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Database: UniProt
Entry: A0A0H4VMI3_9BACT
LinkDB: A0A0H4VMI3_9BACT
Original site: A0A0H4VMI3_9BACT 
ID   A0A0H4VMI3_9BACT        Unreviewed;       143 AA.
AC   A0A0H4VMI3;
DT   14-OCT-2015, integrated into UniProtKB/TrEMBL.
DT   14-OCT-2015, sequence version 1.
DT   24-JAN-2024, entry version 31.
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=TH63_17745 {ECO:0000313|EMBL:AKQ47065.1};
OS   Rufibacter radiotolerans.
OC   Bacteria; Bacteroidota; Cytophagia; Cytophagales; Hymenobacteraceae;
OC   Rufibacter.
OX   NCBI_TaxID=1379910 {ECO:0000313|EMBL:AKQ47065.1, ECO:0000313|Proteomes:UP000036458};
RN   [1] {ECO:0000313|EMBL:AKQ47065.1, ECO:0000313|Proteomes:UP000036458}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DG31D {ECO:0000313|EMBL:AKQ47065.1,
RC   ECO:0000313|Proteomes:UP000036458};
RA   Kim M.K., Srinivasan S., Lee J.-J.;
RT   "Rufibacter sp./DG31D/ whole genome sequencing.";
RL   Submitted (JAN-2015) to the EMBL/GenBank/DDBJ databases.
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; CP010777; AKQ47065.1; -; Genomic_DNA.
DR   RefSeq; WP_048922122.1; NZ_CP010777.1.
DR   AlphaFoldDB; A0A0H4VMI3; -.
DR   STRING; 1379910.TH63_17745; -.
DR   KEGG; ruf:TH63_17745; -.
DR   PATRIC; fig|1379910.4.peg.3868; -.
DR   OrthoDB; 9811984at2; -.
DR   Proteomes; UP000036458; 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: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; ENDORIBONUCLEASE YBEY, CHLOROPLASTIC; 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   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};
KW   Nuclease {ECO:0000256|ARBA:ARBA00022722, ECO:0000256|HAMAP-Rule:MF_00009};
KW   Reference proteome {ECO:0000313|Proteomes:UP000036458};
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   BINDING         111
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00009"
FT   BINDING         115
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00009"
FT   BINDING         121
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00009"
SQ   SEQUENCE   143 AA;  16777 MW;  53F16515DAF22253 CRC64;
     MQELPIEFFT EEVDFEVKNE TKVKEWLFEI ISEYSFEVES LNYIFCSDEY LHQMNVEYLD
     HDTLTDVITF DNSDIEGVIE GDVFISIDRI VDNATTFNTP IEKELHRVMA HGLLHLLGFD
     DKTPEKQAIM QSKEEECLAL IKF
//
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