PDBsum entry 1mbt

Oxidoreductase

PDB id: 1mbt

Contents

Protein chain

340 a.a. *

Ligands

SO4

FAD

Waters ×4

* Residue conservation analysis

PDB id:

1mbt

Name:

Oxidoreductase

Title:

Oxidoreductase

Structure:

Uridine diphospho-n-acetylenolpyruvylglucosamine reductase. Chain: a. Synonym: murb. Other_details: bound flavin-adenine dinucleotide, ph 8.0

Source:

Escherichia coli. Organism_taxid: 562. Strain: ab1157 (atcc)

Resolution:

3.00Å R-factor: 0.209 R-free: 0.322

Authors:

T.E.Benson,C.T.Walsh,J.M.Hogle

Key ref:

T.E.Benson et al. (1996). The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls. Structure, 4, 47-54. PubMed id: 8805513 DOI: 10.1016/S0969-2126(96)00008-1

Date:

28-Nov-95 Release date: 14-Oct-96

Protein chain

P08373  (MURB_ECOLI) -  UDP-N-acetylenolpyruvoylglucosamine reductase from Escherichia coli (strain K12)

Seq: 342 a.a.

Struc: 340 a.a.

Enzyme reactions

• Enzyme class: E.C.1.3.1.98 - UDP-N-acetylmuramate dehydrogenase.
• Reaction: UDP-N-acetyl-alpha-D-muramate + NADP⁺ = UDP-N-acetyl-3- O-(1-carboxyvinyl)-alpha-D-glucosamine + NADPH + H⁺
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0969-2126(96)00008-1

Structure 4:47-54 (1996)

PubMed id: 8805513

The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls.

T.E.Benson, C.T.Walsh, J.M.Hogle.

ABSTRACT

BACKGROUND: The repeating disaccharide and pentapeptide units of the bacterial peptidoglycan layer are connected by a lactyl ether bridge biosynthesized from UDP-N-acetylglucosamine and phosphoenolpyruvate in sequential enol ether transfer and reduction steps catalyzed by MurA and MurB respectively. Knowledge of the structure and mechanism of the MurB enzyme will permit analysis of this unusual enol ether reduction reaction and may facilitate the design of inhibitors as candidate next-generation antimicrobial agents. RESULTS: The crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase, MurB, has been solved at 3.0 A and compared with our previously reported structure of MurB complexed with its substrate enolpyruvyl-UDP-N- acetylglucosamine. Comparison of the liganded structure of MurB with this unliganded form reveals that the binding of substrate induces a substantial movement of domain 3 (residues 219-319) of the enzyme and a significant rearrangement of a loop within this domain. These ligand induced changes disrupt a stacking interaction between two tyrosines (Tyr190 and Tyr254) which lie at the side of the channel leading to the active site of the free enzyme. CONCLUSIONS: The conformational change induced by enolpyruvyl-UDP-N- acetylglucosamine binding to MurB results in the closure of the substrate-binding channel over the substrate. Tyr190 swings over the channel opening and establishes a hydrogen bond with an oxygen of the alpha-phosphate of the sugar nucleotide substrate which is critical to substrate binding.

Selected figure(s)

Figure 1.
Figure 1. Proposed mechanism of reduction of the enolpyruvyl group of EP-UDP-GlcNAc by MurB [3 and 5]. Hydride transfer to C3 is proposed to generate a carbanion equivalent that can be stabilized by protonation from Glu325 and/or Arg159. Quenching of the carbanion is proposed to be mediated by Ser229. Figure 1. Proposed mechanism of reduction of the enolpyruvyl group of EP-UDP-GlcNAc by MurB [[3]3 and [4]5]. Hydride transfer to C3 is proposed to generate a carbanion equivalent that can be stabilized by protonation from Glu325 and/or Arg159. Quenching of the carbanion is proposed to be mediated by Ser229.

Figure 5.
Figure 5. Surface representations of the substrate-free and EP-UDP-GlcNAc-bound MurB structures. (a) Molecular and charge surfaces of the substrate-free MurB with a view of the uracil portion of the bound flavin. This representation shows access to the flavin and the charge distribution at the channel (positively charged areas shown in blue, negatively charged areas shown in red, and neutral areas shown in white). (b) The EP-UDP-GlcNAc–MurB complex. The substrate-bound MurB shows structural and charge-distribution changes induced upon substrate binding. Figure 5. Surface representations of the substrate-free and EP-UDP-GlcNAc-bound MurB structures. (a) Molecular and charge surfaces of the substrate-free MurB with a view of the uracil portion of the bound flavin. This representation shows access to the flavin and the charge distribution at the channel (positively charged areas shown in blue, negatively charged areas shown in red, and neutral areas shown in white). (b) The EP-UDP-GlcNAc–MurB complex. The substrate-bound MurB shows structural and charge-distribution changes induced upon substrate binding. (Figure generated using GRASP [[4]27].)

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 47-54) copyright 1996.

Figures were selected by an automated process.