DACD_ECOLI
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 03-AUG-2022, entry version 170.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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};
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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_LN832404.1.
DR PDB; 5FSR; X-ray; 2.40 A; A/B=22-374.
DR PDBsum; 5FSR; -.
DR AlphaFoldDB; P33013; -.
DR SMR; P33013; -.
DR BioGRID; 4260413; 266.
DR STRING; 511145.b2010; -.
DR MEROPS; S11.009; -.
DR PaxDb; P33013; -.
DR PRIDE; P33013; -.
DR EnsemblBacteria; AAC75071; AAC75071; b2010.
DR EnsemblBacteria; BAA15838; BAA15838; BAA15838.
DR GeneID; 946518; -.
DR KEGG; ecj:JW5329; -.
DR KEGG; eco:b2010; -.
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 PhylomeDB; P33013; -.
DR BioCyc; EcoCyc:RPOA-MON; -.
DR BioCyc; MetaCyc:RPOA-MON; -.
DR UniPathway; UPA00219; -.
DR PRO; PR:P33013; -.
DR Proteomes; UP000000318; Chromosome.
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: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; IDA:EcoCyc.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 2.60.410.10; -; 1.
DR Gene3D; 3.40.710.10; -; 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 Pfam; PF07943; PBP5_C; 1.
DR Pfam; PF00768; Peptidase_S11; 1.
DR PRINTS; PR00725; DADACBPTASE1.
DR SMART; SM00936; PBP5_C; 1.
DR SUPFAM; SSF56601; SSF56601; 1.
DR SUPFAM; SSF69189; SSF69189; 1.
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 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..332
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
