ID DACB_ECOLI Reviewed; 477 AA. AC P24228; Q2M930; DT 01-MAR-1992, integrated into UniProtKB/Swiss-Prot. DT 01-NOV-1995, sequence version 2. DT 24-JAN-2024, entry version 177. DE RecName: Full=D-alanyl-D-alanine carboxypeptidase DacB; DE Short=DD-carboxypeptidase; DE Short=DD-peptidase; DE EC=3.4.16.4; DE AltName: Full=D-alanyl-D-alanine endopeptidase; DE Short=DD-endopeptidase; DE EC=3.4.21.-; DE AltName: Full=Penicillin-binding protein 4; DE Short=PBP-4; DE Flags: Precursor; GN Name=dacB; OrderedLocusNames=b3182, JW3149; OS Escherichia coli (strain K12). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 21-31. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=2040429; DOI=10.1016/0378-1097(91)90160-c; RA Mottl H., Terpstra P., Keck W.; RT "Penicillin-binding protein 4 of Escherichia coli shows a novel type of RT primary structure among penicillin-interacting proteins."; RL FEMS Microbiol. Lett. 62:213-220(1991). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=K12; RA Wang R., Kushner S.R.; RL Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases. RN [3] 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 [4] 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 [5] RP PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND X-RAY CRYSTALLOGRAPHY (1.55 RP ANGSTROMS) OF 21-477 OF APOENZYME AND IN COMPLEX WITH PENICILLIN RP ANTIBIOTICS. RC STRAIN=K12; RX PubMed=16411754; DOI=10.1021/bi051533t; RA Kishida H., Unzai S., Roper D.I., Lloyd A., Park S.-Y., Tame J.R.H.; RT "Crystal structure of penicillin binding protein 4 (dacB) from Escherichia RT coli, both in the native form and covalently linked to various RT antibiotics."; RL Biochemistry 45:783-792(2006). RN [6] RP FUNCTION. RX PubMed=2046551; DOI=10.1111/j.1365-2958.1991.tb00739.x; RA Korat B., Mottl H., Keck W.; RT "Penicillin-binding protein 4 of Escherichia coli: molecular cloning of the RT dacB gene, controlled overexpression, and alterations in murein RT composition."; RL Mol. Microbiol. 5:675-684(1991). CC -!- FUNCTION: Not involved in transpeptidation but exclusively catalyzes a CC DD-carboxypeptidase and DD-endopeptidase reaction. CC {ECO:0000269|PubMed:2046551}. CC -!- CATALYTIC ACTIVITY: CC Reaction=Preferential cleavage: (Ac)2-L-Lys-D-Ala-|-D-Ala. Also CC transpeptidation of peptidyl-alanyl moieties that are N-acyl CC substituents of D-alanine.; EC=3.4.16.4; CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis. CC -!- INTERACTION: CC P24228; P0A6E4: argG; NbExp=2; IntAct=EBI-1131834, EBI-1120296; CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000305}. CC -!- MISCELLANEOUS: In E.coli there are three murein endopeptidases: two are CC penicillin sensitive (DacB and PbpG), the other (MepA) not. CC -!- SIMILARITY: Belongs to the peptidase S13 family. {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; X59460; CAA42070.1; -; Genomic_DNA. DR EMBL; X60038; CAA42643.1; -; Genomic_DNA. DR EMBL; U01376; AAA97505.1; -; Genomic_DNA. DR EMBL; U18997; AAA57983.1; -; Genomic_DNA. DR EMBL; U00096; AAC76214.1; -; Genomic_DNA. DR EMBL; AP009048; BAE77226.1; -; Genomic_DNA. DR PIR; A54535; A54535. DR RefSeq; NP_417649.1; NC_000913.3. DR RefSeq; WP_001212619.1; NZ_SSZK01000007.1. DR PDB; 2EX2; X-ray; 1.55 A; A=21-477. DR PDB; 2EX6; X-ray; 1.60 A; A=21-477. DR PDB; 2EX8; X-ray; 1.60 A; A=21-477. DR PDB; 2EX9; X-ray; 1.65 A; A=21-477. DR PDB; 2EXA; X-ray; 1.70 A; A=21-477. DR PDB; 2EXB; X-ray; 1.75 A; A=21-477. DR PDBsum; 2EX2; -. DR PDBsum; 2EX6; -. DR PDBsum; 2EX8; -. DR PDBsum; 2EX9; -. DR PDBsum; 2EXA; -. DR PDBsum; 2EXB; -. DR AlphaFoldDB; P24228; -. DR SMR; P24228; -. DR BioGRID; 4262437; 332. DR BioGRID; 852006; 1. DR IntAct; P24228; 1. DR STRING; 511145.b3182; -. DR ChEMBL; CHEMBL2354204; -. DR DrugBank; DB01602; Bacampicillin. DR DrugBank; DB00578; Carbenicillin. DR DrugBank; DB09319; Carindacillin. DR DrugBank; DB14879; Cefiderocol. DR DrugBank; DB01328; Cefonicid. DR DrugBank; DB01329; Cefoperazone. DR DrugBank; DB01331; Cefoxitin. DR DrugBank; DB09050; Ceftolozane. DR DrugBank; DB01000; Cyclacillin. DR DrugBank; DB00303; Ertapenem. DR DrugBank; DB04570; Latamoxef. DR DrugBank; DB00760; Meropenem. DR DrugBank; DB00417; Phenoxymethylpenicillin. DR DrugCentral; P24228; -. DR MEROPS; S13.001; -. DR MoonProt; P24228; -. DR jPOST; P24228; -. DR PaxDb; 511145-b3182; -. DR EnsemblBacteria; AAC76214; AAC76214; b3182. DR GeneID; 75173356; -. DR GeneID; 947693; -. DR KEGG; ecj:JW3149; -. DR KEGG; eco:b3182; -. DR PATRIC; fig|511145.12.peg.3275; -. DR EchoBASE; EB0198; -. DR eggNOG; COG2027; Bacteria. DR HOGENOM; CLU_017692_1_1_6; -. DR InParanoid; P24228; -. DR OMA; DGTMRKR; -. DR OrthoDB; 9802627at2; -. DR PhylomeDB; P24228; -. DR BioCyc; EcoCyc:EG10202-MONOMER; -. DR BioCyc; MetaCyc:EG10202-MONOMER; -. DR BRENDA; 3.4.16.4; 2165. DR BRENDA; 3.4.17.14; 2026. DR UniPathway; UPA00219; -. DR EvolutionaryTrace; P24228; -. DR PRO; PR:P24228; -. DR Proteomes; UP000000318; Chromosome. DR Proteomes; UP000000625; Chromosome. DR GO; GO:0042597; C:periplasmic space; IDA:EcoCyc. DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc. DR GO; GO:0004180; F:carboxypeptidase activity; IMP:EcoCyc. DR GO; GO:0004175; F:endopeptidase activity; IDA:EcoCyc. DR GO; GO:0008658; F:penicillin binding; IDA:EcoCyc. DR GO; GO:0004185; F:serine-type carboxypeptidase activity; ISM:EcoCyc. DR GO; GO:0009002; F:serine-type D-Ala-D-Ala carboxypeptidase activity; IMP:EcoliWiki. DR GO; GO:0004252; F:serine-type endopeptidase activity; ISM:EcoCyc. DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW. DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW. DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW. DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway. DR GO; GO:0000270; P:peptidoglycan metabolic process; IMP:EcoCyc. DR GO; GO:0006508; P:proteolysis; IEA:InterPro. DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW. DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW. DR Gene3D; 3.50.80.20; D-Ala-D-Ala carboxypeptidase C, peptidase S13; 1. DR Gene3D; 3.40.710.10; DD-peptidase/beta-lactamase superfamily; 1. DR InterPro; IPR012338; Beta-lactam/transpept-like. DR InterPro; IPR000667; Peptidase_S13. DR NCBIfam; TIGR00666; PBP4; 1. DR PANTHER; PTHR30023; D-ALANYL-D-ALANINE CARBOXYPEPTIDASE; 1. DR PANTHER; PTHR30023:SF0; PENICILLIN-SENSITIVE CARBOXYPEPTIDASE A; 1. DR Pfam; PF02113; Peptidase_S13; 1. DR PRINTS; PR00922; DADACBPTASE3. DR SUPFAM; SSF56601; beta-lactamase/transpeptidase-like; 1. PE 1: Evidence at protein level; KW 3D-structure; Antibiotic resistance; Cell cycle; Cell division; Cell shape; KW Cell wall biogenesis/degradation; Direct protein sequencing; Hydrolase; KW Peptidoglycan synthesis; Periplasm; Reference proteome; Signal. FT SIGNAL 1..20 FT /evidence="ECO:0000269|PubMed:2040429" FT CHAIN 21..477 FT /note="D-alanyl-D-alanine carboxypeptidase DacB" FT /id="PRO_0000027241" FT REGION 90..263 FT /note="Absent in class-A beta-lactamases" FT ACT_SITE 62 FT /note="Acyl-ester intermediate" FT /evidence="ECO:0000250|UniProtKB:P39844" FT ACT_SITE 65 FT /note="Proton acceptor" FT /evidence="ECO:0000250|UniProtKB:P39844" FT ACT_SITE 306 FT /evidence="ECO:0000250|UniProtKB:P39844" FT BINDING 417 FT /ligand="substrate" FT /evidence="ECO:0000250" FT CONFLICT 261 FT /note="D -> Y (in Ref. 5)" FT /evidence="ECO:0000305" FT CONFLICT 427 FT /note="L -> Q (in Ref. 1; CAA42643)" FT /evidence="ECO:0000305" FT HELIX 23..27 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 35..42 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 49..53 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 61..63 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 64..75 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 83..93 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 96..104 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 113..125 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 130..133 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 135..138 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 153..155 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 159..161 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 170..172 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 173..179 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 189..191 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 199..207 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 209..211 FT /evidence="ECO:0007829|PDB:2EX9" FT TURN 213..216 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 219..224 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 225..227 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 228..236 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 242..247 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 251..265 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 269..272 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 274..277 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 285..291 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 295..305 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 308..323 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 329..342 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 356..358 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 367..379 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 381..384 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 387..389 FT /evidence="ECO:0007829|PDB:2EX2" FT TURN 393..395 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 397..399 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 403..407 FT /evidence="ECO:0007829|PDB:2EX2" FT TURN 411..413 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 414..421 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 424..432 FT /evidence="ECO:0007829|PDB:2EX2" FT STRAND 438..447 FT /evidence="ECO:0007829|PDB:2EX2" FT HELIX 452..454 FT /evidence="ECO:0007829|PDB:2EX2" FT TURN 455..457 FT /evidence="ECO:0007829|PDB:2EX6" FT HELIX 460..475 FT /evidence="ECO:0007829|PDB:2EX2" SQ SEQUENCE 477 AA; 51798 MW; 4EF5E43D2BEC4E5B CRC64; MRFSRFIIGL TSCIAFSVQA ANVDEYITQL PAGANLALMV QKVGASAPAI DYHSQQMALP ASTQKVITAL AALIQLGPDF RFTTTLETKG NVENGVLKGD LVARFGADPT LKRQDIRNMV ATLKKSGVNQ IDGNVLIDTS IFASHDKAPG WPWNDMTQCF SAPPAAAIVD RNCFSVSLYS APKPGDMAFI RVASYYPVTM FSQVRTLPRG SAEAQYCELD VVPGDLNRFT LTGCLPQRSE PLPLAFAVQD GASYAGAILK DELKQAGITW SGTLLRQTQV NEPGTVVASK QSAPLHDLLK IMLKKSDNMI ADTVFRMIGH ARFNVPGTWR AGSDAVRQIL RQQAGVDIGN TIIADGSGLS RHNLIAPATM MQVLQYIAQH DNELNFISML PLAGYDGSLQ YRAGLHQAGV DGKVSAKTGS LQGVYNLAGF ITTASGQRMA FVQYLSGYAV EPADQRNRRI PLVRFESRLY KDIYQNN //