YBAK_ECOLI
ID YBAK_ECOLI Reviewed; 159 AA.
AC P0AAR3; P37175; P77281; Q2MBU6;
DT 11-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2005, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
DE EC=4.2.-.-;
GN Name=ybaK; OrderedLocusNames=b0481, JW0470;
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 / 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 [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 149-159.
RX PubMed=3012467; DOI=10.1093/nar/14.10.4325;
RA Burns D.M., Beacham I.R.;
RT "Nucleotide sequence and transcriptional analysis of the E. coli ushA gene,
RT encoding periplasmic UDP-sugar hydrolase (5'-nucleotidase): regulation of
RT the ushA gene, and the signal sequence of its encoded protein product.";
RL Nucleic Acids Res. 14:4325-4342(1986).
RN [5]
RP IDENTIFICATION.
RA Jimenez S., Bairoch A.;
RL Unpublished observations (AUG-1994).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=B / BL21;
RX PubMed=10493123;
RX DOI=10.1002/(sici)1522-2683(19990801)20:11<2181::aid-elps2181>3.0.co;2-q;
RA Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.;
RT "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite
RT chromatography.";
RL Electrophoresis 20:2181-2195(1999).
RN [7]
RP LACK OF EDITING ACTIVITY ON MISCHARGED ALA-TRNA(PRO).
RX PubMed=14663147; DOI=10.1073/pnas.2136934100;
RA Ahel I., Korencic D., Ibba M., Soll D.;
RT "Trans-editing of mischarged tRNAs.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:15422-15427(2003).
RN [8]
RP FUNCTION AS A DEACYLASE, SUBSTRATE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=15886196; DOI=10.1074/jbc.m502174200;
RA Ruan B., Soll D.;
RT "The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase.";
RL J. Biol. Chem. 280:25887-25891(2005).
RN [9]
RP FUNCTION, REACTION MECHANISM, AND MUTAGENESIS OF GLY-30 AND ASP-136.
RX PubMed=23185990; DOI=10.1021/jp308628y;
RA Kumar S., Das M., Hadad C.M., Musier-Forsyth K.;
RT "Aminoacyl-tRNA substrate and enzyme backbone atoms contribute to
RT translational quality control by YbaK.";
RL J. Phys. Chem. B 117:4521-4527(2013).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.58 ANGSTROMS).
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure of trans editing enzyme ProX from E.coli.";
RL Submitted (FEB-2009) to the PDB data bank.
CC -!- FUNCTION: Functions in trans to edit the amino acid from incorrectly
CC charged Cys-tRNA(Pro) via a Cys-tRNA(Pro) deacylase activity. May
CC compensate for the lack of Cys-tRNA(Pro) editing by ProRS. Is also able
CC to deacylate Cys-tRNA(Cys), and displays weak deacylase activity in
CC vitro against Gly-tRNA(Gly), as well as, at higher concentrations, some
CC other correctly charged tRNAs. Unlike some of its orthologs it is not
CC able to remove the amino acid moiety from incorrectly charged Ala-
CC tRNA(Pro). {ECO:0000269|PubMed:15886196, ECO:0000269|PubMed:23185990}.
CC -!- INTERACTION:
CC P0AAR3; P0A9P0: lpdA; NbExp=2; IntAct=EBI-559987, EBI-542856;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Non-essential gene.
CC {ECO:0000269|PubMed:15886196}.
CC -!- MISCELLANEOUS: Has been suggested to be potentially involved in
CC suppression of transcription of ushA.
CC -!- MISCELLANEOUS: Reaction mechanism involves exclusion of catalytic water
CC from the active site and substrate-mediated catalysis: the sulfhydryl
CC side chain of the Cys substrate acts as a nucleophile and attacks the
CC carbonyl center of the ester bond, leading to the cleavage of the Cys-
CC tRNA ester bond and formation of a cyclic cysteine thiolactone
CC intermediate. In contrast, the INS editing domain of ProRS catalyzes
CC Ala-tRNA(Pro) hydrolysis via nucleophilic attack by a catalytic water
CC molecule (PubMed:23185990). {ECO:0000305|PubMed:23185990}.
CC -!- SIMILARITY: Belongs to the prolyl-tRNA editing family. YbaK/EbsC
CC subfamily. {ECO:0000305}.
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DR EMBL; U82664; AAB40235.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73583.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76260.1; -; Genomic_DNA.
DR EMBL; X03895; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; H64778; H64778.
DR RefSeq; NP_415014.1; NC_000913.3.
DR RefSeq; WP_000186631.1; NZ_STEB01000007.1.
DR PDB; 2DXA; X-ray; 1.58 A; A=1-159.
DR PDBsum; 2DXA; -.
DR AlphaFoldDB; P0AAR3; -.
DR SMR; P0AAR3; -.
DR BioGRID; 4263284; 32.
DR DIP; DIP-48133N; -.
DR IntAct; P0AAR3; 17.
DR STRING; 511145.b0481; -.
DR jPOST; P0AAR3; -.
DR PaxDb; P0AAR3; -.
DR PRIDE; P0AAR3; -.
DR EnsemblBacteria; AAC73583; AAC73583; b0481.
DR EnsemblBacteria; BAE76260; BAE76260; BAE76260.
DR GeneID; 66671217; -.
DR GeneID; 947083; -.
DR KEGG; ecj:JW0470; -.
DR KEGG; eco:b0481; -.
DR PATRIC; fig|511145.12.peg.501; -.
DR EchoBASE; EB2348; -.
DR eggNOG; COG2606; Bacteria.
DR HOGENOM; CLU_094875_1_1_6; -.
DR InParanoid; P0AAR3; -.
DR OMA; PYDYVEH; -.
DR PhylomeDB; P0AAR3; -.
DR BioCyc; EcoCyc:EG12454-MON; -.
DR EvolutionaryTrace; P0AAR3; -.
DR PRO; PR:P0AAR3; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0002161; F:aminoacyl-tRNA editing activity; IDA:UniProtKB.
DR GO; GO:0043907; F:Cys-tRNA(Pro) hydrolase activity; IDA:EcoCyc.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0010165; P:response to X-ray; IMP:EcoCyc.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
DR CDD; cd00002; YbaK_deacylase; 1.
DR Gene3D; 3.90.960.10; -; 1.
DR InterPro; IPR004369; Prolyl-tRNA_editing_YbaK/EbsC.
DR InterPro; IPR036754; YbaK/aa-tRNA-synt-asso_dom_sf.
DR InterPro; IPR007214; YbaK/aa-tRNA-synth-assoc-dom.
DR Pfam; PF04073; tRNA_edit; 1.
DR PIRSF; PIRSF006181; EbsC_YbaK; 1.
DR SUPFAM; SSF55826; SSF55826; 1.
DR TIGRFAMs; TIGR00011; YbaK_EbsC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Lyase; Protein biosynthesis; Reference proteome.
FT CHAIN 1..159
FT /note="Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK"
FT /id="PRO_0000168620"
FT SITE 29
FT /note="Participates in proton transfer during catalysis"
FT MUTAGEN 30
FT /note="G->C,I,V: >100-fold decrease in Cys-tRNA(Pro)
FT deacylation activity. Fails to gain Ala-tRNA(Pro)
FT deacylation activity."
FT /evidence="ECO:0000269|PubMed:23185990"
FT MUTAGEN 136
FT /note="D->A,C: 6-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:23185990"
FT HELIX 3..10
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 16..19
FT /evidence="ECO:0007829|PDB:2DXA"
FT HELIX 32..37
FT /evidence="ECO:0007829|PDB:2DXA"
FT TURN 41..43
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 44..52
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 55..65
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:2DXA"
FT HELIX 72..79
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:2DXA"
FT HELIX 89..96
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:2DXA"
FT HELIX 118..122
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 135..139
FT /evidence="ECO:0007829|PDB:2DXA"
FT HELIX 141..148
FT /evidence="ECO:0007829|PDB:2DXA"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:2DXA"
SQ SEQUENCE 159 AA; 17093 MW; 45CD6A2226F2AA01 CRC64;
MTPAVKLLEK NKISFQIHTY EHDPAETNFG DEVVKKLGLN PDQVYKTLLV AVNGDMKHLA
VAVTPVAGQL DLKKVAKALG AKKVEMADPM VAQRSTGYLV GGISPLGQKK RLPTIIDAPA
QEFATIYVSG GKRGLDIELA AGDLAKILDA KFADIARRD
