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Q87M06

- PNP_VIBPA

UniProt

Q87M06 - PNP_VIBPA

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Protein
Polyribonucleotide nucleotidyltransferase
Gene
pnp, VP2452
Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
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 bindingi487 – 4871Magnesium By similarity
Metal bindingi493 – 4931Magnesium By similarity

GO - Molecular functioni

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

GO - Biological processi

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

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-2509-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:VP2452
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493: 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 – 711711Polyribonucleotide nucleotidyltransferaseUniRule annotation
PRO_0000329931Add
BLAST

Interactioni

Subunit structurei

Component of the RNA degradosome, which is a multiprotein complex involved in RNA processing and mRNA degradation By similarity.

Protein-protein interaction databases

STRINGi223926.VP2452.

Structurei

3D structure databases

ProteinModelPortaliQ87M06.
SMRiQ87M06. Positions 618-693.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini554 – 61360KH
Add
BLAST
Domaini623 – 69169S1 motif
Add
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.

Q87M06-1 [UniParc]FASTAAdd to Basket

« Hide

MFEKPVVKTF QYGNHTVTLE TGVIARQATA AVMVTMDDTA VFVSVVGKKE    50
AVAGQDFFPL TVNYQERTYA AGKIPGGFFK REGRPSEGET LTARLIDRPI 100
RPLFPDAFKN EVQVIATVVS VNPDVQPDIP TMIGTSAALA ISGIPFNGPI 150
GAARVGHIDG QLVLNPSQTE LNASRLDLVV AGTESAVLMV ESEADNLTEE 200
EMLAAVVFGH DQQQVVINAI NEFKAEVATP AWDWVAPEEN TALKTKIAEL 250
AEAKLVEAYQ ITEKMARYDR IHEIAAEVNE ALLAQDPEAD TKEIHTIFHD 300
LEKTVVRRSI IAGNPRIDGR EKDMVRALDV RTGVLPRTHG SALFTRGETQ 350
ALVTATLGTQ RDAQIIDELT GERKDHFLLH YNFPPYCVGE TGFVGSPKRR 400
EIGHGKLAKR GIAAVMPSVD EFPYTVRVVS EITESNGSSS MASVCGTSLA 450
LMDAGVPIKA SVAGIAMGLV KEGDDFVVLS DILGDEDHLG DMDFKVAGTS 500
TGVTALQMDI KIEGITKEIM QIALNQAQGA RKHILSVMDE ALAGARDDIS 550
EFAPRIHTMK ISAEKIKDVI GKGGAVIRAL TEETGTTIEI EDDGTIKIAA 600
TEGAAAKEAI RRIEEITAEV EVGRIYTGKV ARLADFGAFV TVLPGKDGLV 650
HISQIAEKRV EKVSDYLTEG QEVQVKVLEI DRQGRVRLSM KEAVEKPAEE 700
AAAEAPAAKE E 711
Length:711
Mass (Da):76,738
Last modified:June 1, 2003 - v1
Checksum:iBBF41F227161F563
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000031 Genomic DNA. Translation: BAC60715.1.
RefSeqiNP_798831.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC60715; BAC60715; BAC60715.
GeneIDi1189965.
KEGGivpa:VP2452.
PATRICi20143048. VBIVibPar50997_2353.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000031 Genomic DNA. Translation: BAC60715.1 .
RefSeqi NP_798831.1. NC_004603.1.

3D structure databases

ProteinModelPortali Q87M06.
SMRi Q87M06. Positions 618-693.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 223926.VP2452.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAC60715 ; BAC60715 ; BAC60715 .
GeneIDi 1189965.
KEGGi vpa:VP2452.
PATRICi 20143048. VBIVibPar50997_2353.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci VPAR223926:GHK4-2509-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. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiPNP_VIBPA
AccessioniPrimary (citable) accession number: Q87M06
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 29, 2008
Last sequence update: June 1, 2003
Last modified: May 14, 2014
This is version 69 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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