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Protein

Ribonuclease BN

Gene

rbn

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Zinc phosphodiesterase, which has both exoribonuclease and endoribonuclease activities, depending on the nature of the substrate and of the added divalent cation, and on its 3'-terminal structure. Can process the 3' termini of both CCA-less and CCA-containing tRNA precursors. CCA-less tRNAs are cleaved endonucleolytically after the discriminator base, whereas residues following the CCA sequence can be removed exonucleolytically or endonucleolytically in CCA-containing molecules. Does not remove the CCA sequence. May also be involved in the degradation of mRNAs. In vitro, hydrolyzes bis(p-nitrophenyl)phosphate and thymidine-5'-p-nitrophenyl phosphate.5 Publications

Cofactori

Zn2+1 PublicationNote: Binds 2 Zn2+ ions.1 Publication

Enzyme regulationi

Activated by cobalt and manganese. Strongly inhibited by the presence of a 3'-CCA sequence or a 3'-phosphoryl group.3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi64 – 641Zinc 1; catalyticUniRule annotation1 Publication
Metal bindingi66 – 661Zinc 1; catalyticUniRule annotation1 Publication
Active sitei68 – 681Proton acceptorUniRule annotation
Metal bindingi68 – 681Zinc 2; catalyticUniRule annotation1 Publication
Metal bindingi69 – 691Zinc 2; catalyticUniRule annotation1 Publication
Metal bindingi141 – 1411Zinc 1; catalyticUniRule annotation1 Publication
Metal bindingi212 – 2121Zinc 1; catalyticUniRule annotation1 Publication
Metal bindingi212 – 2121Zinc 2; catalyticUniRule annotation1 Publication
Metal bindingi270 – 2701Zinc 2; catalyticUniRule annotation1 Publication

GO - Molecular functioni

  • 3'-tRNA processing endoribonuclease activity Source: GO_Central
  • exoribonuclease activity Source: EcoliWiki
  • nuclease activity Source: EcoliWiki
  • zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  • tRNA processing Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G7175-MONOMER.
ECOL316407:JW2263-MONOMER.
MetaCyc:G7175-MONOMER.
BRENDAi3.1.26.11. 2026.
SABIO-RKP0A8V0.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease BNUniRule annotation (EC:3.1.-.-UniRule annotation)
Short name:
RNase BNUniRule annotation
Alternative name(s):
Ribonuclease Z homologUniRule annotation
Short name:
RNase Z homologUniRule annotation
Gene namesi
Name:rbn
Synonyms:elaC, rnz
Ordered Locus Names:b2268, JW2263
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14260. rbn.

Pathology & Biotechi

Disruption phenotypei

Mutants are unaffected in growth.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 305305Ribonuclease BNPRO_0000155863Add
BLAST

Proteomic databases

PaxDbiP0A8V0.
PRIDEiP0A8V0.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

BioGridi4263118. 10 interactions.
DIPiDIP-9498N.
IntActiP0A8V0. 7 interactions.
MINTiMINT-1275952.
STRINGi511145.b2268.

Structurei

Secondary structure

1
305
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76Combined sources
Beta strandi9 – 124Combined sources
Beta strandi21 – 255Combined sources
Beta strandi34 – 374Combined sources
Helixi43 – 486Combined sources
Turni54 – 563Combined sources
Beta strandi57 – 615Combined sources
Helixi67 – 704Combined sources
Helixi73 – 8210Combined sources
Beta strandi89 – 946Combined sources
Helixi97 – 10711Combined sources
Beta strandi116 – 1205Combined sources
Beta strandi123 – 1286Combined sources
Beta strandi130 – 1389Combined sources
Beta strandi140 – 1434Combined sources
Beta strandi146 – 1527Combined sources
Helixi161 – 1666Combined sources
Helixi173 – 1808Combined sources
Turni187 – 1893Combined sources
Helixi194 – 1963Combined sources
Beta strandi206 – 2094Combined sources
Helixi219 – 2235Combined sources
Beta strandi227 – 2326Combined sources
Helixi237 – 2393Combined sources
Helixi240 – 2456Combined sources
Helixi251 – 26111Combined sources
Beta strandi264 – 2696Combined sources
Helixi277 – 28812Combined sources
Beta strandi294 – 2963Combined sources
Beta strandi302 – 3043Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CBNX-ray2.90A1-305[»]
ProteinModelPortaliP0A8V0.
SMRiP0A8V0. Positions 1-305.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8V0.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase Z family. RNase BN subfamily.UniRule annotationCurated

Phylogenomic databases

eggNOGiENOG4105IES. Bacteria.
COG1234. LUCA.
HOGENOMiHOG000272419.
InParanoidiP0A8V0.
KOiK00784.
OMAiSYAFCSD.
OrthoDBiEOG61P6TK.
PhylomeDBiP0A8V0.

Family and domain databases

Gene3Di3.60.15.10. 2 hits.
HAMAPiMF_01818. RNase_Z_BN.
InterProiIPR001279. Metallo-B-lactamas.
IPR013469. Rbn.
IPR013471. RNase_Z/BN.
[Graphical view]
PfamiPF12706. Lactamase_B_2. 2 hits.
[Graphical view]
SMARTiSM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.
TIGRFAMsiTIGR02651. RNase_Z. 1 hit.
TIGR02649. true_RNase_BN. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A8V0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELIFLGTSA GVPTRTRNVT AILLNLQHPT QSGLWLFDCG EGTQHQLLHT
60 70 80 90 100
AFNPGKLDKI FISHLHGDHL FGLPGLLCSR SMSGIIQPLT IYGPQGIREF
110 120 130 140 150
VETALRISGS WTDYPLEIVE IGAGEILDDG LRKVTAYPLE HPLECYGYRI
160 170 180 190 200
EEHDKPGALN AQALKAAGVP PGPLFQELKA GKTITLEDGR QINGADYLAA
210 220 230 240 250
PVPGKALAIF GDTGPCDAAL DLAKGVDVMV HEATLDITME AKANSRGHSS
260 270 280 290 300
TRQAATLARE AGVGKLIITH VSSRYDDKGC QHLLRECRSI FPATELANDF

TVFNV
Length:305
Mass (Da):32,930
Last modified:June 7, 2005 - v1
Checksum:i69A55EAE8BDDEF68
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti154 – 1541D → Y in AAB02732 (Ref. 1) Curated
Sequence conflicti217 – 2171D → N in AAB02732 (Ref. 1) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U58768 Genomic DNA. Translation: AAB02732.1.
U00096 Genomic DNA. Translation: AAC75328.2.
AP009048 Genomic DNA. Translation: BAA16095.2.
PIRiB64998.
RefSeqiNP_416771.4. NC_000913.3.
WP_001300687.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75328; AAC75328; b2268.
BAA16095; BAA16095; BAA16095.
GeneIDi946760.
KEGGiecj:JW2263.
eco:b2268.
PATRICi32119903. VBIEscCol129921_2361.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U58768 Genomic DNA. Translation: AAB02732.1.
U00096 Genomic DNA. Translation: AAC75328.2.
AP009048 Genomic DNA. Translation: BAA16095.2.
PIRiB64998.
RefSeqiNP_416771.4. NC_000913.3.
WP_001300687.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CBNX-ray2.90A1-305[»]
ProteinModelPortaliP0A8V0.
SMRiP0A8V0. Positions 1-305.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263118. 10 interactions.
DIPiDIP-9498N.
IntActiP0A8V0. 7 interactions.
MINTiMINT-1275952.
STRINGi511145.b2268.

Proteomic databases

PaxDbiP0A8V0.
PRIDEiP0A8V0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75328; AAC75328; b2268.
BAA16095; BAA16095; BAA16095.
GeneIDi946760.
KEGGiecj:JW2263.
eco:b2268.
PATRICi32119903. VBIEscCol129921_2361.

Organism-specific databases

EchoBASEiEB4008.
EcoGeneiEG14260. rbn.

Phylogenomic databases

eggNOGiENOG4105IES. Bacteria.
COG1234. LUCA.
HOGENOMiHOG000272419.
InParanoidiP0A8V0.
KOiK00784.
OMAiSYAFCSD.
OrthoDBiEOG61P6TK.
PhylomeDBiP0A8V0.

Enzyme and pathway databases

BioCyciEcoCyc:G7175-MONOMER.
ECOL316407:JW2263-MONOMER.
MetaCyc:G7175-MONOMER.
BRENDAi3.1.26.11. 2026.
SABIO-RKP0A8V0.

Miscellaneous databases

EvolutionaryTraceiP0A8V0.
PROiP0A8V0.

Family and domain databases

Gene3Di3.60.15.10. 2 hits.
HAMAPiMF_01818. RNase_Z_BN.
InterProiIPR001279. Metallo-B-lactamas.
IPR013469. Rbn.
IPR013471. RNase_Z/BN.
[Graphical view]
PfamiPF12706. Lactamase_B_2. 2 hits.
[Graphical view]
SMARTiSM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.
TIGRFAMsiTIGR02651. RNase_Z. 1 hit.
TIGR02649. true_RNase_BN. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Huisman G.W.
    Submitted (JUN-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. Cited for: FUNCTION, DIMERIZATION, COFACTOR.
    Strain: K12 / DH5-alpha.
  6. "The RNase Z homologue encoded by Escherichia coli elaC gene is RNase BN."
    Ezraty B., Dahlgren B., Deutscher M.P.
    J. Biol. Chem. 280:16542-16545(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION AS RNASE BN, FUNCTION, ENZYME REGULATION, SUBUNIT, DISRUPTION PHENOTYPE.
    Strain: K12.
  7. "RNase Z in Escherichia coli plays a significant role in mRNA decay."
    Perwez T., Kushner S.R.
    Mol. Microbiol. 60:723-737(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN MRNA DECAY.
    Strain: K12.
  8. "Catalytic properties of RNase BN/RNase Z from Escherichia coli: RNase BN is both an exo- and endoribonuclease."
    Dutta T., Deutscher M.P.
    J. Biol. Chem. 284:15425-15431(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION.
  9. "Mode of action of RNase BN/RNase Z on tRNA precursors: RNase BN does not remove the CCA sequence from tRNA."
    Dutta T., Deutscher M.P.
    J. Biol. Chem. 285:22874-22881(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION.
  10. "The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins."
    Kostelecky B., Pohl E., Vogel A., Schilling O., Meyer-Klaucke W.
    J. Bacteriol. 188:1607-1614(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 3-305 IN COMPLEX WITH ZINC IONS, SUBUNIT.

Entry informationi

Entry nameiRBN_ECOLI
AccessioniPrimary (citable) accession number: P0A8V0
Secondary accession number(s): P77449, Q47012
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: July 6, 2016
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was initially thought to be an arylsulfatase, given its similarity with the AtsA family. PubMed:12029081 however showed that it is a zinc phosphodiesterase.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.