DACB_ECOLI
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 03-AUG-2022, entry version 171.
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; Proteobacteria; 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}.
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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; P24228; -.
DR PRIDE; P24228; -.
DR EnsemblBacteria; AAC76214; AAC76214; b3182.
DR EnsemblBacteria; BAE77226; BAE77226; BAE77226.
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 PhylomeDB; P24228; -.
DR BioCyc; EcoCyc:EG10202-MON; -.
DR BioCyc; MetaCyc:EG10202-MON; -.
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; 3.40.710.10; -; 1.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR000667; Peptidase_S13.
DR PANTHER; PTHR30023; PTHR30023; 1.
DR Pfam; PF02113; Peptidase_S13; 1.
DR PRINTS; PR00922; DADACBPTASE3.
DR SUPFAM; SSF56601; SSF56601; 1.
DR TIGRFAMs; TIGR00666; PBP4; 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
