nameiPNP_DESVM
    AccessioniPrimary (citable) accession number: B8DN07
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 14, 2009
    Last sequence update: March 3, 2009
    Last modified: October 1, 2014
    This is version 41 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3