YBXI_BACSU
ID YBXI_BACSU Reviewed; 267 AA.
AC P54427; O31439;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Probable beta-lactamase YbxI;
DE EC=3.5.2.6;
DE Flags: Precursor;
GN Name=ybxI; Synonyms=ybdS; OrderedLocusNames=BSU02090;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RA Haga K., Liu H., Yasumoto K., Takahashi H., Yoshikawa H.;
RT "Sequence analysis of the 70kb region between 17 and 23 degree of the
RT Bacillus subtilis chromosome.";
RL Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 129-267.
RC STRAIN=168 / PY79;
RX PubMed=9016963; DOI=10.1016/s0378-1119(96)00603-8;
RA Shcheptov M., Chyu G., Bagyan I., Cutting S.M.;
RT "Characterization of csgA, a new member of the forespore-expressed sigmaG-
RT regulon from Bacillus subtilis.";
RL Gene 184:133-140(1997).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a beta-lactam + H2O = a substituted beta-amino acid;
CC Xref=Rhea:RHEA:20401, ChEBI:CHEBI:15377, ChEBI:CHEBI:35627,
CC ChEBI:CHEBI:140347; EC=3.5.2.6; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU10103};
CC -!- SIMILARITY: Belongs to the class-D beta-lactamase family.
CC {ECO:0000305}.
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DR EMBL; AB006424; BAA33106.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12003.1; -; Genomic_DNA.
DR EMBL; X92859; CAA63445.1; -; Genomic_DNA.
DR PIR; B69752; B69752.
DR RefSeq; NP_388091.1; NC_000964.3.
DR RefSeq; WP_003246349.1; NZ_JNCM01000030.1.
DR PDB; 5E2F; X-ray; 1.30 A; A/B=1-267.
DR PDB; 6W5E; X-ray; 1.30 A; A=1-267.
DR PDB; 6W5F; X-ray; 1.50 A; A/B/C/D=1-267.
DR PDBsum; 5E2F; -.
DR PDBsum; 6W5E; -.
DR PDBsum; 6W5F; -.
DR AlphaFoldDB; P54427; -.
DR SMR; P54427; -.
DR STRING; 224308.BSU02090; -.
DR PaxDb; P54427; -.
DR PRIDE; P54427; -.
DR EnsemblBacteria; CAB12003; CAB12003; BSU_02090.
DR GeneID; 938466; -.
DR KEGG; bsu:BSU02090; -.
DR PATRIC; fig|224308.179.peg.215; -.
DR eggNOG; COG2602; Bacteria.
DR InParanoid; P54427; -.
DR OMA; WNRDHTL; -.
DR PhylomeDB; P54427; -.
DR BioCyc; BSUB:BSU02090-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005887; C:integral component of plasma membrane; IBA:GO_Central.
DR GO; GO:0008800; F:beta-lactamase activity; IEA:UniProtKB-EC.
DR GO; GO:0008658; F:penicillin binding; IBA:GO_Central.
DR GO; GO:0017001; P:antibiotic catabolic process; IEA:InterPro.
DR GO; GO:0071555; P:cell wall organization; IBA:GO_Central.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR Gene3D; 3.40.710.10; -; 1.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR002137; Beta-lactam_class-D_AS.
DR InterPro; IPR001460; PCN-bd_Tpept.
DR Pfam; PF00905; Transpeptidase; 1.
DR SUPFAM; SSF56601; SSF56601; 1.
DR PROSITE; PS00337; BETA_LACTAMASE_D; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic resistance; Hydrolase; Reference proteome; Signal.
FT SIGNAL 1..23
FT /evidence="ECO:0000255"
FT CHAIN 24..267
FT /note="Probable beta-lactamase YbxI"
FT /id="PRO_0000017049"
FT ACT_SITE 76
FT /note="Acyl-ester intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10103"
FT BINDING 214..216
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 79
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000250"
FT CONFLICT 129..137
FT /note="YQALARDIG -> IISISERYR (in Ref. 3)"
FT /evidence="ECO:0000305"
FT CONFLICT 169
FT /note="T -> A (in Ref. 3; CAA63445)"
FT /evidence="ECO:0000305"
FT HELIX 34..36
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 40..43
FT /evidence="ECO:0007829|PDB:5E2F"
FT STRAND 44..46
FT /evidence="ECO:0007829|PDB:6W5F"
FT STRAND 48..54
FT /evidence="ECO:0007829|PDB:5E2F"
FT TURN 55..58
FT /evidence="ECO:0007829|PDB:5E2F"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 65..68
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 81..88
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 109..111
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 117..122
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 126..136
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 138..147
FT /evidence="ECO:0007829|PDB:5E2F"
FT TURN 159..163
FT /evidence="ECO:0007829|PDB:5E2F"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 172..183
FT /evidence="ECO:0007829|PDB:5E2F"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 191..200
FT /evidence="ECO:0007829|PDB:5E2F"
FT STRAND 202..205
FT /evidence="ECO:0007829|PDB:5E2F"
FT STRAND 207..217
FT /evidence="ECO:0007829|PDB:5E2F"
FT TURN 219..222
FT /evidence="ECO:0007829|PDB:5E2F"
FT STRAND 225..233
FT /evidence="ECO:0007829|PDB:5E2F"
FT STRAND 236..246
FT /evidence="ECO:0007829|PDB:5E2F"
FT HELIX 248..261
FT /evidence="ECO:0007829|PDB:5E2F"
SQ SEQUENCE 267 AA; 30644 MW; BBE3E698CD46E6ED CRC64;
MKKWIYVVLV LSIAGIGGFS VHAASSAHEK HLNVSKMNVD DEFKDTDGTF ILHDLQKDQT
FVYNRKRANQ RQTPQSTFKV VNALIGLQVK AVRDEYDVKR WDGVKREFES WNRDHTLGSA
MRESAIWYYQ ALARDIGEER MKTWLHTLSY GNEDISGGID QFWLQSSLTI SPLEQETFLE
KLAKEELPFD KPVMKIVKRM MIQEEGDHYT LYGKTGTRLT DMGLGWFVGF IKTEHGSYVF
VTNVDDSGTK AKNITVDILK KYGLITS
