D-alanyl-D-alanine carboxypeptidase dacA (P0AEB2)

Identification
Name:D-alanyl-D-alanine carboxypeptidase dacA
Synonyms:
  • DD-carboxypeptidase
  • DD-peptidase
  • Beta-lactamase
  • Penicillin-binding protein 5
  • PBP-5
Gene Name:dacA
Enzyme Class:
Biological Properties
General Function:Involved in carboxypeptidase activity
Specific Function:Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors
Cellular Location:Cell inner membrane; Peripheral membrane protein; Cytoplasmic side.
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Reactions:
1.0a lipid II+1.0Thumb ? 1.0a N-acetylglucosamine--N-acetylmuramyl-(tetrapeptide) pyrophosphoryl-undecaprenol+1.0Thumb
1.0a lipid II + 1.0Water ? 1.0a N-acetylglucosamine--N-acetylmuramyl-(tetrapeptide) pyrophosphoryl-undecaprenol + 1.0D-Alanine
ReactionCard
1.0Thumb+1.0a β-lactam → 1.0a substituted β-amino acid
1.0Water + 1.0a β-lactam → 1.0a substituted β-amino acid
ReactionCard
Complex Reactions:
1.0Thumb+1.0three disacharide linked murein units (pentapeptide crosslinked tetrapeptide (A2pm->D-ala) tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain) → 1.0Thumb+1.0three disacharide linked murein units (tetrapeptide crosslinked tetrapeptide (A2pm->D-ala) & tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain)
1.0Water + 1.0three disacharide linked murein units (pentapeptide crosslinked tetrapeptide (A2pm->D-ala) tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain) → 1.0D-Alanine + 1.0three disacharide linked murein units (tetrapeptide crosslinked tetrapeptide (A2pm->D-ala) & tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain)
ReactionCard
1.0Thumb+1.0two disacharide linked murein units, pentapeptide crosslinked tetrapeptide (A2pm->D-ala) (middle of chain) → 1.0Thumb+1.0two disacharide linked murein units, tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)
1.0Water + 1.0two disacharide linked murein units, pentapeptide crosslinked tetrapeptide (A2pm->D-ala) (middle of chain) → 1.0D-Alanine + 1.0two disacharide linked murein units, tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)
ReactionCard
1.0Thumb+1.0two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain) → 1.0Thumb+1.0two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain)
1.0Water + 1.0two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain) → 1.0D-Alanine + 1.0two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain)
ReactionCard
1.0Thumb+1.0two linked disacharide pentapeptide and tripeptide murein units (uncrosslinked, middle of chain) → 1.0Thumb+1.0two linked disacharide tetrapeptide and tripeptide murein units (uncrosslinked, middle of chain)
1.0Water + 1.0two linked disacharide pentapeptide and tripeptide murein units (uncrosslinked, middle of chain) → 1.0D-Alanine + 1.0two linked disacharide tetrapeptide and tripeptide murein units (uncrosslinked, middle of chain)
ReactionCard
1.0Thumb+1.0two linked disacharide pentapeptide murein units (uncrosslinked, middle of chain) → 1.0Thumb+1.0two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain)
1.0Water + 1.0two linked disacharide pentapeptide murein units (uncrosslinked, middle of chain) → 1.0D-Alanine + 1.0two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain)
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB01310D-AlanineMetaboCard
ECMDB00494WaterMetaboCard
GO Classification:
Function
carboxypeptidase activity
catalytic activity
exopeptidase activity
hydrolase activity
peptidase activity
peptidase activity, acting on L-amino acid peptides
serine-type carboxypeptidase activity
serine-type D-Ala-D-Ala carboxypeptidase activity
Process
macromolecule metabolic process
metabolic process
protein metabolic process
proteolysis
Gene Properties
Blattner:b0632
Gene OrientationCounterclockwise
Centisome Percentage:14.27
Left Sequence End661975
Right Sequence End663186
Gene Sequence:
>1212 bp
ATGTCGACTCGTACCCCTTCATCATCTTCATCCCGCCTGATGCTGACCATCGGGCTTTGT
TTTTTGGTCGCTCTGATGGAAGGGCTGGATCTTCAGGCGGCTGGCATTGCGGCGGGTGGC
ATCGCCCAGGCTTTCGCACTCGATAAAATGCAAATGGGCTGGATATTTAGCGCCGGAATA
CTCGGTTTGCTACCCGGCGCGTTGGTTGGCGGAATGCTGGCGGACCGTTATGGTCGCAAG
CGCATTTTGATTGGCTCAGTTGCGCTGTTTGGTTTGTTCTCACTGGCAACGGCGATTGCC
TGGGATTTCCCCTCACTGGTCTTTGCGCGGCTGATGACCGGTGTCGGGCTGGGGGCGGCG
TTGCCGAATCTTATCGCCCTGACGTCTGAAGCCGCGGGTCCACGTTTTCGTGGGACGGCA
GTGAGCCTGATGTATTGCGGTGTTCCCATTGGCGCGGCGCTGGCGGCGACACTGGGTTTC
GCGGGGGCAAACTTAGCATGGCAAACGGTGTTTTGGGTAGGTGGTGTGGTGCCGTTGATT
CTGGTGCCGCTATTAATGCGCTGGCTGCCGGAGTCGGCGGTTTTCGCTGGCGAAAAACAG
TCTGCGCCACCACTGCGTGCCTTATTTGCGCCAGAAACGGCAACCGCGACGCTGCTGCTG
TGGTTGTGTTATTTCTTCACTCTGCTGGTGGTCTACATGTTGATCAACTGGCTACCGCTA
CTTTTGGTGGAGCAAGGATTCCAGCCATCGCAGGCGGCAGGGGTGATGTTTGCCCTGCAA
ATGGGGGCGGCAAGCGGGACGTTAATGTTGGGCGCATTGATGGATAAGCTGCGTCCAGTA
ACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGCTGCTGGCGCTTGGAACGGTG
TCGTCATTTAACGGTATGTTGCTGGCGGGATTTGTCGCGGGGTTGTTTGCGACAGGTGGG
CAAAGCGTTTTGTATGCCCTGGCACCGTTGTTTTACAGTTCGCAGATCCGCGCAACAGGT
GTGGGAACAGCCGTGGCGGTAGGGCGTCTGGGGGCTATGAGCGGTCCGTTACTGGCCGGG
AAAATGCTGGCATTAGGCACTGGCACGGTCGGCGTAATGGCCGCTTCTGCACCGGGTATT
CTTGTTGCTGGGTTGGCGGTGTTTATTTTGATGAGCCGGAGATCACGAATACAGCCGTGC
GCCGATGCCTGA
Protein Properties
Pfam Domain Function:
Protein Residues:403
Protein Molecular Weight:44444
Protein Theoretical pI:9
PDB File:1NZU
Signaling Regions:
  • 1-29
Transmembrane Regions:
  • None
Protein Sequence:
>D-alanyl-D-alanine carboxypeptidase dacA
MNTIFSARIMKRLALTTALCTAFISAAHADDLNIKTMIPGVPQIDAESYILIDYNSGKVL
AEQNADVRRDPASLTKMMTSYVIGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFL
KPGMQVPVSQLIRGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVH
GLDADGQYSSARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDG
IKTGHTDKAGYNLVASATEGQMRLISAVMGGRTFKGREAESKKLLTWGFRFFETVNPLKV
GKEFASEPVWFGDSDRASLGVDKDVYLTIPRGRMKDLKASYVLNSSELHAPLQKNQVVGT
INFQLDGKTIEQRPLVVLQEIPEGNFFGKIIDYIKLMFHHWFG
References
External Links:
ResourceLink
Uniprot ID:P0AEB2
Uniprot Name:DACA_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:85674495
PDB ID:1NZU
Ecogene ID:EG10201
Ecocyc:EG10201
ColiBase:b0632
Kegg Gene:b0632
EchoBASE ID:EB0197
CCDB:DACA_ECOLI
BacMap:16128615
General Reference:
  • Blattner, F. R., Plunkett, G. 3rd, 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. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Broome-Smith, J. K., Ioannidis, I., Edelman, A., Spratt, B. G. (1988). "Nucleotide sequences of the penicillin-binding protein 5 and 6 genes of Escherichia coli." Nucleic Acids Res 16:1617. Pubmed: 3279397
  • Broome-Smith, J., Spratt, B. G. (1984). "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. Pubmed: 6319180
  • Davies, C., White, S. W., Nicholas, R. A. (2001). "Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3-A resolution." J Biol Chem 276:616-623. Pubmed: 10967102
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Malhotra, K. T., Nicholas, R. A. (1992). "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. Pubmed: 1597468
  • Nicholas, R. A., Krings, S., Tomberg, J., Nicola, G., Davies, C. (2003). "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. Pubmed: 14555648
  • Nicola, G., Peddi, S., Stefanova, M., Nicholas, R. A., Gutheil, W. G., Davies, C. (2005). "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. Pubmed: 15938610
  • 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., Horiuchi, T., et, a. l. .. (1996). "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. Pubmed: 8905232
  • Takase, I., Ishino, F., Wachi, M., Kamata, H., Doi, M., Asoh, S., Matsuzawa, H., Ohta, T., Matsuhashi, M. (1987). "Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome." J Bacteriol 169:5692-5699. Pubmed: 3316191
  • van der Linden, M. P., de Haan, L., Keck, W. (1993). "Domain organization of penicillin-binding protein 5 from Escherichia coli analysed by C-terminal truncation." Biochem J 289 ( Pt 2):593-598. Pubmed: 8424800
  • Waxman, D. J., Amanuma, H., Strominger, J. L. (1982). "Amino acid sequence homologies between Escherichia coli penicillin-binding protein 5 and class A beta-lactamases." FEBS Lett 139:159-163. Pubmed: 7042389