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C5CT24

- PNP_VARPS

UniProt

C5CT24 - PNP_VARPS

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Protein

Polyribonucleotide nucleotidyltransferase

Gene
pnp, Vapar_3514
Organism
Variovorax paradoxus (strain S110)
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 bindingi488 – 4881Magnesium By similarity
Metal bindingi494 – 4941Magnesium 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

BioCyciVPAR543728:GHLL-3546-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:Vapar_3514
OrganismiVariovorax paradoxus (strain S110)
Taxonomic identifieri543728 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeVariovorax
ProteomesiUP000000453: Chromosome 1

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 – 772772Polyribonucleotide nucleotidyltransferaseUniRule annotationPRO_1000215672Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi543728.Vapar_3514.

Structurei

3D structure databases

ProteinModelPortaliC5CT24.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini555 – 61460KHAdd
BLAST
Domaini624 – 69269S1 motifAdd
BLAST

Sequence similaritiesi

Contains 1 KH domain.
Contains 1 S1 motif domain.

Phylogenomic databases

eggNOGiCOG1185.
HOGENOMiHOG000218326.
KOiK00962.
OMAiPRWDWVA.
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]
SUPFAMiSSF50249. 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.

C5CT24-1 [UniParc]FASTAAdd to Basket

« Hide

MSLFNKVTKS FQWGDKTVVM ETGEIARQAS GAVVVDIDGT VILATVVASK    50
TAKPGQDFFP LTVDYIEKTY AAGKIPGSFF KREAKPSEHE TLTSRLIDRP 100
IRPLFPEGFL NEVHVVIHTL SLNPEVDADI AAMIGVSAAL SISGIPFSGP 150
IGAARVGYIN GQYVLNPGQT ARKDSQMDLV VAGTEAAVLM VESEAQQLSE 200
EIMLGGVVFG HEQANIAINA IHELVRDAGK PVWDWQAPAE DEAFVAKVKS 250
LAEEKLRAVY QIRSKQARTQ ALREANASVM NTLKESGEPF DAGKVNDLLF 300
AIESKIVRSQ ILSGEPRIDG RDTRTVRPIE IRNSVLPRTH GSALFTRGET 350
QGLVVTTLGT ERDAQRIDAL AGEYEDRFLF HYNMPPFATG EVGRMGSTKR 400
REIGHGRLAK RALVAVLPTK EEFPYTIRVV SEITESNGSS SMASVCGGCL 450
SMMDAGVPMK AHVAGIAMGL IKEDNRFAVL TDILGDEDHL GDMDFKVAGT 500
TNGITALQMD IKIQGITKEI MQVALAQAKE ARMHILGKMQ EAMGEAKTEV 550
SQFAPRLTTL KINPEKIRDV IGKGGAVIRG LQEETGTTIN IDEDGTITIA 600
STDPEKAEFA KKRIEQITAE VEIGKVYEGP VTKILDFGAL INLLPGKDGL 650
LHISQIAHER VEKVTDYLSE GQIVKVKVLE TDEKGRVKLS MKALTERPAG 700
MEYSERPPRE DRGDRGDRGG ERRERSDRGD RGGDRGERAP RFNSEQQQQP 750
RSNEQQPAPV GEQPYAPRDS QE 772
Length:772
Mass (Da):84,330
Last modified:July 28, 2009 - v1
Checksum:i0CE933ACBD8CB6B5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001635 Genomic DNA. Translation: ACS20131.1.
RefSeqiYP_002945397.1. NC_012791.1.

Genome annotation databases

EnsemblBacteriaiACS20131; ACS20131; Vapar_3514.
GeneIDi7972140.
KEGGivap:Vapar_3514.
PATRICi24007479. VBIVarPar36677_3525.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001635 Genomic DNA. Translation: ACS20131.1 .
RefSeqi YP_002945397.1. NC_012791.1.

3D structure databases

ProteinModelPortali C5CT24.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 543728.Vapar_3514.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACS20131 ; ACS20131 ; Vapar_3514 .
GeneIDi 7972140.
KEGGi vap:Vapar_3514.
PATRICi 24007479. VBIVarPar36677_3525.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci VPAR543728:GHLL-3546-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 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 genome sequence of the metabolically versatile plant growth-promoting endophyte, Variovorax paradoxus S110."
    Han J.I., Choi H.K., Lee S.W., Orwin P.M., Kim J., Laroe S.L., Kim T.G., O'Neil J., Leadbetter J.R., Lee S.Y., Hur C.G., Spain J.C., Ovchinnikova G., Goodwin L., Han C.
    J. Bacteriol. 193:1183-1190(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: S110.

Entry informationi

Entry nameiPNP_VARPS
AccessioniPrimary (citable) accession number: C5CT24
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 28, 2009
Last modified: May 14, 2014
This is version 35 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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