YBEY_THEMA
ID YBEY_THEMA Reviewed; 150 AA.
AC Q9X1J7;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Endoribonuclease YbeY {ECO:0000255|HAMAP-Rule:MF_00009};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_00009};
GN Name=ybeY {ECO:0000255|HAMAP-Rule:MF_00009}; OrderedLocusNames=TM_1509;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP STRUCTURE BY NMR, COFACTOR, AND ZINC BINDING.
RX PubMed=15965736; DOI=10.1007/s10969-005-5277-z;
RA Penhoat C.H., Li Z., Atreya H.S., Kim S., Yee A., Xiao R., Murray D.,
RA Arrowsmith C.H., Szyperski T.;
RT "NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-
RT metalloprotease-like tertiary structure.";
RL J. Struct. Funct. Genomics 6:51-62(2005).
CC -!- FUNCTION: Single strand-specific metallo-endoribonuclease involved in
CC late-stage 70S ribosome quality control and in maturation of the 3'
CC terminus of the 16S rRNA. {ECO:0000255|HAMAP-Rule:MF_00009}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00009,
CC ECO:0000269|PubMed:15965736};
CC Note=Binds 1 zinc ion. {ECO:0000255|HAMAP-Rule:MF_00009,
CC ECO:0000269|PubMed:15965736};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00009}.
CC -!- SIMILARITY: Belongs to the endoribonuclease YbeY family.
CC {ECO:0000255|HAMAP-Rule:MF_00009}.
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DR EMBL; AE000512; AAD36576.1; -; Genomic_DNA.
DR PIR; F72244; F72244.
DR RefSeq; NP_229309.1; NC_000853.1.
DR RefSeq; WP_004081854.1; NZ_CP011107.1.
DR PDB; 1TVI; NMR; -; A=1-150.
DR PDBsum; 1TVI; -.
DR AlphaFoldDB; Q9X1J7; -.
DR BMRB; Q9X1J7; -.
DR SMR; Q9X1J7; -.
DR STRING; 243274.THEMA_06755; -.
DR EnsemblBacteria; AAD36576; AAD36576; TM_1509.
DR KEGG; tma:TM1509; -.
DR eggNOG; COG0319; Bacteria.
DR InParanoid; Q9X1J7; -.
DR OMA; INYIFCD; -.
DR OrthoDB; 1830156at2; -.
DR EvolutionaryTrace; Q9X1J7; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004521; F:endoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.390.30; -; 1.
DR HAMAP; MF_00009; Endoribonucl_YbeY; 1.
DR InterPro; IPR023091; MetalPrtase_cat_dom_sf_prd.
DR InterPro; IPR002036; YbeY.
DR InterPro; IPR020549; YbeY_CS.
DR Pfam; PF02130; YbeY; 1.
DR TIGRFAMs; TIGR00043; TIGR00043; 1.
DR PROSITE; PS01306; UPF0054; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Endonuclease; Hydrolase; Metal-binding; Nuclease;
KW Reference proteome; Ribosome biogenesis; rRNA processing; Zinc.
FT CHAIN 1..150
FT /note="Endoribonuclease YbeY"
FT /id="PRO_0000102553"
FT BINDING 102
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00009"
FT BINDING 106
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00009"
FT BINDING 112
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00009"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:1TVI"
FT HELIX 11..16
FT /evidence="ECO:0007829|PDB:1TVI"
FT HELIX 18..28
FT /evidence="ECO:0007829|PDB:1TVI"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:1TVI"
FT HELIX 41..49
FT /evidence="ECO:0007829|PDB:1TVI"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:1TVI"
FT STRAND 67..69
FT /evidence="ECO:0007829|PDB:1TVI"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:1TVI"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:1TVI"
FT HELIX 92..108
FT /evidence="ECO:0007829|PDB:1TVI"
FT HELIX 120..137
FT /evidence="ECO:0007829|PDB:1TVI"
SQ SEQUENCE 150 AA; 17550 MW; 5BDE227C0BE6DCC5 CRC64;
MIRILGEGKG SKLLENLKEK LEEIVKKEIG DVHVNVILVS EDEIKELNQQ FRGQDRPTDV
LTFPLMEEDV YGEIYVCPLI VEENAREFNN TFEKELLEVV IHGILHLAGY DHEFEDKNSK
EMFEKQKKYV EEVWGEWRSN PSEDSDPGKR
