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Literature summary extracted from

  • Sink, R.; Kotnik, M.; Zega, A.; Barreteau, H.; Gobec, S.; Blanot, D.; Dessen, A.; Contreras-Martel, C.
    Crystallographic study of peptidoglycan biosynthesis enzyme MurD: domain movement revisited (2016), PLoS ONE, 11, e0152075 .
    View publication on PubMedView publication on EuropePMC

Application

EC Number Application Comment Organism
6.3.2.9 drug development the enzyme is a target in the development of potential antibiotics designed to target the peptidoglycan biosynthetic pathway Escherichia coli

Cloned(Commentary)

EC Number Cloned (Comment) Organism
6.3.2.9 gene murD, recombinant expression of His6-tagged enzyme in Escherichia coli strain DH5alpha Escherichia coli

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
6.3.2.9 purified free MurD and MurD complexed with the tetrahedral reaction intermediate, hanging drop vapor diffusion method, for free enzyme crystals: mixing of 0.002 ml of 3 mg/ml protein in 20 mM HEPES, pH 5.6, 1 mM DTT, and 1 mM NaN3, with 0.002 ml of reservoir solution containing 1.8 M (NH4)2SO4, 7% v/v 2-methyl-2,4-pentanediol, and 0.1 MMES, pH 5.6, 15°C, 48 h, for complexed enzyme crystals: mixing of 0.002 ml of 4 mg/ml protein in 20 mM HEPES, pH 7.4, 1 mM DTT, 1 mM NaN3, 5 mMAMP-PNP, and 1 mM UDP-N-acetyl-alpha-D-muramoyl-L-alanine, with 0.002 ml of reservoir solution containing 1.8 M Na-malonate, pH 7.0, 15°C, 48 h, X-ray diffraction structure determination and analysis at 1.84-1.90 A resolution Escherichia coli

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
6.3.2.9 additional information
-
 additional information ordered kinetic mechanism Escherichia coli

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
6.3.2.9 cytoplasm
-
 Escherichia coli 5737
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
6.3.2.9 Mg2+ required Escherichia coli

Organism

EC Number Organism UniProt Comment Textmining
6.3.2.9 Escherichia coli P14900
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
6.3.2.9 recombinant His6-tagged enzyme from Escherichia coli strain DH5alpha by nickel affinity chromatography and dialysis Escherichia coli

Reaction

EC Number Reaction Comment Organism Reaction ID
6.3.2.9 ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate reaction via tetrahedral intermediate. The enzyme performs binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. Reaction mechanism and structure analysis, overview Escherichia coli
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
6.3.2.9 ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate
-
 Escherichia coli ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
-
 ?
6.3.2.9 additional information enzyme MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP Escherichia coli ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
6.3.2.9 MurD
-
 Escherichia coli

Cofactor

EC Number Cofactor Comment Organism Structure
6.3.2.9 ATP ATP binding to the enzyme causes conformational changes, overview Escherichia coli

General Information

EC Number General Information Comment Organism
6.3.2.9 metabolism the enzyme is involved in the peptidoglycan biosynthesis Escherichia coli
6.3.2.9 additional information conformational changes of MurD occur upon ligand binding. Upon binding of ATP and UDP-N-acetyl-alpha-D-muramoyl-L-alanine, there is a closing rotation of the C-terminal domain, which does not occur before ATP is bound, targeted molecular dynamics simulation Escherichia coli
6.3.2.9 physiological function MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala, generating the dipeptide moiety L-Ala-D-Glu in peptidoglycan biosynthesis Escherichia coli