YBEY_ECOLI
ID YBEY_ECOLI Reviewed; 155 AA.
AC P0A898; P77385;
DT 26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT 26-APR-2005, sequence version 1.
DT 03-AUG-2022, entry version 132.
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};
GN OrderedLocusNames=b0659, JW0656;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP INDUCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16818608; DOI=10.1101/gad.1428206;
RA Nonaka G., Blankschien M., Herman C., Gross C.A., Rhodius V.A.;
RT "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32,
RT reveals a multifaceted cellular response to heat stress.";
RL Genes Dev. 20:1776-1789(2006).
RN [6]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=19181801; DOI=10.1128/jb.01663-08;
RA Rasouly A., Schonbrun M., Shenhar Y., Ron E.Z.;
RT "YbeY, a heat shock protein involved in translation in Escherichia coli.";
RL J. Bacteriol. 191:2649-2655(2009).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=20639334; DOI=10.1128/jb.00448-10;
RA Rasouly A., Davidovich C., Ron E.Z.;
RT "The heat shock protein YbeY is required for optimal activity of the 30S
RT ribosomal subunit.";
RL J. Bacteriol. 192:4592-4596(2010).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ARG-59; HIS-114; HIS-118
RP AND HIS-124.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=20807199; DOI=10.1111/j.1365-2958.2010.07351.x;
RA Davies B.W., Kohrer C., Jacob A.I., Simmons L.A., Zhu J., Aleman L.M.,
RA Rajbhandary U.L., Walker G.C.;
RT "Role of Escherichia coli YbeY, a highly conserved protein, in rRNA
RT processing.";
RL Mol. Microbiol. 78:506-518(2010).
RN [9]
RP FUNCTION, ACTIVITY REGULATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP ARG-59 AND HIS-114.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=23273979; DOI=10.1016/j.molcel.2012.11.025;
RA Jacob A.I., Kohrer C., Davies B.W., Rajbhandary U.L., Walker G.C.;
RT "Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality
RT control and 16S rRNA maturation.";
RL Mol. Cell 49:427-438(2013).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH DIVALENT METAL
RP CATIONS, AND FUNCTION.
RX PubMed=16511207; DOI=10.1107/s1744309105031131;
RA Zhan C., Fedorov E.V., Shi W., Ramagopal U.A., Thirumuruhan R.,
RA Manjasetty B.A., Almo S.C., Fiser A., Chance M.R., Fedorov A.A.;
RT "The ybeY protein from Escherichia coli is a metalloprotein.";
RL Acta Crystallogr. F 61:959-963(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. Acts together with the RNase R to eliminate
CC defective 70S ribosomes, but not properly matured 70S ribosomes or
CC individual subunits, by a process mediated specifically by the 30S
CC ribosomal subunit. Involved in the processing of 16S, 23S and 5S rRNAs,
CC with a particularly strong effect on maturation at both the 5'- and 3'-
CC ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S
CC rRNAs. {ECO:0000255|HAMAP-Rule:MF_00009, ECO:0000269|PubMed:16511207,
CC ECO:0000269|PubMed:20639334, ECO:0000269|PubMed:20807199,
CC ECO:0000269|PubMed:23273979}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00009};
CC Note=Binds 1 zinc ion. {ECO:0000255|HAMAP-Rule:MF_00009};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA. {ECO:0000269|PubMed:23273979}.
CC -!- INTERACTION:
CC P0A898; P0DTT0: bipA; NbExp=2; IntAct=EBI-560240, EBI-562154;
CC P0A898; P0A9K3: ybeZ; NbExp=2; IntAct=EBI-560240, EBI-560255;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00009,
CC ECO:0000269|PubMed:20639334}.
CC -!- INDUCTION: By heat shock. {ECO:0000269|PubMed:16818608}.
CC -!- DISRUPTION PHENOTYPE: Mutants show defects in 16S rRNA maturation,
CC ribosome activity, translational fidelity, and ribosome assembly. They
CC have severe growth defect at high temperatures, essentially no
CC thermotolerance at lethal temperatures. They also show a decrease in
CC polysomes and a large increase in both free 50S and free 30S ribosomal
CC subunits relative to 70S ribosomes. {ECO:0000269|PubMed:19181801,
CC ECO:0000269|PubMed:20639334, ECO:0000269|PubMed:20807199,
CC ECO:0000269|PubMed:23273979}.
CC -!- SIMILARITY: Belongs to the endoribonuclease YbeY family.
CC {ECO:0000255|HAMAP-Rule:MF_00009}.
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DR EMBL; U82598; AAB40861.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73760.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35314.1; -; Genomic_DNA.
DR PIR; A64801; A64801.
DR RefSeq; NP_415192.1; NC_000913.3.
DR RefSeq; WP_000084469.1; NZ_SSZK01000037.1.
DR PDB; 1XM5; X-ray; 2.70 A; A/B/C/D=1-155.
DR PDBsum; 1XM5; -.
DR AlphaFoldDB; P0A898; -.
DR SMR; P0A898; -.
DR BioGRID; 4261388; 68.
DR DIP; DIP-48144N; -.
DR IntAct; P0A898; 15.
DR STRING; 511145.b0659; -.
DR jPOST; P0A898; -.
DR PaxDb; P0A898; -.
DR PRIDE; P0A898; -.
DR DNASU; 946430; -.
DR EnsemblBacteria; AAC73760; AAC73760; b0659.
DR EnsemblBacteria; BAA35314; BAA35314; BAA35314.
DR GeneID; 67416301; -.
DR GeneID; 946430; -.
DR KEGG; ecj:JW0656; -.
DR KEGG; eco:b0659; -.
DR PATRIC; fig|1411691.4.peg.1609; -.
DR EchoBASE; EB3419; -.
DR eggNOG; COG0319; Bacteria.
DR HOGENOM; CLU_106710_0_1_6; -.
DR InParanoid; P0A898; -.
DR OMA; RMRIHPL; -.
DR PhylomeDB; P0A898; -.
DR BioCyc; EcoCyc:G6362-MON; -.
DR EvolutionaryTrace; P0A898; -.
DR PRO; PR:P0A898; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016892; F:endoribonuclease activity, producing 3'-phosphomonoesters; IDA:EcoCyc.
DR GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro.
DR GO; GO:0016151; F:nickel cation binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000478; P:endonucleolytic cleavage involved in rRNA processing; IMP:EcoCyc.
DR GO; GO:0030490; P:maturation of SSU-rRNA; IMP:EcoCyc.
DR GO; GO:0009408; P:response to heat; IMP:EcoCyc.
DR GO; GO:0042274; P:ribosomal small subunit biogenesis; IMP:EcoCyc.
DR GO; GO:0042254; P:ribosome biogenesis; IMP:UniProtKB.
DR GO; GO:0006364; P:rRNA processing; IMP:UniProtKB.
DR GO; GO:0031564; P:transcription antitermination; IMP:EcoCyc.
DR GO; GO:0006412; P:translation; IMP:EcoCyc.
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 PANTHER; PTHR46986; PTHR46986; 1.
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..155
FT /note="Endoribonuclease YbeY"
FT /id="PRO_0000102449"
FT BINDING 114
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305"
FT BINDING 118
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305"
FT BINDING 124
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305"
FT MUTAGEN 59
FT /note="R->A,E: Loss of activity."
FT /evidence="ECO:0000269|PubMed:20807199,
FT ECO:0000269|PubMed:23273979"
FT MUTAGEN 114
FT /note="H->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:20807199,
FT ECO:0000269|PubMed:23273979"
FT MUTAGEN 118
FT /note="H->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:20807199"
FT MUTAGEN 124
FT /note="H->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:20807199"
FT STRAND 3..10
FT /evidence="ECO:0007829|PDB:1XM5"
FT STRAND 12..14
FT /evidence="ECO:0007829|PDB:1XM5"
FT HELIX 21..29
FT /evidence="ECO:0007829|PDB:1XM5"
FT HELIX 33..36
FT /evidence="ECO:0007829|PDB:1XM5"
FT STRAND 37..46
FT /evidence="ECO:0007829|PDB:1XM5"
FT HELIX 48..59
FT /evidence="ECO:0007829|PDB:1XM5"
FT STRAND 66..71
FT /evidence="ECO:0007829|PDB:1XM5"
FT STRAND 82..89
FT /evidence="ECO:0007829|PDB:1XM5"
FT HELIX 90..99
FT /evidence="ECO:0007829|PDB:1XM5"
FT HELIX 104..119
FT /evidence="ECO:0007829|PDB:1XM5"
FT HELIX 127..143
FT /evidence="ECO:0007829|PDB:1XM5"
SQ SEQUENCE 155 AA; 17526 MW; C0DAC40266F846A5 CRC64;
MSQVILDLQL ACEDNSGLPE ESQFQTWLNA VIPQFQEESE VTIRVVDTAE SHSLNLTYRG
KDKPTNVLSF PFEVPPGMEM SLLGDLVICR QVVEKEAQEQ GKPLEAHWAH MVVHGSLHLL
GYDHIEDDEA EEMEALETEI MLALGYEDPY IAEKE
