ID A0A0B4Y6F0_9PROT Unreviewed; 200 AA.
AC A0A0B4Y6F0;
DT 01-APR-2015, integrated into UniProtKB/TrEMBL.
DT 01-APR-2015, sequence version 1.
DT 27-MAR-2024, entry version 37.
DE RecName: Full=Endoribonuclease YbeY {ECO:0000256|HAMAP-Rule:MF_00009};
DE EC=3.1.-.- {ECO:0000256|HAMAP-Rule:MF_00009};
GN Name=ybeY {ECO:0000256|HAMAP-Rule:MF_00009};
GN ORFNames=TH3_20400 {ECO:0000313|EMBL:AJD54182.1};
OS Thalassospira xiamenensis M-5 = DSM 17429.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales;
OC Thalassospiraceae; Thalassospira.
OX NCBI_TaxID=1123366 {ECO:0000313|EMBL:AJD54182.1, ECO:0000313|Proteomes:UP000007127};
RN [1] {ECO:0000313|EMBL:AJD54182.1, ECO:0000313|Proteomes:UP000007127}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=M-5 {ECO:0000313|EMBL:AJD54182.1,
RC ECO:0000313|Proteomes:UP000007127};
RX PubMed=23209216; DOI=10.1128/JB.01904-12;
RA Lai Q., Shao Z.;
RT "Genome sequence of Thalassospira xiamenensis type strain M-5.";
RL J. Bacteriol. 194:6957-6957(2012).
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:0000256|HAMAP-Rule:MF_00009}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00009};
CC Note=Binds 1 zinc ion. {ECO:0000256|HAMAP-Rule:MF_00009};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00009}.
CC -!- SIMILARITY: Belongs to the endoribonuclease YbeY family.
CC {ECO:0000256|ARBA:ARBA00010875, ECO:0000256|HAMAP-Rule:MF_00009}.
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DR EMBL; CP004388; AJD54182.1; -; Genomic_DNA.
DR RefSeq; WP_007088433.1; NZ_FTON01000001.1.
DR AlphaFoldDB; A0A0B4Y6F0; -.
DR STRING; 1123366.TH3_20400; -.
DR GeneID; 31929755; -.
DR KEGG; txi:TH3_20400; -.
DR eggNOG; COG0319; Bacteria.
DR HOGENOM; CLU_106710_0_0_5; -.
DR Proteomes; UP000007127; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro.
DR GO; GO:0004521; F:RNA endonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.390.30; Metalloproteases ('zincins'), catalytic domain; 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 NCBIfam; TIGR00043; rRNA maturation RNase YbeY; 1.
DR PANTHER; PTHR46986; ENDORIBONUCLEASE YBEY, CHLOROPLASTIC; 1.
DR PANTHER; PTHR46986:SF1; YBEY METALLOENDORIBONUCLEASE; 1.
DR Pfam; PF02130; YbeY; 1.
DR SUPFAM; SSF55486; Metalloproteases ('zincins'), catalytic domain; 1.
DR PROSITE; PS01306; UPF0054; 1.
PE 3: Inferred from homology;
KW Coiled coil {ECO:0000256|SAM:Coils};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00009};
KW Endonuclease {ECO:0000256|ARBA:ARBA00022759, ECO:0000256|HAMAP-
KW Rule:MF_00009};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00009};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00009}; Metalloprotease {ECO:0000313|EMBL:AJD54182.1};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722, ECO:0000256|HAMAP-Rule:MF_00009};
KW Protease {ECO:0000313|EMBL:AJD54182.1};
KW Ribosome biogenesis {ECO:0000256|HAMAP-Rule:MF_00009};
KW rRNA processing {ECO:0000256|HAMAP-Rule:MF_00009};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_00009}.
FT COILED 157..184
FT /evidence="ECO:0000256|SAM:Coils"
FT BINDING 152
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00009"
FT BINDING 156
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00009"
FT BINDING 162
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00009"
SQ SEQUENCE 200 AA; 21641 MW; F9A92CA3DC00143B CRC64;
MTAPLDLDLD VEAGNWTKAD IDAIENAVRA ALDGAVRDGA LWEEDAAPAD GTPDQGDGAS
LLSIAPVVEV GVRLSDDASV RILNRDYRGK DSPTNVLSFA ALESADDTAA FMMSSDMPLM
LGDIVIARET CEREAVEQNK TLINHLVHLT VHGTLHLVGY DHMVDDEAEE MEELERQILA
ALGIDDPYEP IEDQDIETGQ
//
