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D-alanyl-D-alanine carboxypeptidase DacC (DD-carboxypeptidase) (DD-peptidase) (EC 3.4.16.4) (Penicillin-binding protein 6) (PBP-6)

 DACC_ECOLI              Reviewed;         400 AA.
P08506; P77287;
01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 2.
28-MAR-2018, entry version 167.
RecName: Full=D-alanyl-D-alanine carboxypeptidase DacC;
Short=DD-carboxypeptidase;
Short=DD-peptidase;
EC=3.4.16.4;
AltName: Full=Penicillin-binding protein 6;
Short=PBP-6;
Flags: Precursor;
Name=dacC; OrderedLocusNames=b0839, JW0823;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
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).
[2]
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).
[3]
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).
[4]
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).
[5]
PROTEIN SEQUENCE OF 28-52.
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).
[6]
SUBCELLULAR LOCATION, AND DOMAIN.
PubMed=3330754; DOI=10.1111/j.1365-2958.1987.tb00522.x;
Jackson M.E., Pratt J.M.;
"An 18 amino acid amphiphilic helix forms the membrane-anchoring
domain of the Escherichia coli penicillin-binding protein 5.";
Mol. Microbiol. 1:23-28(1987).
-!- 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.
-!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
-!- SUBCELLULAR LOCATION: Cell inner membrane
{ECO:0000269|PubMed:3330754}; Peripheral membrane protein
{ECO:0000269|PubMed:3330754}; Periplasmic side
{ECO:0000269|PubMed:3330754}. Note=N-terminus lies in the
periplasmic space, targeted there by the C-terminal amphiphilic
helix (PMID:3330754).
-!- DOMAIN: The C-terminus forms an amphiphilic helix that targets the
protein to the periplasmic side of the inner cell membrane.
{ECO:0000269|PubMed:3330754}.
-!- SIMILARITY: Belongs to the peptidase S11 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X06480; CAA29775.1; -; Genomic_DNA.
EMBL; U00096; AAC73926.1; -; Genomic_DNA.
EMBL; AP009048; BAA35542.1; -; Genomic_DNA.
PIR; G64821; G64821.
RefSeq; NP_415360.1; NC_000913.3.
RefSeq; WP_001300708.1; NZ_LN832404.1.
PDB; 3IT9; X-ray; 2.10 A; A/B/C/D=28-378.
PDB; 3ITA; X-ray; 1.80 A; A/B/C/D=28-378.
PDB; 3ITB; X-ray; 1.80 A; A/B/C/D=28-378.
PDBsum; 3IT9; -.
PDBsum; 3ITA; -.
PDBsum; 3ITB; -.
ProteinModelPortal; P08506; -.
SMR; P08506; -.
BioGrid; 4262825; 228.
IntAct; P08506; 2.
MINT; P08506; -.
STRING; 316385.ECDH10B_0908; -.
ChEMBL; CHEMBL2354204; -.
DrugBank; DB00274; Cefmetazole.
DrugBank; DB01329; Cefoperazone.
DrugBank; DB01331; Cefoxitin.
DrugBank; DB00430; Cefpiramide.
DrugBank; DB00303; Ertapenem.
MEROPS; S11.003; -.
EPD; P08506; -.
PaxDb; P08506; -.
PRIDE; P08506; -.
EnsemblBacteria; AAC73926; AAC73926; b0839.
EnsemblBacteria; BAA35542; BAA35542; BAA35542.
GeneID; 945455; -.
KEGG; ecj:JW0823; -.
KEGG; eco:b0839; -.
PATRIC; fig|1411691.4.peg.1439; -.
EchoBASE; EB0199; -.
EcoGene; EG10203; dacC.
eggNOG; ENOG4105DZ1; Bacteria.
eggNOG; COG1686; LUCA.
HOGENOM; HOG000086623; -.
InParanoid; P08506; -.
KO; K07258; -.
OMA; TGWTNEA; -.
PhylomeDB; P08506; -.
BioCyc; EcoCyc:EG10203-MONOMER; -.
BioCyc; MetaCyc:EG10203-MONOMER; -.
UniPathway; UPA00219; -.
EvolutionaryTrace; P08506; -.
PRO; PR:P08506; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005887; C:integral component of plasma membrane; IDA:EcoliWiki.
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; IEA:UniProtKB-EC.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0009252; P:peptidoglycan biosynthetic process; IDA:EcoCyc.
GO; GO:0008360; P:regulation of cell shape; IGI:EcoCyc.
GO; GO:0042493; P:response to drug; IMP: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 27 {ECO:0000269|PubMed:7042389}.
CHAIN 28 400 D-alanyl-D-alanine carboxypeptidase DacC.
/FTId=PRO_0000027233.
REGION 383 400 Required for inner membrane binding.
ACT_SITE 66 66 Acyl-ester intermediate. {ECO:0000250}.
ACT_SITE 69 69 Proton acceptor. {ECO:0000250}.
ACT_SITE 132 132 {ECO:0000250}.
BINDING 235 235 Substrate. {ECO:0000250}.
CONFLICT 231 231 V -> E (in Ref. 1; CAA29775).
{ECO:0000305}.
STRAND 39 46 {ECO:0000244|PDB:3ITA}.
TURN 47 49 {ECO:0000244|PDB:3ITA}.
STRAND 52 57 {ECO:0000244|PDB:3ITA}.
HELIX 65 67 {ECO:0000244|PDB:3ITA}.
HELIX 68 81 {ECO:0000244|PDB:3ITA}.
STRAND 90 92 {ECO:0000244|PDB:3ITA}.
HELIX 95 97 {ECO:0000244|PDB:3ITA}.
TURN 99 101 {ECO:0000244|PDB:3ITA}.
HELIX 103 105 {ECO:0000244|PDB:3ITA}.
STRAND 118 120 {ECO:0000244|PDB:3ITA}.
HELIX 121 129 {ECO:0000244|PDB:3ITA}.
HELIX 134 145 {ECO:0000244|PDB:3ITA}.
HELIX 148 161 {ECO:0000244|PDB:3ITA}.
STRAND 171 173 {ECO:0000244|PDB:3ITB}.
HELIX 184 197 {ECO:0000244|PDB:3ITA}.
HELIX 199 202 {ECO:0000244|PDB:3ITA}.
HELIX 203 206 {ECO:0000244|PDB:3ITA}.
STRAND 209 212 {ECO:0000244|PDB:3ITA}.
STRAND 215 218 {ECO:0000244|PDB:3ITA}.
HELIX 222 225 {ECO:0000244|PDB:3ITA}.
STRAND 230 239 {ECO:0000244|PDB:3ITA}.
TURN 240 242 {ECO:0000244|PDB:3ITA}.
STRAND 243 252 {ECO:0000244|PDB:3ITA}.
STRAND 255 266 {ECO:0000244|PDB:3ITA}.
HELIX 267 284 {ECO:0000244|PDB:3ITA}.
STRAND 285 288 {ECO:0000244|PDB:3ITA}.
STRAND 297 313 {ECO:0000244|PDB:3ITA}.
HELIX 315 317 {ECO:0000244|PDB:3ITA}.
STRAND 320 323 {ECO:0000244|PDB:3ITA}.
HELIX 327 329 {ECO:0000244|PDB:3ITA}.
STRAND 330 343 {ECO:0000244|PDB:3ITA}.
STRAND 350 358 {ECO:0000244|PDB:3ITA}.
STRAND 361 370 {ECO:0000244|PDB:3ITA}.
SEQUENCE 400 AA; 43609 MW; 4D7F3BDCEA64C775 CRC64;
MTQYSSLLRG LAAGSAFLFL FAPTAFAAEQ TVEAPSVDAR AWILMDYASG KVLAEGNADE
KLDPASLTKI MTSYVVGQAL KADKIKLTDM VTVGKDAWAT GNPALRGSSV MFLKPGDQVS
VADLNKGVII QSGNDACIAL ADYVAGSQES FIGLMNGYAK KLGLTNTTFQ TVHGLDAPGQ
FSTARDMALL GKALIHDVPE EYAIHKEKEF TFNKIRQPNR NRLLWSSNLN VDGMKTGTTA
GAGYNLVASA TQGDMRLISV VLGAKTDRIR FNESEKLLTW GFRFFETVTP IKPDATFVTQ
RVWFGDKSEV NLGAGEAGSV TIPRGQLKNL KASYTLTEPQ LTAPLKKGQV VGTIDFQLNG
KSIEQRPLIV MENVEEGGFF GRVWDFVMMK FHQWFGSWFS


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