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D-alanyl-D-alanine carboxypeptidase DacA (DD-carboxypeptidase) (DD-peptidase) (EC 3.4.16.4) (Beta-lactamase) (EC 3.5.2.6) (Penicillin-binding protein 5) (PBP-5)

 DACA_ECOLI              Reviewed;         403 AA.
P0AEB2; P04287; P77106;
20-MAR-1987, integrated into UniProtKB/Swiss-Prot.
20-MAR-1987, sequence version 1.
28-MAR-2018, entry version 123.
RecName: Full=D-alanyl-D-alanine carboxypeptidase DacA;
Short=DD-carboxypeptidase;
Short=DD-peptidase;
EC=3.4.16.4;
AltName: Full=Beta-lactamase;
EC=3.5.2.6;
AltName: Full=Penicillin-binding protein 5;
Short=PBP-5;
Flags: Precursor;
Name=dacA; Synonyms=pfv; OrderedLocusNames=b0632, JW0627;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Broome-Smith J.K.;
Submitted (APR-1984) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=3279397; DOI=10.1093/nar/16.4.1617;
Broome-Smith J.K., Ioannidis I., Edelman A., Spratt B.G.;
"Nucleotide sequences of the penicillin-binding protein 5 and 6 genes
of Escherichia coli.";
Nucleic Acids Res. 16:1617-1617(1988).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=8905232; DOI=10.1093/dnares/3.3.137;
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A.,
Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K.,
Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K.,
Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N.,
Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y.,
Yano M., Horiuchi T.;
"A 718-kb DNA sequence of the Escherichia coli K-12 genome
corresponding to the 12.7-28.0 min region on the linkage map.";
DNA Res. 3:137-155(1996).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
"Sequence of minutes 4-25 of Escherichia coli.";
Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 108-336, AND MUTANT DACA11191.
PubMed=6319180; DOI=10.1016/0014-5793(84)80166-0;
Broome-Smith J.K., Spratt B.G.;
"An amino acid substitution that blocks the deacylation step in the
enzyme mechanism of penicillin-binding protein 5 of Escherichia
coli.";
FEBS Lett. 165:185-189(1984).
[8]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-39.
STRAIN=K12;
PubMed=3316191; DOI=10.1128/jb.169.12.5692-5699.1987;
Takase I., Ishino F., Wachi M., Kamata H., Doi M., Asoh S.,
Matsuzawa H., Ohta T., Matsuhashi M.;
"Genes encoding two lipoproteins in the leuS-dacA region of the
Escherichia coli chromosome.";
J. Bacteriol. 169:5692-5699(1987).
[9]
PROTEIN SEQUENCE OF 30-57.
PubMed=7042389; DOI=10.1016/0014-5793(82)80840-5;
Waxman D.J., Amanuma H., Strominger J.L.;
"Amino acid sequence homologies between Escherichia coli penicillin-
binding protein 5 and class A beta-lactamases.";
FEBS Lett. 139:159-163(1982).
[10]
MUTAGENESIS OF LYS-213.
PubMed=1597468;
Malhotra K.T., Nicholas R.A.;
"Substitution of lysine 213 with arginine in penicillin-binding
protein 5 of Escherichia coli abolishes D-alanine carboxypeptidase
activity without affecting penicillin binding.";
J. Biol. Chem. 267:11386-11391(1992).
[11]
DOMAINS.
PubMed=8424800;
van der Linden M.P.G., de Haan L., Keck W.;
"Domain organization of penicillin-binding protein 5 from Escherichia
coli analysed by C-terminal truncation.";
Biochem. J. 289:593-598(1993).
[12]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[13]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 30-386 OF MUTANT ASP-134.
PubMed=10967102; DOI=10.1074/jbc.M004471200;
Davies C., White S.W., Nicholas R.A.;
"Crystal structure of a deacylation-defective mutant of penicillin-
binding protein 5 at 2.3-A resolution.";
J. Biol. Chem. 276:616-623(2001).
[14]
X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 30-386 OF WILD-TYPE AND
MUTANT ASP-134, AND MUTAGENESIS OF 101-GLY--LYS-121.
PubMed=14555648; DOI=10.1074/jbc.M310177200;
Nicholas R.A., Krings S., Tomberg J., Nicola G., Davies C.;
"Crystal structure of wild-type penicillin-binding protein 5 from
Escherichia coli. Implications for deacylation of the acyl-enzyme
complex.";
J. Biol. Chem. 278:52826-52833(2003).
[15]
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 30-386 IN COMPLEX WITH
SUBSTRATE ANALOG, AND REACTION MECHANISM.
PubMed=15938610; DOI=10.1021/bi0473004;
Nicola G., Peddi S., Stefanova M., Nicholas R.A., Gutheil W.G.,
Davies C.;
"Crystal structure of Escherichia coli penicillin-binding protein 5
bound to a tripeptide boronic acid inhibitor: a role for Ser-110 in
deacylation.";
Biochemistry 44:8207-8217(2005).
-!- FUNCTION: Removes C-terminal D-alanyl residues from sugar-peptide
cell wall precursors.
-!- CATALYTIC ACTIVITY: Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-
D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are
N-acyl substituents of D-alanine.
-!- CATALYTIC ACTIVITY: A beta-lactam + H(2)O = a substituted beta-
amino acid.
-!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
-!- SUBCELLULAR LOCATION: Cell inner membrane; Peripheral membrane
protein; Cytoplasmic side. Note=N-terminal lies in the periplasmic
space.
-!- SIMILARITY: Belongs to the peptidase S11 family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAB40832.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; X06479; CAA29774.1; -; Genomic_DNA.
EMBL; M18276; AAA24553.1; -; Genomic_DNA.
EMBL; U82598; AAB40832.1; ALT_INIT; Genomic_DNA.
EMBL; U00096; AAC73733.1; -; Genomic_DNA.
EMBL; AP009048; BAA35275.1; -; Genomic_DNA.
EMBL; L07636; AAA66340.1; -; Genomic_DNA.
PIR; A28536; ZPECP5.
RefSeq; NP_415165.1; NC_000913.3.
RefSeq; WP_001092082.1; NZ_LN832404.1.
PDB; 1HD8; X-ray; 2.30 A; A=30-386.
PDB; 1NJ4; X-ray; 1.90 A; A=30-392.
PDB; 1NZO; X-ray; 1.85 A; A=30-392.
PDB; 1NZU; X-ray; 2.00 A; A=30-392.
PDB; 1SDN; X-ray; 2.50 A; A=30-392.
PDB; 1Z6F; X-ray; 1.60 A; A=30-392.
PDB; 3BEB; X-ray; 2.00 A; A=30-386.
PDB; 3BEC; X-ray; 1.60 A; A=30-386.
PDB; 3MZD; X-ray; 1.90 A; A=30-386.
PDB; 3MZE; X-ray; 2.10 A; A=30-386.
PDB; 3MZF; X-ray; 1.50 A; A=30-386.
PDB; 5J8X; X-ray; 2.53 A; A=30-392.
PDBsum; 1HD8; -.
PDBsum; 1NJ4; -.
PDBsum; 1NZO; -.
PDBsum; 1NZU; -.
PDBsum; 1SDN; -.
PDBsum; 1Z6F; -.
PDBsum; 3BEB; -.
PDBsum; 3BEC; -.
PDBsum; 3MZD; -.
PDBsum; 3MZE; -.
PDBsum; 3MZF; -.
PDBsum; 5J8X; -.
ProteinModelPortal; P0AEB2; -.
SMR; P0AEB2; -.
BioGrid; 4260698; 270.
DIP; DIP-47947N; -.
IntAct; P0AEB2; 9.
STRING; 316385.ECDH10B_0701; -.
ChEMBL; CHEMBL2354204; -.
DrugBank; DB04647; BOC-GAMMA-D-GLU-L-LYS(CBZ)-D-BOROALA.
DrugBank; DB00274; Cefmetazole.
DrugBank; DB01329; Cefoperazone.
DrugBank; DB01331; Cefoxitin.
MEROPS; S11.008; -.
EPD; P0AEB2; -.
PaxDb; P0AEB2; -.
PRIDE; P0AEB2; -.
EnsemblBacteria; AAC73733; AAC73733; b0632.
EnsemblBacteria; BAA35275; BAA35275; BAA35275.
GeneID; 945222; -.
KEGG; ecj:JW0627; -.
KEGG; eco:b0632; -.
PATRIC; fig|511145.12.peg.662; -.
EchoBASE; EB0197; -.
EcoGene; EG10201; dacA.
eggNOG; ENOG4105DZ1; Bacteria.
eggNOG; COG1686; LUCA.
HOGENOM; HOG000086623; -.
InParanoid; P0AEB2; -.
KO; K07258; -.
OMA; LQNTHFQ; -.
PhylomeDB; P0AEB2; -.
BioCyc; EcoCyc:EG10201-MONOMER; -.
BioCyc; MetaCyc:EG10201-MONOMER; -.
BRENDA; 3.4.16.4; 2026.
UniPathway; UPA00219; -.
EvolutionaryTrace; P0AEB2; -.
PRO; PR:P0AEB2; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005887; C:integral component of plasma membrane; IDA:EcoliWiki.
GO; GO:0008800; F:beta-lactamase activity; IEA:UniProtKB-EC.
GO; GO:0004180; F:carboxypeptidase activity; IDA:EcoCyc.
GO; GO:0004175; F:endopeptidase activity; IBA:GO_Central.
GO; GO:0008658; F:penicillin binding; IDA:EcoCyc.
GO; GO:0009002; F:serine-type D-Ala-D-Ala carboxypeptidase activity; IDA:CACAO.
GO; GO:0044036; P:cell wall macromolecule metabolic process; IDA:EcoCyc.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway.
GO; GO:0000270; P:peptidoglycan metabolic process; IDA:EcoCyc.
GO; GO:0008360; P:regulation of cell shape; IGI:EcoCyc.
Gene3D; 2.60.410.10; -; 1.
InterPro; IPR012338; Beta-lactam/transpept-like.
InterPro; IPR015956; Peniciliin-bd_prot_C_sf.
InterPro; IPR018044; Peptidase_S11.
InterPro; IPR012907; Peptidase_S11_C.
InterPro; IPR037167; Peptidase_S11_C_sf.
InterPro; IPR001967; Peptidase_S11_N.
Pfam; PF07943; PBP5_C; 1.
Pfam; PF00768; Peptidase_S11; 1.
PRINTS; PR00725; DADACBPTASE1.
SMART; SM00936; PBP5_C; 1.
SUPFAM; SSF56601; SSF56601; 1.
SUPFAM; SSF69189; SSF69189; 1.
1: Evidence at protein level;
3D-structure; Carboxypeptidase; Cell inner membrane; Cell membrane;
Cell shape; Cell wall biogenesis/degradation; Complete proteome;
Direct protein sequencing; Hydrolase; Membrane;
Peptidoglycan synthesis; Protease; Reference proteome; Signal.
SIGNAL 1 29 {ECO:0000269|PubMed:7042389}.
CHAIN 30 403 D-alanyl-D-alanine carboxypeptidase DacA.
/FTId=PRO_0000027231.
ACT_SITE 73 73 Acyl-ester intermediate.
ACT_SITE 76 76 Proton acceptor.
ACT_SITE 139 139
BINDING 242 242 Substrate.
VARIANT 134 134 G -> D (in mutant dacA11191; inactive but
still binds penicillin. Blocked in the
release of the bound penicilloyl moiety;
the mutant also fails to catalyze the D-
alanine carboxypeptidase reaction as the
hydrolysis of the acyl-enzyme formed with
substrate is also blocked and the acyl-
enzyme accumulates).
MUTAGEN 101 121 Missing: Complete loss of enzyme
activity. No effect on penicillin
binding. {ECO:0000269|PubMed:14555648}.
MUTAGEN 213 213 K->R: Complete loss of enzyme activity.
No effect on penicillin binding.
{ECO:0000269|PubMed:1597468}.
MUTAGEN 213 213 K->X: Complete loss of activity.
{ECO:0000269|PubMed:1597468}.
TURN 33 35 {ECO:0000244|PDB:3MZF}.
STRAND 46 53 {ECO:0000244|PDB:3MZF}.
TURN 54 56 {ECO:0000244|PDB:3MZF}.
STRAND 59 64 {ECO:0000244|PDB:3MZF}.
HELIX 72 74 {ECO:0000244|PDB:3MZF}.
HELIX 75 88 {ECO:0000244|PDB:3MZF}.
STRAND 97 99 {ECO:0000244|PDB:3MZF}.
HELIX 102 104 {ECO:0000244|PDB:3MZF}.
HELIX 106 108 {ECO:0000244|PDB:3MZF}.
HELIX 110 112 {ECO:0000244|PDB:3MZF}.
STRAND 125 127 {ECO:0000244|PDB:3MZF}.
HELIX 128 136 {ECO:0000244|PDB:3MZF}.
HELIX 141 152 {ECO:0000244|PDB:3MZF}.
HELIX 155 168 {ECO:0000244|PDB:3MZF}.
STRAND 179 183 {ECO:0000244|PDB:3MZF}.
HELIX 191 204 {ECO:0000244|PDB:3MZF}.
HELIX 206 209 {ECO:0000244|PDB:3MZF}.
HELIX 210 213 {ECO:0000244|PDB:3MZF}.
STRAND 216 219 {ECO:0000244|PDB:3MZF}.
STRAND 222 225 {ECO:0000244|PDB:3MZF}.
HELIX 229 232 {ECO:0000244|PDB:3MZF}.
STRAND 236 246 {ECO:0000244|PDB:3MZF}.
TURN 247 249 {ECO:0000244|PDB:3MZF}.
STRAND 250 259 {ECO:0000244|PDB:3MZF}.
STRAND 262 271 {ECO:0000244|PDB:3MZF}.
HELIX 274 276 {ECO:0000244|PDB:3MZF}.
HELIX 279 291 {ECO:0000244|PDB:3MZF}.
STRAND 292 298 {ECO:0000244|PDB:3MZF}.
STRAND 304 320 {ECO:0000244|PDB:3MZF}.
STRAND 325 330 {ECO:0000244|PDB:3MZF}.
HELIX 334 336 {ECO:0000244|PDB:3MZF}.
STRAND 338 350 {ECO:0000244|PDB:3MZF}.
STRAND 357 365 {ECO:0000244|PDB:3MZF}.
STRAND 368 379 {ECO:0000244|PDB:3MZF}.
SEQUENCE 403 AA; 44444 MW; 7FAAB8E98452FF22 CRC64;
MNTIFSARIM KRLALTTALC TAFISAAHAD DLNIKTMIPG VPQIDAESYI LIDYNSGKVL
AEQNADVRRD PASLTKMMTS YVIGQAMKAG KFKETDLVTI GNDAWATGNP VFKGSSLMFL
KPGMQVPVSQ LIRGINLQSG NDACVAMADF AAGSQDAFVG LMNSYVNALG LKNTHFQTVH
GLDADGQYSS ARDMALIGQA LIRDVPNEYS IYKEKEFTFN GIRQLNRNGL LWDNSLNVDG
IKTGHTDKAG YNLVASATEG QMRLISAVMG GRTFKGREAE SKKLLTWGFR FFETVNPLKV
GKEFASEPVW FGDSDRASLG VDKDVYLTIP RGRMKDLKAS YVLNSSELHA PLQKNQVVGT
INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH WFG


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