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Protein

Endoribonuclease YbeY

Gene

ybeY

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

Functioni

Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Acts together with the RNase R to eliminate defective 70S ribosomes, but not properly matured 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. Involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs.UniRule annotation4 Publications

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion.UniRule annotation

Enzyme regulationi

Inhibited by EDTA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi114 – 1141Zinc; catalyticCurated
Metal bindingi118 – 1181Zinc; catalyticCurated
Metal bindingi124 – 1241Zinc; catalyticCurated

GO - Molecular functioni

  • endoribonuclease activity, producing 3'-phosphomonoesters Source: EcoCyc
  • metalloendopeptidase activity Source: InterPro
  • nickel cation binding Source: EcoCyc
  • zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  • endonucleolytic cleavage involved in rRNA processing Source: EcoCyc
  • maturation of SSU-rRNA Source: EcoCyc
  • response to heat Source: EcoCyc
  • ribosomal small subunit biogenesis Source: EcoCyc
  • ribosome biogenesis Source: UniProtKB
  • rRNA processing Source: UniProtKB
  • transcription antitermination Source: EcoCyc
  • translation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G6362-MONOMER.
ECOL316407:JW0656-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease YbeYUniRule annotation (EC:3.1.-.-UniRule annotation)
Gene namesi
Name:ybeYUniRule annotation
Ordered Locus Names:b0659, JW0656
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13655. ybeY.

Subcellular locationi

  • Cytoplasm UniRule annotation1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Mutants show defects in 16S rRNA maturation, ribosome activity, translational fidelity, and ribosome assembly. They have severe growth defect at high temperatures, essentially no thermotolerance at lethal temperatures. They also show a decrease in polysomes and a large increase in both free 50S and free 30S ribosomal subunits relative to 70S ribosomes.4 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi59 – 591R → A or E: Loss of activity. 2 Publications
Mutagenesisi114 – 1141H → A: Loss of activity. 2 Publications
Mutagenesisi118 – 1181H → A: No change in activity. 1 Publication
Mutagenesisi124 – 1241H → A: No change in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 155155Endoribonuclease YbeYPRO_0000102449Add
BLAST

Proteomic databases

PaxDbiP0A898.
PRIDEiP0A898.

Expressioni

Inductioni

By heat shock.1 Publication

Interactioni

Protein-protein interaction databases

BioGridi4261388. 63 interactions.
DIPiDIP-48144N.
IntActiP0A898. 14 interactions.
MINTiMINT-1241301.
STRINGi511145.b0659.

Structurei

Secondary structure

1
155
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 108Combined sources
Beta strandi12 – 143Combined sources
Helixi21 – 299Combined sources
Helixi33 – 364Combined sources
Beta strandi37 – 4610Combined sources
Helixi48 – 5912Combined sources
Beta strandi66 – 716Combined sources
Beta strandi82 – 898Combined sources
Helixi90 – 9910Combined sources
Helixi104 – 11916Combined sources
Helixi127 – 14317Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XM5X-ray2.70A/B/C/D1-155[»]
ProteinModelPortaliP0A898.
SMRiP0A898. Positions 1-152.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A898.

Family & Domainsi

Sequence similaritiesi

Belongs to the endoribonuclease YbeY family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105KGE. Bacteria.
COG0319. LUCA.
HOGENOMiHOG000132870.
InParanoidiP0A898.
KOiK07042.
OMAiEESHHLN.
PhylomeDBiP0A898.

Family and domain databases

Gene3Di3.40.390.30. 1 hit.
HAMAPiMF_00009. Endoribonucl_YbeY. 1 hit.
InterProiIPR023091. MetalPrtase_cat_dom_prd.
IPR002036. YbeY.
IPR020549. YbeY_CS.
[Graphical view]
PfamiPF02130. UPF0054. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00043. TIGR00043. 1 hit.
PROSITEiPS01306. UPF0054. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A898-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQVILDLQL ACEDNSGLPE ESQFQTWLNA VIPQFQEESE VTIRVVDTAE
60 70 80 90 100
SHSLNLTYRG KDKPTNVLSF PFEVPPGMEM SLLGDLVICR QVVEKEAQEQ
110 120 130 140 150
GKPLEAHWAH MVVHGSLHLL GYDHIEDDEA EEMEALETEI MLALGYEDPY

IAEKE
Length:155
Mass (Da):17,526
Last modified:April 26, 2005 - v1
Checksum:iC0DAC40266F846A5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82598 Genomic DNA. Translation: AAB40861.1.
U00096 Genomic DNA. Translation: AAC73760.1.
AP009048 Genomic DNA. Translation: BAA35314.1.
PIRiA64801.
RefSeqiNP_415192.1. NC_000913.3.
WP_000084469.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73760; AAC73760; b0659.
BAA35314; BAA35314; BAA35314.
GeneIDi946430.
KEGGiecj:JW0656.
eco:b0659.
PATRICi32116507. VBIEscCol129921_0693.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82598 Genomic DNA. Translation: AAB40861.1.
U00096 Genomic DNA. Translation: AAC73760.1.
AP009048 Genomic DNA. Translation: BAA35314.1.
PIRiA64801.
RefSeqiNP_415192.1. NC_000913.3.
WP_000084469.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XM5X-ray2.70A/B/C/D1-155[»]
ProteinModelPortaliP0A898.
SMRiP0A898. Positions 1-152.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261388. 63 interactions.
DIPiDIP-48144N.
IntActiP0A898. 14 interactions.
MINTiMINT-1241301.
STRINGi511145.b0659.

Proteomic databases

PaxDbiP0A898.
PRIDEiP0A898.

Protocols and materials databases

DNASUi946430.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73760; AAC73760; b0659.
BAA35314; BAA35314; BAA35314.
GeneIDi946430.
KEGGiecj:JW0656.
eco:b0659.
PATRICi32116507. VBIEscCol129921_0693.

Organism-specific databases

EchoBASEiEB3419.
EcoGeneiEG13655. ybeY.

Phylogenomic databases

eggNOGiENOG4105KGE. Bacteria.
COG0319. LUCA.
HOGENOMiHOG000132870.
InParanoidiP0A898.
KOiK07042.
OMAiEESHHLN.
PhylomeDBiP0A898.

Enzyme and pathway databases

BioCyciEcoCyc:G6362-MONOMER.
ECOL316407:JW0656-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A898.
PROiP0A898.

Family and domain databases

Gene3Di3.40.390.30. 1 hit.
HAMAPiMF_00009. Endoribonucl_YbeY. 1 hit.
InterProiIPR023091. MetalPrtase_cat_dom_prd.
IPR002036. YbeY.
IPR020549. YbeY_CS.
[Graphical view]
PfamiPF02130. UPF0054. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00043. TIGR00043. 1 hit.
PROSITEiPS01306. UPF0054. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYBEY_ECOLI
AccessioniPrimary (citable) accession number: P0A898
Secondary accession number(s): P77385
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2005
Last sequence update: April 26, 2005
Last modified: September 7, 2016
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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.