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Protein

Ribonuclease 3

Gene

rnc

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism.UniRule annotation

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphomonoester.UniRule annotation

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi63 – 631MagnesiumUniRule annotation
Active sitei67 – 671UniRule annotation
Metal bindingi136 – 1361MagnesiumUniRule annotation
Active sitei139 – 1391UniRule annotation
Metal bindingi139 – 1391MagnesiumUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, rRNA processing, tRNA processing

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-5098-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease 3UniRule annotation (EC:3.1.26.3UniRule annotation)
Alternative name(s):
Ribonuclease IIIUniRule annotation
Short name:
RNase IIIUniRule annotation
Gene namesi
Name:rncUniRule annotation
Ordered Locus Names:bll5061
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
ProteomesiUP000002526 Componenti: Chromosome

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 – 250250Ribonuclease 3PRO_0000180377Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224911.bll5061.

Structurei

3D structure databases

ProteinModelPortaliO69161.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini22 – 150129RNase IIIUniRule annotationAdd
BLAST
Domaini175 – 24470DRBMUniRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 DRBM (double-stranded RNA-binding) domain.UniRule annotation
Contains 1 RNase III domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG0571.
HOGENOMiHOG000246809.
InParanoidiO69161.
KOiK03685.
OrthoDBiEOG6T1WVS.

Family and domain databases

Gene3Di1.10.1520.10. 1 hit.
3.30.160.20. 1 hit.
HAMAPiMF_00104. RNase_III.
InterProiIPR014720. dsRNA-bd_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]
PANTHERiPTHR11207. PTHR11207. 1 hit.
PfamiPF00035. dsrm. 1 hit.
PF00636. Ribonuclease_3. 1 hit.
[Graphical view]
SMARTiSM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
[Graphical view]
SUPFAMiSSF69065. SSF69065. 1 hit.
TIGRFAMsiTIGR02191. RNaseIII. 1 hit.
PROSITEiPS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O69161-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKTPAKKKR ARSSKAKGTD ANAALEARIG HSFADPNLLM QGITHVSALK
60 70 80 90 100
SGRKRGDSYQ RLEFLGDHVL GLVVSDMLYH AFPNADEGEL SKRLAELVRK
110 120 130 140 150
ESCADVAKSL GLLDDIKLGS VGPSADARLR KSVLGDICEA VIGAIFLDGG
160 170 180 190 200
HAAAAEFVKR NWTERMHKPR RPLRDPKTVL QEWAQGKGLP TPVYREVERT
210 220 230 240 250
GPHHDPQFRV AVDLPGLAPA EGIGGSKRAA EKVAASVMIE REGVGGGNDG
Length:250
Mass (Da):26,856
Last modified:February 28, 2003 - v2
Checksum:i19E6FE9D2DDDC930
GO

Sequence cautioni

The sequence BAC50326.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1 – 3232MTKTP…RIGHS → MRTRRLRRASGHT in AAD02939 (Ref. 1) CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF065159 Genomic DNA. Translation: AAD02939.1.
BA000040 Genomic DNA. Translation: BAC50326.1. Different initiation.
RefSeqiNP_771701.1. NC_004463.1.

Genome annotation databases

EnsemblBacteriaiBAC50326; BAC50326; BAC50326.
GeneIDi1051815.
KEGGibja:bll5061.
PATRICi21193792. VBIBraJap65052_5141.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF065159 Genomic DNA. Translation: AAD02939.1.
BA000040 Genomic DNA. Translation: BAC50326.1. Different initiation.
RefSeqiNP_771701.1. NC_004463.1.

3D structure databases

ProteinModelPortaliO69161.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224911.bll5061.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC50326; BAC50326; BAC50326.
GeneIDi1051815.
KEGGibja:bll5061.
PATRICi21193792. VBIBraJap65052_5141.

Phylogenomic databases

eggNOGiCOG0571.
HOGENOMiHOG000246809.
InParanoidiO69161.
KOiK03685.
OrthoDBiEOG6T1WVS.

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-5098-MONOMER.

Family and domain databases

Gene3Di1.10.1520.10. 1 hit.
3.30.160.20. 1 hit.
HAMAPiMF_00104. RNase_III.
InterProiIPR014720. dsRNA-bd_dom.
IPR011907. RNase_III.
IPR000999. RNase_III_dom.
[Graphical view]
PANTHERiPTHR11207. PTHR11207. 1 hit.
PfamiPF00035. dsrm. 1 hit.
PF00636. Ribonuclease_3. 1 hit.
[Graphical view]
SMARTiSM00358. DSRM. 1 hit.
SM00535. RIBOc. 1 hit.
[Graphical view]
SUPFAMiSSF69065. SSF69065. 1 hit.
TIGRFAMsiTIGR02191. RNaseIII. 1 hit.
PROSITEiPS50137. DS_RBD. 1 hit.
PS00517. RNASE_3_1. 1 hit.
PS50142. RNASE_3_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "sipF, the second functional type I signal peptidase of Bradyrhizobium japonicum, is encoded in the vicinity of essential genes involved in RNA processing and cell division."
    Bairl A., Mueller P.
    Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: USDA 110spc4.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.

Entry informationi

Entry nameiRNC_BRADU
AccessioniPrimary (citable) accession number: O69161
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: February 28, 2003
Last modified: January 7, 2015
This is version 91 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

External Data

Dasty 3

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 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.