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Protein

Endoribonuclease YbeY

Gene

ybeY

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: Annotation score: 2 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.UniRule annotation

Cofactori

Zn2+UniRule annotation1 PublicationNote: Binds 1 zinc ion.UniRule annotation1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi102 – 1021Zinc; catalyticUniRule annotation
Metal bindingi106 – 1061Zinc; catalyticUniRule annotation
Metal bindingi112 – 1121Zinc; catalyticUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease YbeYUniRule annotation (EC:3.1.-.-UniRule annotation)
Gene namesi
Name:ybeYUniRule annotation
Ordered Locus Names:TM_1509
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 150150Endoribonuclease YbeYPRO_0000102553Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi243274.TM1509.

Structurei

Secondary structure

1
150
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 64Combined sources
Helixi11 – 166Combined sources
Helixi18 – 2811Combined sources
Beta strandi35 – 384Combined sources
Helixi41 – 499Combined sources
Beta strandi59 – 613Combined sources
Beta strandi67 – 693Combined sources
Beta strandi72 – 765Combined sources
Helixi78 – 8710Combined sources
Helixi92 – 10817Combined sources
Helixi120 – 13718Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TVINMR-A1-150[»]
ProteinModelPortaliQ9X1J7.
SMRiQ9X1J7. Positions 1-150.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9X1J7.

Family & Domainsi

Sequence similaritiesi

Belongs to the endoribonuclease YbeY family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105KGE. Bacteria.
COG0319. LUCA.
InParanoidiQ9X1J7.
KOiK07042.
OMAiEENAREF.
OrthoDBiEOG680X6D.

Family and domain databases

Gene3Di3.40.390.30. 1 hit.
HAMAPiMF_00009. Endoribonucl_YbeY.
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.

Q9X1J7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIRILGEGKG SKLLENLKEK LEEIVKKEIG DVHVNVILVS EDEIKELNQQ
60 70 80 90 100
FRGQDRPTDV LTFPLMEEDV YGEIYVCPLI VEENAREFNN TFEKELLEVV
110 120 130 140 150
IHGILHLAGY DHEFEDKNSK EMFEKQKKYV EEVWGEWRSN PSEDSDPGKR
Length:150
Mass (Da):17,550
Last modified:November 1, 1999 - v1
Checksum:i5BDE227C0BE6DCC5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36576.1.
PIRiF72244.
RefSeqiNP_229309.1. NC_000853.1.
WP_004081854.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD36576; AAD36576; TM_1509.
GeneIDi898186.
KEGGitma:TM1509.
PATRICi23937976. VBITheMar51294_1526.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36576.1.
PIRiF72244.
RefSeqiNP_229309.1. NC_000853.1.
WP_004081854.1. NZ_CP011107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TVINMR-A1-150[»]
ProteinModelPortaliQ9X1J7.
SMRiQ9X1J7. Positions 1-150.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM1509.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD36576; AAD36576; TM_1509.
GeneIDi898186.
KEGGitma:TM1509.
PATRICi23937976. VBITheMar51294_1526.

Phylogenomic databases

eggNOGiENOG4105KGE. Bacteria.
COG0319. LUCA.
InParanoidiQ9X1J7.
KOiK07042.
OMAiEENAREF.
OrthoDBiEOG680X6D.

Miscellaneous databases

EvolutionaryTraceiQ9X1J7.

Family and domain databases

Gene3Di3.40.390.30. 1 hit.
HAMAPiMF_00009. Endoribonucl_YbeY.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
  2. "NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure."
    Penhoat C.H., Li Z., Atreya H.S., Kim S., Yee A., Xiao R., Murray D., Arrowsmith C.H., Szyperski T.
    J. Struct. Funct. Genomics 6:51-62(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR, COFACTOR, ZINC BINDING.

Entry informationi

Entry nameiYBEY_THEMA
AccessioniPrimary (citable) accession number: Q9X1J7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: April 13, 2016
This is version 115 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.