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C5CT24

- PNP_VARPS

UniProt

C5CT24 - PNP_VARPS

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Protein

Polyribonucleotide nucleotidyltransferase

Gene

pnp

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.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi488 – 4881MagnesiumUniRule annotation
Metal bindingi494 – 4941MagnesiumUniRule 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
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 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:Vapar_3514
OrganismiVariovorax paradoxus (strain S110)
Taxonomic identifieri543728 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeVariovorax
ProteomesiUP000000453: Chromosome 1

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 772772Polyribonucleotide nucleotidyltransferasePRO_1000215672Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi543728.Vapar_3514.

Structurei

3D structure databases

ProteinModelPortaliC5CT24.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini555 – 61460KHUniRule annotationAdd
BLAST
Domaini624 – 69269S1 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.
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. S1_dom.
[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

        10         20         30         40         50
MSLFNKVTKS FQWGDKTVVM ETGEIARQAS GAVVVDIDGT VILATVVASK
60 70 80 90 100
TAKPGQDFFP LTVDYIEKTY AAGKIPGSFF KREAKPSEHE TLTSRLIDRP
110 120 130 140 150
IRPLFPEGFL NEVHVVIHTL SLNPEVDADI AAMIGVSAAL SISGIPFSGP
160 170 180 190 200
IGAARVGYIN GQYVLNPGQT ARKDSQMDLV VAGTEAAVLM VESEAQQLSE
210 220 230 240 250
EIMLGGVVFG HEQANIAINA IHELVRDAGK PVWDWQAPAE DEAFVAKVKS
260 270 280 290 300
LAEEKLRAVY QIRSKQARTQ ALREANASVM NTLKESGEPF DAGKVNDLLF
310 320 330 340 350
AIESKIVRSQ ILSGEPRIDG RDTRTVRPIE IRNSVLPRTH GSALFTRGET
360 370 380 390 400
QGLVVTTLGT ERDAQRIDAL AGEYEDRFLF HYNMPPFATG EVGRMGSTKR
410 420 430 440 450
REIGHGRLAK RALVAVLPTK EEFPYTIRVV SEITESNGSS SMASVCGGCL
460 470 480 490 500
SMMDAGVPMK AHVAGIAMGL IKEDNRFAVL TDILGDEDHL GDMDFKVAGT
510 520 530 540 550
TNGITALQMD IKIQGITKEI MQVALAQAKE ARMHILGKMQ EAMGEAKTEV
560 570 580 590 600
SQFAPRLTTL KINPEKIRDV IGKGGAVIRG LQEETGTTIN IDEDGTITIA
610 620 630 640 650
STDPEKAEFA KKRIEQITAE VEIGKVYEGP VTKILDFGAL INLLPGKDGL
660 670 680 690 700
LHISQIAHER VEKVTDYLSE GQIVKVKVLE TDEKGRVKLS MKALTERPAG
710 720 730 740 750
MEYSERPPRE DRGDRGDRGG ERRERSDRGD RGGDRGERAP RFNSEQQQQP
760 770
RSNEQQPAPV GEQPYAPRDS QE
Length:772
Mass (Da):84,330
Last modified:July 28, 2009 - v1
Checksum:i0CE933ACBD8CB6B5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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. S1_dom.
[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: November 26, 2014
This is version 38 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