ID   YBAK_HAEIN              Reviewed;         158 AA.
AC   P45202; Q9RP30;
DT   01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT   21-FEB-2001, sequence version 2.
DT   02-SEP-2026, entry version 148.
DE   RecName: Full=Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
DE            EC=4.2.-.-;
GN   Name=ybaK; OrderedLocusNames=HI_1434;
OS   Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Pasteurellales; Pasteurellaceae; Haemophilus.
OX   NCBI_TaxID=71421;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX   PubMed=7542800; DOI=10.1126/science.7542800;
RA   Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F.,
RA   Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.,
RA   McKenney K., Sutton G.G., FitzHugh W., Fields C.A., Gocayne J.D.,
RA   Scott J.D., Shirley R., Liu L.-I., Glodek A., Kelley J.M., Weidman J.F.,
RA   Phillips C.A., Spriggs T., Hedblom E., Cotton M.D., Utterback T.R.,
RA   Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C., Fine L.D.,
RA   Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M., Gnehm C.L., McDonald L.A.,
RA   Small K.V., Fraser C.M., Smith H.O., Venter J.C.;
RT   "Whole-genome random sequencing and assembly of Haemophilus influenzae
RT   Rd.";
RL   Science 269:496-512(1995).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RA   Bonander N., Eisenstein E.;
RL   Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   FUNCTION IN CYS-TRNA(PRO) EDITING, AND MUTAGENESIS OF LYS-46.
RX   PubMed=15322138; DOI=10.1074/jbc.c400304200;
RA   An S., Musier-Forsyth K.;
RT   "Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein.";
RL   J. Biol. Chem. 279:42359-42362(2004).
RN   [4]
RP   FUNCTION AS A DEACYLASE, AND SUBSTRATE SPECIFICITY.
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   [5]
RP   SUBUNIT.
RX   PubMed=16087664; DOI=10.1074/jbc.m507550200;
RA   An S., Musier-Forsyth K.;
RT   "Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel
RT   synthetase.YbaK.tRNA ternary complex.";
RL   J. Biol. Chem. 280:34465-34472(2005).
RN   [6]
RP   FUNCTION, REACTION MECHANISM, SUBSTRATE SPECIFICITY, AND MUTAGENESIS OF
RP   TYR-20; PHE-29; LYS-46; THR-47; GLY-101; SER-129; GLY-131; GLY-134 AND
RP   SER-136.
RX   PubMed=21768119; DOI=10.1074/jbc.m111.232611;
RA   So B.R., An S., Kumar S., Das M., Turner D.A., Hadad C.M.,
RA   Musier-Forsyth K.;
RT   "Substrate-mediated fidelity mechanism ensures accurate decoding of proline
RT   codons.";
RL   J. Biol. Chem. 286:31810-31820(2011).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
RX   PubMed=10813833;
RX   DOI=10.1002/(sici)1097-0134(20000701)40:1<86::aid-prot100>3.0.co;2-y;
RA   Zhang H., Huang K., Li Z., Banerjei L., Fisher K.E., Grishin N.V.,
RA   Eisenstein E., Herzberg O.;
RT   "Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at
RT   1.8-A resolution: functional implications.";
RL   Proteins 40:86-97(2000).
CC   -!- FUNCTION: Functions in trans to edit the amino acid from incorrectly
CC       charged Cys-tRNA(Pro) via a Cys-tRNA(Pro) deacylase activity. Probably
CC       compensates for the lack of Cys-tRNA(Pro) editing by ProRS. Is also
CC       able to deacylate Cys-tRNA(Cys), and displays weak deacylase activity
CC       in vitro against Gly-tRNA(Gly), as well as, at higher concentrations,
CC       some other correctly charged tRNAs. Does not cleave Pro-tRNA(Pro).
CC       {ECO:0000269|PubMed:15322138, ECO:0000269|PubMed:15886196,
CC       ECO:0000269|PubMed:21768119}.
CC   -!- SUBUNIT: May form a tertiary complex with ProRS and tRNA(Pro), as it
CC       can be cross-linked to E.coli ProRS and to E.coli tRNA(Pro) in vitro.
CC       It cannot compete with Ef-Tu for aminoacyl-tRNA binding, suggesting it
CC       acts before release of the charged aminoacyl-tRNA from the synthetase.
CC       {ECO:0000269|PubMed:16087664}.
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 (PubMed:21768119). {ECO:0000305|PubMed:21768119}.
CC   -!- SIMILARITY: Belongs to the prolyl-tRNA editing family. YbaK/EbsC
CC       subfamily. {ECO:0000305}.
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DR   EMBL; L42023; AAC23081.1; -; Genomic_DNA.
DR   EMBL; AF174386; AAD54290.1; -; Genomic_DNA.
DR   PIR; H64171; H64171.
DR   PDB; 1DBU; X-ray; 1.80 A; A=1-158.
DR   PDB; 1DBX; X-ray; 1.80 A; A/B=1-158.
DR   AlphaFoldDB; P45202; -.
DR   SMR; P45202; -.
DR   STRING; 71421.HI_1434; -.
DR   EnsemblBacteria; AAC23081; AAC23081; HI_1434.
DR   KEGG; hin:HI_1434; -.
DR   PATRIC; fig|71421.8.peg.1491; -.
DR   eggNOG; COG2606; Bacteria.
DR   HOGENOM; CLU_094875_1_1_6; -.
DR   OrthoDB; 9809296at2; -.
DR   PhylomeDB; P45202; -.
DR   BioCyc; HINF71421:G1GJ1-1457-MONOMER; -.
DR   EvolutionaryTrace; P45202; -.
DR   Proteomes; UP000000579; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0043906; F:Ala-tRNA(Pro) deacylase activity; IDA:UniProtKB.
DR   GO; GO:0002161; F:aminoacyl-tRNA deacylase activity; IBA:GO_Central.
DR   GO; GO:0106074; P:aminoacyl-tRNA metabolism involved in translational fidelity; IBA:GO_Central.
DR   CDD; cd00002; YbaK_deacylase; 1.
DR   FunFam; 3.90.960.10:FF:000002; Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase; 1.
DR   Gene3D; 3.90.960.10; YbaK/aminoacyl-tRNA synthetase-associated domain; 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   NCBIfam; TIGR00011; YbaK_EbsC; 1.
DR   PANTHER; PTHR30411:SF0; CYS-TRNA(PRO)_CYS-TRNA(CYS) DEACYLASE YBAK; 1.
DR   PANTHER; PTHR30411; CYTOPLASMIC PROTEIN; 1.
DR   Pfam; PF04073; tRNA_edit; 1.
DR   PIRSF; PIRSF006181; EbsC_YbaK; 1.
DR   SUPFAM; SSF55826; YbaK/ProRS associated domain; 1.
DR   PDBsum; 1DBU; -.
DR   PDBsum; 1DBX; -.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Lyase; Protein biosynthesis; Reference proteome.
FT   CHAIN           1..158
FT                   /note="Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK"
FT                   /id="PRO_0000168623"
FT   SITE            29
FT                   /note="Participates in proton transfer during catalysis"
FT                   /evidence="ECO:0000250"
FT   MUTAGEN         20
FT                   /note="Y->A: 45-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   MUTAGEN         29
FT                   /note="F->A: 29-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   MUTAGEN         46
FT                   /note="K->A: 66-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:15322138,
FT                   ECO:0000269|PubMed:21768119"
FT   MUTAGEN         46
FT                   /note="K->I: 38-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:15322138,
FT                   ECO:0000269|PubMed:21768119"
FT   MUTAGEN         46
FT                   /note="K->R: 44-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:15322138,
FT                   ECO:0000269|PubMed:21768119"
FT   MUTAGEN         47
FT                   /note="T->A: 21-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   MUTAGEN         101
FT                   /note="G->A: 36-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   MUTAGEN         129
FT                   /note="S->A: 5.6-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   MUTAGEN         131
FT                   /note="G->A: 28-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   MUTAGEN         134
FT                   /note="G->A: 7.4-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   MUTAGEN         136
FT                   /note="S->A: 3.6-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   MUTAGEN         136
FT                   /note="S->H: 16-fold decrease in Cys-tRNA(Pro) deacylation
FT                   activity."
FT                   /evidence="ECO:0000269|PubMed:21768119"
FT   CONFLICT        117
FT                   /note="N -> K (in Ref. 1; AAC23081)"
FT                   /evidence="ECO:0000305"
FT   HELIX           3..11
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          16..19
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   HELIX           32..37
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   HELIX           41..43
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          44..52
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          58..65
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   HELIX           72..79
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          84..86
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   HELIX           89..96
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          105..107
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          114..117
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   HELIX           118..122
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          126..129
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          135..139
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   HELIX           141..148
FT                   /evidence="ECO:0007829|PDB:1DBU"
FT   STRAND          151..153
FT                   /evidence="ECO:0007829|PDB:1DBU"
SQ   SEQUENCE   158 AA;  17155 MW;  45723E9DFC99535A CRC64;
     MTPAIDLLKK QKIPFILHTY DHDPNNQHFG DEAAEKLGID PNRSFKTLLV AENGDQKKLA
     CFVLATANML NLKKAAKSIG VKKVEMADKD AAQKSTGYLV GGISPLGQKK RVKTVINSTA
     LEFETIYVSG GKRGLSVEIA PQDLAKVLGA EFTDIVDE
//