C5CSF5 (RNC_VARPS) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribonuclease 3
EC=3.1.26.3

Alternative name(s):
Ribonuclease III
Short name=RNase III

Gene names

Name:	rnc
Ordered Locus Names:	Vapar_1402

Organism

Variovorax paradoxus (strain S110) [Complete proteome] [HAMAP]

Taxonomic identifier

543728 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Comamonadaceae › Variovorax › Variovorax paradoxus

Protein attributes

Sequence length	228 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	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). Also processes some mRNAs, and tRNAs when they are encoded in the rRNA operon By similarity. HAMAP-Rule MF_00104
Catalytic activity	Endonucleolytic cleavage to 5'-phosphomonoester. HAMAP-Rule MF_00104
Cofactor	Mg2+ By similarity.
Subunit structure	Homodimer By similarity.
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Contains 1 DRBM (double-stranded RNA-binding) domain. Contains 1 RNase III domain.

Ontologies

Keywords
Biological process	mRNA processing rRNA processing tRNA processing
Cellular component	Cytoplasm
Ligand	Magnesium Metal-binding RNA-binding rRNA-binding
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	mRNA processing Inferred from electronic annotation. Source: HAMAP nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC rRNA catabolic process Inferred from electronic annotation. Source: InterPro rRNA processing Inferred from electronic annotation. Source: HAMAP tRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	double-stranded RNA binding Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW rRNA binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease III activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 228	228	Ribonuclease 3 HAMAP-Rule MF_00104		PRO_1000202847
Regions
	Domain	5 – 127	123	RNase III
	Domain	154 – 224	71	DRBM
Sites
	Active site	44	1	Potential
	Active site	116	1	By similarity
	Metal binding	40	1	Magnesium By similarity
	Metal binding	113	1	Magnesium By similarity
	Metal binding	116	1	Magnesium By similarity

Sequences

	Sequence		Length	Mass (Da)
	C5CSF5 [UniParc]. Last modified July 28, 2009. Version 1. Checksum: 81FA9E801F426F7A	FASTA	228	24,876
	10 20 30 40 50 60 MDGGLTALQE RLKHSFSDTR LLQLALTHRS FSADHNERLE FLGDSVLNLA VSHLLYTRLS 70 80 90 100 110 120 ALPEGDLSRV RANLVKQDTL HRLALELQLS PLLRLGEGEA RSGGPNRPSI LADALEALIG 130 140 150 160 170 180 AVYLDAGFSA AEALVRRLYE SVEINPRMDA VAKDPKTELQ EWLQGHKMKL PVYRVAATLG 190 200 210 220 AAHKQTFDVE CEVPELGLRE RGIGGSRRAG EQAAAAAMLI RLKARGAA

References

[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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001635 Genomic DNA. Translation: ACS18053.1.
RefSeq	YP_002943319.1. NC_012791.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	543728.Vapar_1402.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACS18053; ACS18053; Vapar_1402.
GeneID	7971230.
KEGG	vap:Vapar_1402.
PATRIC	24003232. VBIVarPar36677_1423.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0571.
HOGENOM	HOG000246809.
KO	K03685.
OMA	LTHKSCK.
ProtClustDB	PRK00102.
Family and domain databases
Gene3D	1.10.1520.10. 1 hit. 3.30.160.20. 1 hit.
HAMAP	MF_00104. RNase_III.
InterPro	IPR001159. Ds-RNA-bd. IPR014720. dsRNA-bd-like_dom. IPR011907. RNase_III. IPR000999. RNase_III_dom. [Graphical view]
PANTHER	PTHR11207. PTHR11207. 1 hit.
Pfam	PF00035. dsrm. 1 hit. PF00636. Ribonuclease_3. 1 hit. [Graphical view]
SMART	SM00358. DSRM. 1 hit. SM00535. RIBOc. 1 hit. [Graphical view]
SUPFAM	SSF69065. RNase_III. 1 hit.
TIGRFAMs	TIGR02191. RNaseIII. 1 hit.
PROSITE	PS50137. DS_RBD. 1 hit. PS00517. RNASE_3_1. 1 hit. PS50142. RNASE_3_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RNC_VARPS

Accession

Primary (citable) accession number: C5CSF5

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 22, 2009
Last sequence update:	July 28, 2009
Last modified:	April 3, 2013
This is version 30 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program