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3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase

This is an abbreviated version!
For detailed information about serine-type D-Ala-D-Ala carboxypeptidase, go to the full flat file.

Word Map on EC 3.4.16.4

Reaction

Preferential cleavage: (Ac)2-L-Lys-D-Ala-/-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine =

Synonyms

carboxypeptidase I, CPase, D,D-carboxypeptidase, D,D-carboxypeptidase R39, D,D-dipeptidase, D-Ala-D-Ala carboxypeptidase, D-Ala-D-Ala peptidase, D-Ala-D-Ala(D,D) carboxypeptidase, D-alanine carboxypeptidase, D-alanine carboxypeptidase I, D-alanine-carboxypeptidase, D-alanyl carboxypeptidase, D-alanyl-D-alanine carboxypeptidase, D-alanyl-D-alanine carboxypeptidase/transpeptidase, D-Alanyl-D-alanine hydrolase, D-alanyl-D-alanine peptidase, D-alanyl-D-alanine transpeptidase, D-alanyl-D-alanine-carboxypeptidase, D-alanyl-D-alanine-cleaving peptidase, D-alanyl-D-alanine-cleaving-peptidase, D-alanyl-D-alanine-transpeptidase, D-amino acid amidase, DAA, Dac, dacA, DacA-1, DacB, DacC, DacD, DAP, Dbv7, DD-Carboxypeptidase, DD-CPase, DD-CPase1, DD-peptidase, DD-transpeptidase, DD-transpeptidase/penicillin-binding protein, LMM-PBP, low molecular mass penicillin binding protein, PBP, PBP 2, PBP 3, PBP 4, PBP 5, PBP 6, PBP-5*, PBP-6B, PBP1a, PBP1b, PBP2x, PBP3, PBP4, PBP4a, PBP5, PBP6, PBP6a, PBP6b, penicillin binding protein 4, penicillin binding protein 5, penicillin binding proteins, penicillin-binding protein, penicillin-binding protein 1B, penicillin-binding protein 4a, penicillin-binding protein 5, penicillin-binding protein 5a, R39 PBP, SCO4439, serine type D-alanyl-D-alanine carboxypeptidase/transpeptidase, serine-type D-Ala-D-Ala carboxypeptidase, serine-type-D-Ala-D-Ala carboxypeptidase, transpeptidase, VanX, VanXY, VanY, VanY(D) DD-carboxypeptidase, VanYD, VanYn, VC_0947, VP2468, zinc D-Ala-D-Ala carboxypeptidase

ECTree

     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.16 Serine-type carboxypeptidases
                3.4.16.4 serine-type D-Ala-D-Ala carboxypeptidase

Engineering

Engineering on EC 3.4.16.4 - serine-type D-Ala-D-Ala carboxypeptidase

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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
DELTA74-90
-
deletion of the 74-90 loop markedly diminishes the deacylation rate of penicillin G with a minimal impact on acylation, and abolishes D-alanine carboxypeptidase activity
G105D
S44G
-
active site mutant, isoform PBP5, inactive, mutation changes the conformation of the dimeric state. Contrary to wild-type, the mutant only localized laterally in the cell
S63G
-
active site mutant, isoform PBP6b, inactive, mutation changes the conformation of the dimeric state
S66G
-
active site mutant, isoform PBP6a, inactive, mutation changes the conformation of the dimeric state. Contrary to wild-type, the mutant mostly avoids midcell localization
S86A
-
mutation has little effect on the interaction of the protein with penicillin G, acylation rate constants are nearly identical to wild-type enzyme. The ratio of turnover number to Km-value for the substrate N,N‘-diacetyl-L-Lys-D-Ala-D-Ala is 12% of the wild-type ratio
S86A/S87A
-
mutation has little effect on the interaction of the protein with penicillin G, acylation rate constants are nearly identical to wild-type enzyme. The ratio of turnover number to Km-value for the substrate N,N‘-diacetyl-L-Lys-D-Ala-D-Ala is 8.1% of the wild-type ratio
S87A
-
mutation has little effect on the interaction of the protein with penicillin G, acylation rate constants are nearly identical to wild-type enzyme. The ratio of turnover number to Km-value for the substrate N,N‘-diacetyl-L-Lys-D-Ala-D-Ala is 6.3% of the wild-type ratio
D155A
mutant, constructed for the demonstration of the relative importance of residue Asp155
F160A
mutant, constructed for the demonstration of the relative importance of residue Phe160
Q422A
mutant, constructed for the demonstration of the relative importance of residue Gln422
Q422S
mutant, constructed for the demonstration of the relative importance of residue Gln422
R361A
mutant, constructed for the demonstration of the relative importance of residue Arg361
R361H
mutant, constructed for the demonstration of the relative importance of residue Arg361
L684P
C98A
half-life at 72°C increases to 13 min, compared to 10 min for the wild-type enzyme. Half-life at 60°C increases to 220 min compared to 170 min for the wild-type enzyme. The value of the second-order acylation rate constant is not very different from those of the wild-type enzyme with the exception of the cephalotin, oxacillin and piperacillin values which are increased 5-10fold
C98N
half-life at 72°C decreases to 6 min, compared to 10 min for the wild-type enzyme. Half-life at 60°C decreases to 30 min compared to 170 min for the wild-type enzyme. The acylation rate constants by most of the beta-lactams are increased 10-70fold compared to the wild-type enzyme. The deacylation rate constant values als increases
K38H
half-life at 72°C decreases to 3.5 min, compared to 10 min for the wild-type enzyme. The mutant enzyme fails to bind beta-lactams
S96A
half-life at 72°C decreases to 8 min, compared to 10 min for the wild-type enzyme. Half-life at 60°C decreases to 120 min compared to 170 min for the wild-type enzyme. The mutant enzyme is inactive in terms of beta-lactam binding with the exception of cefoxitin, for which a residual activity is detected.The value of the second-order acylation rate constant is decreased by a factor of 3000, and that of the deacylation rate constant is decreased 120fold
W271L
-
exchanging of tryptophan 271 shows no particular modification of the proteins biophysical and kinetic charcteristics
additional information