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Literature summary for 3.5.1.28 extracted from

  • Genereux, C.; Dehareng, D.; Devreese, B.; Van Beeumen, J.; Frere, J.M.; Joris, B.
    Mutational analysis of the catalytic centre of the Citrobacter freundii AmpD N-acetylmuramyl-L-alanine amidase (2004), Biochem. J., 377, 111-120.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.5.1.28

Cloned(Commentary)

Cloned (Comment) Organism
ampD gene, expression in Escherichia coli Citrobacter freundii

Protein Variants

Protein Variants Comment Organism
D164A inactive mutant with lost ability to bind zinc, kinetics Citrobacter freundii
E116A inactive mutant, residue is not directly involved in catalytic mechanism, but rather in binding of zinc by contributing to the correct orientation of His-34, kinetics Citrobacter freundii
H154A mutation of a zinc ligand residue, kinetics Citrobacter freundii
H154N mutation of a zinc ligand residue, active mutant which can bind zinc, kinetics Citrobacter freundii
H34A inactive mutant with lost ability to bind zinc, kinetics Citrobacter freundii
K162H 0.7% of wild-type activity, residue is probably involved in substrate binding, kinetics Citrobacter freundii
K162Q 0.2% of wild-type activity, residue is probably involved in substrate binding, kinetics Citrobacter freundii
Y63F 16% of wild-type activity, residue is probably involved in substrate binding, kinetics Citrobacter freundii

Inhibitors

Inhibitors Comment Organism Structure
1,10-phenanthroline 0.005 mM, complete inhibition after 30 min, activity can be restored by 0.1 mM ZnSO4 Citrobacter freundii
dipicolinic acid 0.005 mM, complete inhibition after 30 min, activity can be restored by 0.1 mM ZnSO4 Citrobacter freundii
EDTA 0.005 mM, complete inhibition after 30 min, activity can be restored by 0.1 mM ZnSO4 Citrobacter freundii
additional information not inhibited by 1,6-anhydro-beta-D-glucopyranose, 2-bromomethyl-1,3-dioxolane, anhydro-GlcNAc, L-Ala-p-nitroanilide, D-Ala-p-nitroanilide, Gly-p-nitroanilide Citrobacter freundii
MurNAc-L-Ala-D-Gln competitive inhibitor Citrobacter freundii

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information kinetic data Citrobacter freundii

Localization

Localization Comment Organism GeneOntology No. Textmining
intracellular
-
 Citrobacter freundii 5622
-

Metals/Ions

Metals/Ions Comment Organism Structure
additional information not activated by Cu2+, Co2+, Ni2+, Cd2+ or Mn2+ Citrobacter freundii
Zn2+ requirement, contains 0.7 mol of zinc/mol of enzyme with no zinc added to the buffer, His-34 and Asp-164 are presumed to act as zinc ligands, Glu-116 contributes to the correct orientation of His-34 Citrobacter freundii

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
20847
-
 x * 20847, wild-type AmpD, mass spectrometry Citrobacter freundii

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
additional information Citrobacter freundii AmpD is involved in both peptidoglycan recycling and beta-lactamase induction ?
-
 ?

Organism

Organism UniProt Comment Textmining
Citrobacter freundii
-
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant wild-type and mutant AmpD Citrobacter freundii

Reaction

Reaction Comment Organism Reaction ID
GlcNAc-MurNAc-L-Ala-D-isoglutaminyl-meso-diaminopimelyl-D-Ala-D-Ala + H2O = N-acetylglucosaminyl-N-acetylmuramic acid + L-Ala-D-isoglutaminyl-meso-diaminopimelyl-D-Ala-D-Ala catalytic mechanism Citrobacter freundii
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1,6-anhydromuropeptide + H2O AmpD has a strict specificity for 1,6-anhydromuropeptides, three-dimensional structure, active site structure, catalytic mechanism, Lys-162 and Tyr-63 are probably involved in substrate binding Citrobacter freundii ?
-
 ?
additional information AmpD is involved in both peptidoglycan recycling and beta-lactamase induction Citrobacter freundii ?
-
 ?
additional information not: L-Ala-p-nitroanilide, D-Ala-p-nitroanilide, Gly-p-nitroanilide Citrobacter freundii ?
-
 ?
N-acetylglucosaminyl-1,6-anhydro-N-acetylmuramyl-tripeptide + H2O
-
 Citrobacter freundii ?
-
 ?

Subunits

Subunits Comment Organism
? x * 20847, wild-type AmpD, mass spectrometry Citrobacter freundii

Synonyms

Synonyms Comment Organism
1,6-anhydro-N-acetylmuramyl-L-alanine amidase
-
 Citrobacter freundii
AmpD
-
 Citrobacter freundii
anhydroMurNAc-L-Ala amidase
-
 Citrobacter freundii

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
 assay at Citrobacter freundii

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
35
-
 Tm, H34A mutant AmpD + Zn2+ Citrobacter freundii
39
-
 Tm, D164A mutant AmpD + Zn2+ Citrobacter freundii
46
-
 Tm, D164A mutant AmpD Citrobacter freundii
51
-
 Tm, H34A mutant AmpD Citrobacter freundii
52
-
 Tm, H154A mutant AmpD + Zn2+ Citrobacter freundii
55
-
 Tm, Y63F mutant AmpD + Zn2+ Citrobacter freundii
56
-
 Tm, H154A mutant AmpD, K162H mutant AmpD + Zn2+ Citrobacter freundii
57
-
 Tm, H154N mutant AmpD + Zn2+ Citrobacter freundii
59
-
 Tm, K162Q mutant AmpD + Zn2+ Citrobacter freundii
60
-
 Tm, wild-type AmpD, wild-type AmpD + Zn2+, H154N and K162Q mutant AmpD Citrobacter freundii
61
-
 Tm, Y63F mutant AmpD Citrobacter freundii
62
-
 Tm, E116A mutant AmpD + Zn2+, K162H mutant AmpD Citrobacter freundii
66
-
 Tm, E116A mutant AmpD Citrobacter freundii

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
additional information
-
 additional information kinetic data Citrobacter freundii

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7
-
 assay at Citrobacter freundii

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.19
-
 MurNAc-L-Ala-D-Gln
-
 Citrobacter freundii