ID   DACD_ECOLI              Reviewed;         388 AA.
AC   P33013;
DT   01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT   15-JUL-1998, sequence version 3.
DT   02-SEP-2026, entry version 186.
DE   RecName: Full=D-alanyl-D-alanine carboxypeptidase DacD;
DE            Short=DD-carboxypeptidase;
DE            Short=DD-peptidase;
DE            EC=3.4.16.4;
DE   AltName: Full=Penicillin-binding protein 6b;
DE            Short=PBP-6b;
DE   Flags: Precursor;
GN   Name=dacD; Synonyms=phsE, yeeC; OrderedLocusNames=b2010, JW5329;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHARACTERIZATION.
RX   PubMed=8955390; DOI=10.1128/jb.178.24.7106-7111.1996;
RA   Baquero M.-R., Bouzon M., Quintela J.C., Ayala J.A., Moreno F.;
RT   "dacD, an Escherichia coli gene encoding a novel penicillin-binding protein
RT   (PBP6b) with DD-carboxypeptidase activity.";
RL   J. Bacteriol. 178:7106-7111(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / BHB2600;
RA   Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K.,
RA   Church G.M.;
RT   "Automated multiplex sequencing of the E.coli genome.";
RL   Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA   Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA   Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA   Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA   Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA   Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA   Horiuchi T.;
RT   "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT   the 40.1-50.0 min region on the linkage map.";
RL   DNA Res. 3:379-392(1996).
RN   [4]
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   [5]
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).
CC   -!- FUNCTION: Removes C-terminal D-alanyl residues from sugar-peptide cell
CC       wall precursors.
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   -!- SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000305}; Peripheral
CC       membrane protein {ECO:0000305}. Note=N-terminal lies in the periplasmic
CC       space. {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the peptidase S11 family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA16416.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={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; U00009; AAA16416.1; ALT_INIT; Genomic_DNA.
DR   EMBL; U00096; AAC75071.2; -; Genomic_DNA.
DR   EMBL; AP009048; BAA15838.2; -; Genomic_DNA.
DR   PIR; A64966; A64966.
DR   RefSeq; NP_416514.4; NC_000913.3.
DR   RefSeq; WP_000830156.1; NZ_CP009789.1.
DR   PDB; 5FSR; X-ray; 2.40 A; A/B=22-374.
DR   AlphaFoldDB; P33013; -.
DR   SMR; P33013; -.
DR   BioGRID; 4260413; 268.
DR   FunCoup; P33013; 265.
DR   STRING; 511145.b2010; -.
DR   MEROPS; S11.009; -.
DR   PaxDb; 511145-b2010; -.
DR   EnsemblBacteria; AAC75071; AAC75071; b2010.
DR   GeneID; 946518; -.
DR   KEGG; ecj:JW5329; -.
DR   KEGG; eco:b2010; -.
DR   KEGG; ecoc:C3026_11340; -.
DR   PATRIC; fig|1411691.4.peg.242; -.
DR   EchoBASE; EB1839; -.
DR   eggNOG; COG1686; Bacteria.
DR   HOGENOM; CLU_027070_8_1_6; -.
DR   InParanoid; P33013; -.
DR   OMA; IQAGSWV; -.
DR   OrthoDB; 9795979at2; -.
DR   PhylomeDB; P33013; -.
DR   BioCyc; EcoCyc:RPOA-MONOMER; -.
DR   BioCyc; MetaCyc:RPOA-MONOMER; -.
DR   UniPathway; UPA00219; -.
DR   PRO; PR:P33013; -.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0008800; F:beta-lactamase activity; IDA:EcoCyc.
DR   GO; GO:0004180; F:carboxypeptidase activity; IDA:EcoCyc.
DR   GO; GO:0008658; F:penicillin binding; IDA:EcoCyc.
DR   GO; GO:0009002; F:serine-type D-Ala-D-Ala carboxypeptidase activity; ISM:EcoCyc.
DR   GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway.
DR   GO; GO:0000270; P:peptidoglycan metabolic process; IDA:EcoCyc.
DR   GO; GO:0006508; P:proteolysis; IEA:InterPro.
DR   GO; GO:0008360; P:regulation of cell shape; IGI:EcoCyc.
DR   FunFam; 2.60.410.10:FF:000002; D-alanyl-D-alanine carboxypeptidase dacD; 1.
DR   FunFam; 3.40.710.10:FF:000001; D-alanyl-D-alanine serine-type carboxypeptidase; 1.
DR   Gene3D; 2.60.410.10; D-Ala-D-Ala carboxypeptidase, C-terminal domain; 1.
DR   Gene3D; 3.40.710.10; DD-peptidase/beta-lactamase superfamily; 1.
DR   InterPro; IPR012338; Beta-lactam/transpept-like.
DR   InterPro; IPR015956; Peniciliin-bd_prot_C_sf.
DR   InterPro; IPR018044; Peptidase_S11.
DR   InterPro; IPR012907; Peptidase_S11_C.
DR   InterPro; IPR037167; Peptidase_S11_C_sf.
DR   InterPro; IPR001967; Peptidase_S11_N.
DR   NCBIfam; NF008489; PRK11397.1; 1.
DR   PANTHER; PTHR21581; D-ALANYL-D-ALANINE CARBOXYPEPTIDASE; 1.
DR   PANTHER; PTHR21581:SF5; D-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACD; 1.
DR   Pfam; PF07943; PBP5_C; 1.
DR   Pfam; PF00768; Peptidase_S11; 1.
DR   PRINTS; PR00725; DADACBPTASE1.
DR   SMART; SM00936; PBP5_C; 1.
DR   SUPFAM; SSF56601; beta-lactamase/transpeptidase-like; 1.
DR   SUPFAM; SSF69189; Penicillin-binding protein associated domain; 1.
DR   PDBsum; 5FSR; -.
PE   1: Evidence at protein level;
KW   3D-structure; Carboxypeptidase; Cell inner membrane; Cell membrane;
KW   Cell shape; Cell wall biogenesis/degradation; Hydrolase; Membrane;
KW   Peptidoglycan synthesis; Protease; Reference proteome; Signal.
FT   SIGNAL          1..21
FT                   /evidence="ECO:0000255"
FT   CHAIN           22..388
FT                   /note="D-alanyl-D-alanine carboxypeptidase DacD"
FT                   /id="PRO_0000027234"
FT   ACT_SITE        63
FT                   /note="Acyl-ester intermediate"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        66
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        129
FT                   /evidence="ECO:0000250"
FT   BINDING         232
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   HELIX           28..33
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          36..43
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   TURN            44..46
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          49..54
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           62..64
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           65..78
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          87..89
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           92..94
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   TURN            100..104
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          115..117
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           118..126
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           131..142
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           145..158
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          168..171
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           181..192
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           196..200
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           201..203
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          206..209
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          212..215
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           219..222
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          226..228
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          232..235
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          241..249
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          252..263
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           264..281
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          282..291
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          315..320
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   HELIX           321..326
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          327..329
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          349..355
FT                   /evidence="ECO:0007829|PDB:5FSR"
FT   STRAND          358..365
FT                   /evidence="ECO:0007829|PDB:5FSR"
SQ   SEQUENCE   388 AA;  43346 MW;  453FE18C21D207D0 CRC64;
     MKRRLIIAAS LFVFNLSSGF AAENIPFSPQ PPEIHAGSWV LMDYTTGQIL TAGNEHQQRN
     PASLTKLMTG YVVDRAIDSH RITPDDIVTV GRDAWAKDNP VFVGSSLMFL KEGDRVSVRD
     LSRGLIVDSG NDACVALADY IAGGQRQFVE MMNNYAEKLH LKDTHFETVH GLDAPGQHSS
     AYDLAVLSRA IIHGEPEFYH MYSEKSLTWN GITQQNRNGL LWDKTMNVDG LKTGHTSGAG
     FNLIASAVDG QRRLIAVVMG ADSAKGREEE ARKLLRWGQQ NFTTVQILHR GKKVGTERIW
     YGDKENIDLG TEQEFWMVLP KAEIPHIKAK YTLDGKELTA PISAHQRVGE IELYDRDKQV
     AHWPLVTLES VGEGSMFSRL SDYFHHKA
//