Skip Header

Contribute Send feedback
Read comments (?) or add your own

P30850 (RNB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 110. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Exoribonuclease 2
EC=3.1.13.1
Alternative name(s):
Exoribonuclease II
Short name=RNase II
Short name=Ribonuclease II
Gene names
Name:rnb
Ordered Locus Names:b1286, JW1279
OrganismEscherichia coli (strain K12)
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length644 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3' to 5' direction. Ref.6

Catalytic activity

Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. HAMAP MF_01036

Cofactor

Magnesium. Ref.6

Enzyme regulation

Stimulated by the presence of a monovalent cation. Ref.6

Subcellular location

Cytoplasm HAMAP MF_01036.

Sequence similarities

Belongs to the RNR ribonuclease family. RNase II subfamily.

Contains 1 S1 motif domain.

Biophysicochemical properties

Kinetic parameters:

Vmax=109800 nmol/min/mg enzyme with Poly(A) as substrate Ref.6

Vmax=160 nmol/min/mg enzyme with 23S rRNA as substrate

Vmax=30 nmol/min/mg enzyme with 16S rRNA as substrate

Vmax=20 nmol/min/mg enzyme with 5S rRNA as substrate

pH dependence:

Optimum pH is 7.5-9.5.

Temperature dependence:

Optimum temperature is 50 degrees Celsius.

Ontologies

Keywords
   Cellular componentCytoplasm
   LigandRNA-binding
   Molecular functionExonuclease
Hydrolase
Nuclease
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological processRNA catabolic process

Inferred from electronic annotation. Source: InterPro

   Cellular componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular functionRNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

exoribonuclease II activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 644644Exoribonuclease 2 HAMAP MF_01036
PRO_0000166380

Regions

Domain561 – 64383S1 motif

Experimental info

Sequence conflict3841I → N in CAA48112. Ref.1
Sequence conflict3991C → G in CAA48112. Ref.1
Sequence conflict5131A → R in CAA48112. Ref.1

Secondary structure

1 .............................................................................................................. 644
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P30850 [UniParc].

Last modified November 1, 1997. Version 3.
Checksum: 36B16712CDF14394

FASTA64472,491
        10         20         30         40         50         60 
MFQDNPLLAQ LKQQLHSQTP RAEGVVKATE KGFGFLEVDA QKSYFIPPPQ MKKVMHGDRI 

        70         80         90        100        110        120 
IAVIHSEKER ESAEPEELVE PFLTRFVGKV QGKNDRLAIV PDHPLLKDAI PCRAARGLNH 

       130        140        150        160        170        180 
EFKEGDWAVA EMRRHPLKGD RSFYAELTQY ITFGDDHFVP WWVTLARHNL EKEAPDGVAT 

       190        200        210        220        230        240 
EMLDEGLVRE DLTALDFVTI DSASTEDMDD ALFAKALPDD KLQLIVAIAD PTAWIAEGSK 

       250        260        270        280        290        300 
LDKAAKIRAF TNYLPGFNIP MLPRELSDDL CSLRANEVRP VLACRMTLSA DGTIEDNIEF 

       310        320        330        340        350        360 
FAATIESKAK LVYDQVSDWL ENTGDWQPES EAIAEQVRLL AQICQRRGEW RHNHALVFKD 

       370        380        390        400        410        420 
RPDYRFILGE KGEVLDIVAE PRRIANRIVE EAMIAANICA ARVLRDKLGF GIYNVHMGFD 

       430        440        450        460        470        480 
PANADALAAL LKTHGLHVDA EEVLTLDGFC KLRRELDAQP TGFLDSRIRR FQSFAEISTE 

       490        500        510        520        530        540 
PGPHFGLGLE AYATWTSPIR KYGDMINHRL LKAVIKGETA TRPQDEITVQ MAERRRLNRM 

       550        560        570        580        590        600 
AERDVGDWLY ARFLKDKAGT DTRFAAEIVD ISRGGMRVRL VDNGAIAFIP APFLHAVRDE 

       610        620        630        640 
LVCSQENGTV QIKGETVYKV TDVIDVTIAE VRMETRSIIA RPVA

« Hide

References

« Hide 'large scale' references
[1]"DNA sequencing and expression of the gene rnb encoding Escherichia coli ribonuclease II."
Zilhao R., Camelo L., Arraiano C.M.
Mol. Microbiol. 8:43-51(1993) [PubMed: 8497196] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]Zilhao R.
Submitted (OCT-1994) to the EMBL/GenBank/DDBJ databases
Cited for: SEQUENCE REVISION.
[3]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed: 9097039] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]"Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II."
Cheng Z.F., Deutscher M.P.
J. Biol. Chem. 277:21624-21629(2002) [PubMed: 11948193] [Abstract]
Cited for: FUNCTION, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		X67913 Genomic DNA. Translation: CAA48112.1.
U00096 Genomic DNA. Translation: AAC74368.1.
AP009048 Genomic DNA. Translation: BAA14840.1.
PIRA64877.
RefSeqNP_415802.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2ID0X-ray2.35A/B/C/D1-644[»]
2IX0X-ray2.44A6-644[»]
2IX1X-ray2.74A6-644[»]
ProteinModelPortalP30850.
SMRP30850. Positions 5-644.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-10724N.
IntActP30850. 10 interactions.
MINTMINT-1248196.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaEBESCT00000004108; EBESCP00000004108; EBESCG00000003356.
EBESCT00000004109; EBESCP00000004109; EBESCG00000003356.
EBESCT00000015364; EBESCP00000014655; EBESCG00000014424.
GeneID945864.
GenomeReviewsGene locus JW1279 in contig AP009048_GR.
Gene locus b1286 in contig U00096_GR.
KEGGecj:JW1279.
eco:b1286.
PATRIC32117840. VBIEscCol129921_1340.

Organism-specific databases

EchoBASEEB1577.
EcoGeneEG11620. rnb.

Phylogenomic databases

eggNOGCOG4776.
GeneTreeEBGT00050000010946.
HOGENOMHBG401488.
OMAMDDALYI.
PhylomeDBP30850.
ProtClustDBPRK05054.

Enzyme and pathway databases

BioCycEcoCyc:EG11620-MONOMER.
MetaCyc:EG11620-MONOMER.
BRENDA3.1.13.1. 2026.

Gene expression databases

GenevestigatorP30850.

Family and domain databases

HAMAPMF_01036. RNase_II.
[Tree]
InterProIPR011129. Cold_shock_prot.
IPR016027. NA-bd_OB-fold-like.
IPR003029. Rbsml_prot_S1_RNA-bd_dom.
IPR022967. RNA-binding_domain_S1.
IPR013223. RNase_B_OB_dom.
IPR011804. RNase_II.
IPR001900. RNase_II/R.
IPR022966. RNase_II/R_CS.
IPR004476. RNase_II/RNase_R.
[Graphical view]
KOK01147.
PANTHERPTHR23355:SF6. RNase_II_bac. 1 hit.
PfamPF08206. OB_RNB. 1 hit.
PF00773. RNB. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTSM00357. CSP. 1 hit.
SM00955. RNB. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMSSF50249. Nucleic_acid_OB. 1 hit.
TIGRFAMsTIGR00358. 3_prime_RNase. 1 hit.
TIGR02062. RNase_B. 1 hit.
PROSITEPS01175. RIBONUCLEASE_II. 1 hit.
PS50126. S1. False negative.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameRNB_ECOLI
AccessionPrimary (citable) accession number: P30850
Secondary accession number(s): P78280
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: November 1, 1997
Last modified: January 25, 2012
This is version 110 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents