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Protein

Endoribonuclease YbeY

Gene

ybeY

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Metal bindingi114Zinc; catalyticCurated1
Metal bindingi118Zinc; catalyticCurated1
Metal bindingi124Zinc; catalyticCurated1

GO - Molecular functioni

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

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

Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease
Biological processRibosome biogenesis, rRNA processing
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G6362-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13655 ybeY

Subcellular locationi

  • Cytoplasm UniRule annotation1 Publication

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
Mutagenesisi59R → A or E: Loss of activity. 2 Publications1
Mutagenesisi114H → A: Loss of activity. 2 Publications1
Mutagenesisi118H → A: No change in activity. 1 Publication1
Mutagenesisi124H → A: No change in activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001024491 – 155Endoribonuclease YbeYAdd BLAST155

Proteomic databases

PaxDbiP0A898
PRIDEiP0A898

Expressioni

Inductioni

By heat shock.1 Publication

Interactioni

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4261388, 68 interactors
DIPiDIP-48144N
IntActiP0A898, 15 interactors
STRINGi316385.ECDH10B_0728

Structurei

Secondary structure

1155
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 10Combined sources8
Beta strandi12 – 14Combined sources3
Helixi21 – 29Combined sources9
Helixi33 – 36Combined sources4
Beta strandi37 – 46Combined sources10
Helixi48 – 59Combined sources12
Beta strandi66 – 71Combined sources6
Beta strandi82 – 89Combined sources8
Helixi90 – 99Combined sources10
Helixi104 – 119Combined sources16
Helixi127 – 143Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1XM5X-ray2.70A/B/C/D1-155[»]
ProteinModelPortaliP0A898
SMRiP0A898
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
OMAiLGYDHMN
PhylomeDBiP0A898

Family and domain databases

Gene3Di3.40.390.30, 1 hit
HAMAPiMF_00009 Endoribonucl_YbeY, 1 hit
InterProiView protein in InterPro
IPR023091 MetalPrtase_cat_dom_sf_prd
IPR002036 YbeY
IPR020549 YbeY_CS
PfamiView protein in Pfam
PF02130 UPF0054, 1 hit
TIGRFAMsiTIGR00043 TIGR00043, 1 hit
PROSITEiView protein in PROSITE
PS01306 UPF0054, 1 hit

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
PATRICifig|1411691.4.peg.1609

Similar proteinsi

Entry informationi

Entry nameiYBEY_ECOLI
AccessioniPrimary (citable) accession number: P0A898
Secondary accession number(s): P77385
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 26, 2005
Last sequence update: April 26, 2005
Last modified: March 28, 2018
This is version 109 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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