P56123 (RNR_HELPY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribonuclease R
Short name=RNase R
EC=3.1.13.1

Alternative name(s):
VacB protein homolog

Gene names

Name:	rnr
Synonyms:	vacB
Ordered Locus Names:	HP_1248

Organism

Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) [Reference proteome] [HAMAP]

Taxonomic identifier

85962 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Epsilonproteobacteria › Campylobacterales › Helicobacteraceae › Helicobacter › Helicobacter pylori

Protein attributes

Sequence length	644 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs By similarity. HAMAP-Rule MF_01895
Catalytic activity	Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. HAMAP-Rule MF_01895
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01895.
Sequence similarities	Belongs to the RNR ribonuclease family. RNase R subfamily. Contains 1 S1 motif domain.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	RNA-binding
Molecular function	Exonuclease Hydrolase Nuclease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA metabolic process Inferred from electronic annotation. Source: HAMAP nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	RNA binding Inferred from electronic annotation. Source: HAMAP exoribonuclease II 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 – 644	644	Ribonuclease R HAMAP-Rule MF_01895		PRO_0000166404
Regions
	Domain	573 – 644	72	S1 motif

Sequences

	Sequence		Length	Mass (Da)
	P56123 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 960C62605A041EE4	FASTA	644	74,163
	10 20 30 40 50 60 MQGFLRSLFF GVKKIPKPFA PLVEKGVLKE ALELKKDRYF LKEGFDIGKV EKVKDKAFFI 70 80 90 100 110 120 SLAKNYPKDP LIKNLPPSFK TDALILCQIE CSKKRPIAFF KAALLNADHT MIAYLAKKNN 130 140 150 160 170 180 QIVAIPFKEP FKKPVSLKHS QKSLLELPRH CVVKIDTKKR EISEILGALE DPLIDENLSL 190 200 210 220 230 240 SLFDRVKDFS KDCLNLAQHY AQLKASDFKD RINYSHIPFI TIDPKDAKDF DDAIFYDQEK 250 260 270 280 290 300 RVLFVAVADV SEFVPKHSSL DKEARVRGFS VYFPNSVYPM LPLSLSQGAC SLKAFEKRLA 310 320 330 340 350 360 LVYEIPLDNL KNARLSQGVI EVRANCTYEE INHFLSANQS SLDKDLQQSL LGFLEMALKL 370 380 390 400 410 420 KKERLKKGFN FNSFENKLYL NKEGRIEKIE TEKESDAHTL IEEAMLLANQ SSARLLDEHF 430 440 450 460 470 480 HNKGIYRTHK EPSLEQQKRL YDKLFDYEIV RPKNMGFFPF LEHALKIAKE KSIEREVSRL 490 500 510 520 530 540 IIKSQNLALY SPLQESHFGL GFASYTHFTS PIRRYSDLAL HRLLKELLFY QAKGCSYLLE 550 560 570 580 590 600 ETPELCAELN ALQKKAALIE RDFIKRKFAR LALELLEKEF LGVVLEVKDW VVVGLKEFIG 610 620 630 640 LKVLVKTNKV FKPLEKVRVT ITHADLILGQ VRGEITERIK EHVS

References

[1]

"The complete genome sequence of the gastric pathogen Helicobacter pylori." Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A., Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N., Loftus B.J., Richardson D.L., Dodson R.J. , Khalak H.G., Glodek A., McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D., Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S., Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C. Nature 388:539-547(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700392 / 26695.

+

Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE000511 Genomic DNA. Translation: AAD08293.1.
PIR	H64675.
RefSeq	NP_208040.1. NC_000915.1. YP_006935168.1. NC_018939.1.
3D structure databases
ProteinModelPortal	P56123.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-3252N.
MINT	MINT-159708.
STRING	85962.HP1248.
PTM databases
PhosSite	P11071047.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAD08293; AAD08293; HP_1248.
GeneID	13870455. 898781.
KEGG	heo:C694_06450. hpy:HP1248.
PATRIC	20593873. VBIHelPyl33062_1307.
Phylogenomic databases
eggNOG	COG0557.
KO	K12573.
OMA	DCMLLAN.
ProtClustDB	CLSK872530.
Family and domain databases
HAMAP	MF_01895. RNase_R.
InterPro	IPR001900. RNase_II/R. IPR022966. RNase_II/R_CS. IPR011805. RNase_R. [Graphical view]
Pfam	PF00773. RNB. 1 hit. [Graphical view]
SMART	SM00955. RNB. 1 hit. [Graphical view]
PROSITE	PS01175. RIBONUCLEASE_II. 1 hit. PS50126. S1. False negative. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RNR_HELPY

Accession

Primary (citable) accession number: P56123

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program