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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)DescriptionActionsGraphical viewLength
Metal bindingi64Zinc 1; catalyticUniRule annotation1 Publication1
Metal bindingi66Zinc 1; catalyticUniRule annotation1 Publication1
Active sitei68Proton acceptorUniRule annotation1
Metal bindingi68Zinc 2; catalyticUniRule annotation1 Publication1
Metal bindingi69Zinc 2; catalyticUniRule annotation1 Publication1
Metal bindingi141Zinc 1; catalyticUniRule annotation1 Publication1
Metal bindingi212Zinc 1; catalyticUniRule annotation1 Publication1
Metal bindingi212Zinc 2; catalyticUniRule annotation1 Publication1
Metal bindingi270Zinc 2; catalyticUniRule annotation1 Publication1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
ChainiPRO_00001558631 – 305Ribonuclease BNAdd BLAST305

Proteomic databases

PaxDbiP0A8V0.
PRIDEiP0A8V0.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

1305
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Beta strandi9 – 12Combined sources4
Beta strandi21 – 25Combined sources5
Beta strandi34 – 37Combined sources4
Helixi43 – 48Combined sources6
Turni54 – 56Combined sources3
Beta strandi57 – 61Combined sources5
Helixi67 – 70Combined sources4
Helixi73 – 82Combined sources10
Beta strandi89 – 94Combined sources6
Helixi97 – 107Combined sources11
Beta strandi116 – 120Combined sources5
Beta strandi123 – 128Combined sources6
Beta strandi130 – 138Combined sources9
Beta strandi140 – 143Combined sources4
Beta strandi146 – 152Combined sources7
Helixi161 – 166Combined sources6
Helixi173 – 180Combined sources8
Turni187 – 189Combined sources3
Helixi194 – 196Combined sources3
Beta strandi206 – 209Combined sources4
Helixi219 – 223Combined sources5
Beta strandi227 – 232Combined sources6
Helixi237 – 239Combined sources3
Helixi240 – 245Combined sources6
Helixi251 – 261Combined sources11
Beta strandi264 – 269Combined sources6
Helixi277 – 288Combined sources12
Beta strandi294 – 296Combined sources3
Beta strandi302 – 304Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CBNX-ray2.90A1-305[»]
ProteinModelPortaliP0A8V0.
SMRiP0A8V0.
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.
PhylomeDBiP0A8V0.

Family and domain databases

Gene3Di3.60.15.10. 2 hits.
HAMAPiMF_01818. RNase_Z_BN. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti154D → Y in AAB02732 (Ref. 1) Curated1
Sequence conflicti217D → N in AAB02732 (Ref. 1) Curated1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CBNX-ray2.90A1-305[»]
ProteinModelPortaliP0A8V0.
SMRiP0A8V0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263118. 10 interactors.
DIPiDIP-9498N.
IntActiP0A8V0. 7 interactors.
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.
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. 1 hit.
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...

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: November 2, 2016
This is version 105 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.