YBAK_SHIFL
ID YBAK_SHIFL Reviewed; 159 AA.
AC P0AAR4; P37175; P77281;
DT 11-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2005, sequence version 1.
DT 25-MAY-2022, entry version 98.
DE RecName: Full=Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
DE EC=4.2.-.-;
GN Name=ybaK; OrderedLocusNames=SF0426, S0433;
OS Shigella flexneri.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=623;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 / Serotype 2a;
RX PubMed=12384590; DOI=10.1093/nar/gkf566;
RA Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT through comparison with genomes of Escherichia coli K12 and O157.";
RL Nucleic Acids Res. 30:4432-4441(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700930 / 2457T / Serotype 2a;
RX PubMed=12704152; DOI=10.1128/iai.71.5.2775-2786.2003;
RA Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G.,
RA Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T.,
RA Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R.;
RT "Complete genome sequence and comparative genomics of Shigella flexneri
RT serotype 2a strain 2457T.";
RL Infect. Immun. 71:2775-2786(2003).
CC -!- FUNCTION: Functions in trans to edit the amino acid from incorrectly
CC charged Cys-tRNA(Pro) via a Cys-tRNA(Pro) deacylase activity.
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
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 (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the prolyl-tRNA editing family. YbaK/EbsC
CC subfamily. {ECO:0000305}.
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DR EMBL; AE005674; AAN42081.1; -; Genomic_DNA.
DR EMBL; AE014073; AAP15958.1; -; Genomic_DNA.
DR RefSeq; NP_706374.1; NC_004337.2.
DR RefSeq; WP_000186631.1; NZ_WPGW01000015.1.
DR AlphaFoldDB; P0AAR4; -.
DR SMR; P0AAR4; -.
DR STRING; 198214.SF0426; -.
DR EnsemblBacteria; AAN42081; AAN42081; SF0426.
DR EnsemblBacteria; AAP15958; AAP15958; S0433.
DR GeneID; 1027738; -.
DR GeneID; 66671217; -.
DR KEGG; sfl:SF0426; -.
DR KEGG; sfx:S0433; -.
DR PATRIC; fig|198214.7.peg.488; -.
DR HOGENOM; CLU_094875_1_1_6; -.
DR OMA; PYDYVEH; -.
DR OrthoDB; 1503081at2; -.
DR Proteomes; UP000001006; Chromosome.
DR Proteomes; UP000002673; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0002161; F:aminoacyl-tRNA editing activity; IEA:InterPro.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
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 3: Inferred from homology;
KW Cytoplasm; Lyase; Protein biosynthesis; Reference proteome.
FT CHAIN 1..159
FT /note="Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK"
FT /id="PRO_0000168622"
FT SITE 29
FT /note="Participates in proton transfer during catalysis"
FT /evidence="ECO:0000250"
SQ SEQUENCE 159 AA; 17093 MW; 45CD6A2226F2AA01 CRC64;
MTPAVKLLEK NKISFQIHTY EHDPAETNFG DEVVKKLGLN PDQVYKTLLV AVNGDMKHLA
VAVTPVAGQL DLKKVAKALG AKKVEMADPM VAQRSTGYLV GGISPLGQKK RLPTIIDAPA
QEFATIYVSG GKRGLDIELA AGDLAKILDA KFADIARRD
