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B8DN07

- PNP_DESVM

UniProt

B8DN07 - PNP_DESVM

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Protein

Polyribonucleotide nucleotidyltransferase

Gene
pnp, DvMF_2508
Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

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

Catalytic activityi

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

Cofactori

Magnesium By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi492 – 4921Magnesium By similarity
Metal bindingi498 – 4981Magnesium By similarity

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
Complete GO annotation...

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 nucleotidyltransferase (EC:2.7.7.8)
Alternative name(s):
Polynucleotide phosphorylase
Short name:
PNPase
Gene namesi
Name:pnp
Ordered Locus Names:DvMF_2508
OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Taxonomic identifieri883 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000001361: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 756756Polyribonucleotide nucleotidyltransferaseUniRule annotationPRO_1000147916Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi883.DvMF_2508.

Structurei

3D structure databases

ProteinModelPortaliB8DN07.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini559 – 61860KHAdd
BLAST
Domaini628 – 70275S1 motifAdd
BLAST

Sequence similaritiesi

Contains 1 KH domain.
Contains 1 S1 motif domain.

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

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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: September 3, 2014
This is version 40 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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