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 27-MAR-2024, entry version 139. 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; Bacillota; 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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; 224308-BSU02090; -. 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 OrthoDB; 9762883at2; -. DR PhylomeDB; P54427; -. DR BioCyc; BSUB:BSU02090-MONOMER; -. DR Proteomes; UP000001570; Chromosome. 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; DD-peptidase/beta-lactamase superfamily; 1. DR InterPro; IPR012338; Beta-lactam/transpept-like. DR InterPro; IPR002137; Beta-lactam_class-D_AS. DR InterPro; IPR001460; PCN-bd_Tpept. DR PANTHER; PTHR30627:SF6; BETA-LACTAMASE YBXI-RELATED; 1. DR PANTHER; PTHR30627; PEPTIDOGLYCAN D,D-TRANSPEPTIDASE; 1. DR Pfam; PF00905; Transpeptidase; 1. DR SUPFAM; SSF56601; beta-lactamase/transpeptidase-like; 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 //