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Protein

Ribonuclease R

Gene

rnr

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

Functioni

3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs.UniRule annotation

Catalytic activityi

Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.UniRule annotation

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-2901-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease RUniRule annotation (EC:3.1.13.1UniRule annotation)
Short name:
RNase RUniRule annotation
Alternative name(s):
VacB protein homolog
Gene namesi
Name:rnrUniRule annotation
Synonyms:vacB
Ordered Locus Names:VP2807
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000002493 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 835835Ribonuclease RPRO_0000166416Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi223926.VP2807.

Structurei

3D structure databases

ProteinModelPortaliP40611.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini652 – 73382S1 motifUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the RNR ribonuclease family. RNase R subfamily.UniRule annotation
Contains 1 S1 motif domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C40. Bacteria.
COG0557. LUCA.
HOGENOMiHOG000071120.
KOiK12573.
OMAiAMMMATQ.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_01895. RNase_R. 1 hit.
InterProiIPR011129. Cold_shock_prot.
IPR012340. NA-bd_OB-fold.
IPR013223. RNase_B_OB_dom.
IPR022966. RNase_II/R_CS.
IPR004476. RNase_II/RNase_R.
IPR011805. RNase_R.
IPR013668. RNase_R_HTH_12.
IPR022967. S1_dom.
IPR003029. S1_domain.
[Graphical view]
PfamiPF08461. HTH_12. 1 hit.
PF08206. OB_RNB. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTiSM00357. CSP. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 4 hits.
TIGRFAMsiTIGR00358. 3_prime_RNase. 1 hit.
TIGR02063. RNase_R. 1 hit.
PROSITEiPS01175. RIBONUCLEASE_II. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P40611-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDNIPNDPF ADRESQNYEN PIPSREFILE FLEQAGVPMN RNDLFEALKL
60 70 80 90 100
AGEEQYEGLR RRLRAMERDG QLVFTRRQCY ALPEKLEMVK GYVIGHKDGH
110 120 130 140 150
GWVRPEGSVG KDDDILLPHH QMKNIIHGDF VLVQPTDNSK RGRREGRLVR
160 170 180 190 200
VLEERNSQIV GRFFLEYGYS YVVPDDSRIS QDILIPNEHK AGARMGNVVV
210 220 230 240 250
IEITDRGSRS RGMMGKVVEV LGENMAPGME TQIAIRTHQI PYEWPEAVEK
260 270 280 290 300
QIVNLGEEVP EEAKVGRVDL RELPLVTIDG EDARDFDDAV FCEKKKDGGW
310 320 330 340 350
RLWVAIADVS YYVRPDSALD KEAINRGNSV YFPSQVVPML PEVLSNGLCS
360 370 380 390 400
LNPQVDRLCM VCEMTISESG KLSSYKHYEA VMNSHARLTY SKVSAILEGD
410 420 430 440 450
EELRERYQPL VSHLEELHAM YKVLKEARDQ RGAIEFETVE TKFIFNAERK
460 470 480 490 500
IESIEPVIRN DAHKIIEECM ILANIASASL VEKAKEPALY RIHESPGELR
510 520 530 540 550
LQGFRDFLSE LGLELKGGLE PSPTDYADLA RQIAGRQDQE LIQTMLLRSM
560 570 580 590 600
KQAVYNADNA GHFGLALKRY AHFTSPIRRY PDLLLHRAIK YLIAKEEGRN
610 620 630 640 650
QDRWTPTGGY HYSFDDMDFY GEQCSMTERR ADDATREVAD WLKCEYMQDH
660 670 680 690 700
VGDELEGVIA NVTSFGFFVR LTDLHIDGLV HISTLANDYY QFDPIGQRLI
710 720 730 740 750
GESFGNIYRL GDAVKVKVLA VNLDDKQIDF ELVETSRKLR GEGKTAKKRA
760 770 780 790 800
AEAKRKAKEK KRAATRSSSK ESATARAVPA IEPTKRPEQT DSGRKRKGPK
810 820 830
RGDDDSAKKP KVKKAHKKKP HSKPKKTKRT KQDAQ
Length:835
Mass (Da):95,037
Last modified:April 4, 2003 - v2
Checksum:iFA0674C937407F5F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC61070.1.
U09005 Genomic DNA. Translation: AAA62192.1.
RefSeqiNP_799186.1. NC_004603.1.
WP_005480076.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC61070; BAC61070; BAC61070.
GeneIDi1190357.
KEGGivpa:VP2807.
PATRICi20143814. VBIVibPar50997_2699.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC61070.1.
U09005 Genomic DNA. Translation: AAA62192.1.
RefSeqiNP_799186.1. NC_004603.1.
WP_005480076.1. NC_004603.1.

3D structure databases

ProteinModelPortaliP40611.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP2807.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC61070; BAC61070; BAC61070.
GeneIDi1190357.
KEGGivpa:VP2807.
PATRICi20143814. VBIVibPar50997_2699.

Phylogenomic databases

eggNOGiENOG4105C40. Bacteria.
COG0557. LUCA.
HOGENOMiHOG000071120.
KOiK12573.
OMAiAMMMATQ.

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-2901-MONOMER.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_01895. RNase_R. 1 hit.
InterProiIPR011129. Cold_shock_prot.
IPR012340. NA-bd_OB-fold.
IPR013223. RNase_B_OB_dom.
IPR022966. RNase_II/R_CS.
IPR004476. RNase_II/RNase_R.
IPR011805. RNase_R.
IPR013668. RNase_R_HTH_12.
IPR022967. S1_dom.
IPR003029. S1_domain.
[Graphical view]
PfamiPF08461. HTH_12. 1 hit.
PF08206. OB_RNB. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTiSM00357. CSP. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 4 hits.
TIGRFAMsiTIGR00358. 3_prime_RNase. 1 hit.
TIGR02063. RNase_R. 1 hit.
PROSITEiPS01175. RIBONUCLEASE_II. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRNR_VIBPA
AccessioniPrimary (citable) accession number: P40611
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: April 4, 2003
Last modified: September 7, 2016
This is version 101 of the entry and version 2 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.