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"Open" structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase
J A Bertrand1, E Fanchon, L Martin
1Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale Jean-Pierre Ebel (CNRS-CEA), 41, rue Jules Horowitz, Grenoble, Cedex 1, F-38027, France.
Abstract:
UDP-N-acetylmuramoyl-l-alanine:d-glutamate (MurD) ligase catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine (UMA). The crystal structures of Escherichia coli in the substrate-free form and MurD complexed with UMA have been determined at 2.4 A and 1.88 A resolution, respectively. The MurD structure comprises three domains each of a topology reminiscent of nucleotide-binding folds. In the two structures the C-terminal domain undergoes a large rigid-body rotation away from the N-terminal and central domains. These two "open" structures were compared with the four published "closed" structures of MurD. In addition the comparison reveals which regions are affected by the binding of UMA, ATP and d-Glu. Also we compare and discuss two structurally characterized enzymes which belong to the same ligase superfamily: MurD and folylpolyglutamate synthetase (FGS). The analysis allows the identification of key residues involved in the reaction mechanism of FGS. The determination of the two "open" conformation structures represents a new step towards the complete elucidation of the enzymatic mechanism of the MurD ligase.
Insights
Structural analysis of UDP-N-acetylmuramoyl-l-alanine:d-glutamate (MurD) ligase reveals open conformations. This provides new insights into the enzymatic mechanism of MurD ligase and related enzymes.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- UDP-N-acetylmuramoyl-l-alanine:d-glutamate (MurD) ligase is crucial for bacterial cell wall synthesis.
- Understanding MurD ligase's mechanism is key to developing new antibiotics.
Purpose of the Study:
- To determine the crystal structures of Escherichia coli MurD ligase in substrate-free and UMA-bound forms.
- To elucidate the conformational changes and substrate-binding effects on MurD structure.
- To compare MurD with other ligase superfamily members like folylpolyglutamate synthetase (FGS).
Main Methods:
- X-ray crystallography was used to determine the structures of MurD ligase.
- Comparative structural analysis of open and closed MurD conformations.
- Comparison with the structure of folylpolyglutamate synthetase (FGS).
Main Results:
- Crystal structures of substrate-free and UMA-bound MurD were determined at 2.4 Å and 1.88 Å resolution.
- A large rigid-body rotation of the C-terminal domain was observed in the open conformations.
- Identification of regions affected by substrate binding (UMA, ATP, d-Glu) and key residues in FGS.
Conclusions:
- The determined open conformations represent a significant step towards understanding the MurD ligase enzymatic mechanism.
- Structural comparison aids in identifying critical residues for ligase superfamily enzyme function.
- Insights gained could inform the design of novel antibacterial agents targeting MurD.