PDBsum entry 1e7y

Oxidoreductase

PDB id: 1e7y

Contents

Protein chain

485 a.a. *

Ligands

BG6

NDP

Metals

_CA

Waters ×131

* Residue conservation analysis

PDB id:

1e7y

Name:

Oxidoreductase

Title:

Active site mutant (d177->n) of glucose 6-phosphate dehydrogenase from leuconostoc mesenteroides complexed with substrate and NADPH

Structure:

Glucose 6-phosphate 1-dehydrogenase. Chain: a. Synonym: g6pd. Engineered: yes. Mutation: yes

Source:

Leuconostoc mesenteroides. Organism_taxid: 1245. Gene: plmz/d177nurce 9. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: site directed mutagenesis other_details: site directed mutagenesis

Biol. unit:

Dimer (from PDB file)

Resolution:

2.48Å R-factor: 0.205 R-free: 0.296

Authors:

M.J.Adams,M.S.Cosgrove,S.Gover

Key ref:

M.S.Cosgrove et al. (2000). An examination of the role of asp-177 in the His-Asp catalytic dyad of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase: X-ray structure and pH dependence of kinetic parameters of the D177N mutant enzyme. Biochemistry, 39, 15002-15011. PubMed id: 11106478 DOI: 10.1021/bi0014608

Date:

12-Sep-00 Release date: 11-Dec-00

Protein chain

P11411  (G6PD_LEUME) -  Glucose-6-phosphate 1-dehydrogenase from Leuconostoc mesenteroides

Seq: 486 a.a.

Struc: 485 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.1.1.363 - glucose-6-phosphate dehydrogenase [NAD(P)(+)].
• Reaction:
  1. D-glucose 6-phosphate + NADP⁺ = 6-phospho-D-glucono-1,5-lactone + NADPH + H⁺
  2. D-glucose 6-phosphate + NAD⁺ = 6-phospho-D-glucono-1,5-lactone + NADH + H⁺

D-glucose 6-phosphate (Bound ligand (Het Group name = BG6) corresponds exactly) + NADP(+) (Bound ligand (Het Group name = NDP) matches with 56.25% similarity) = 6-phospho-D-glucono-1,5-lactone + NADPH + H(+)

D-glucose 6-phosphate (Bound ligand (Het Group name = BG6) corresponds exactly) + NAD(+) (Bound ligand (Het Group name = NDP) matches with 47.92% similarity) = 6-phospho-D-glucono-1,5-lactone + NADH + H(+)

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

reference

DOI no: 10.1021/bi0014608

Biochemistry 39:15002-15011 (2000)

PubMed id: 11106478

An examination of the role of asp-177 in the His-Asp catalytic dyad of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase: X-ray structure and pH dependence of kinetic parameters of the D177N mutant enzyme.

M.S.Cosgrove, S.Gover, C.E.Naylor, L.Vandeputte-Rutten, M.J.Adams, H.R.Levy.

ABSTRACT

The role of Asp-177 in the His-Asp catalytic dyad of glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides has been investigated by a structural and functional characterization of the D177N mutant enzyme. Its three-dimensional structure has been determined by X-ray cryocrystallography in the presence of NAD(+) and in the presence of glucose 6-phosphate plus NADPH. The structure of a glucose 6-phosphate complex of a mutant (Q365C) with normal enzyme activity has also been determined and substrate binding compared. To understand the effect of Asp-177 on the ionization properties of the catalytic base His-240, the pH dependence of kinetic parameters has been determined for the D177N mutant and compared to that of the wild-type enzyme. The structures give details of glucose 6-phosphate binding and show that replacement of the Asp-177 of the catalytic dyad with asparagine does not affect the overall structure of glucose 6-phosphate dehydrogenase. Additionally, the evidence suggests that the productive tautomer of His-240 in the D177N mutant enzyme is stabilized by a hydrogen bond with Asn-177; hence, the mutation does not affect tautomer stabilization. We conclude, therefore, that the absence of a negatively charged aspartate at 177 accounts for the decrease in catalytic activity at pH 7.8. Structural analysis suggests that the pH dependence of the kinetic parameters of D177N glucose 6-phosphate dehydrogenase results from an ionized water molecule replacing the missing negative charge of the mutated Asp-177 at high pH. Glucose 6-phosphate binding orders and orients His-178 in the D177N-glucose 6-phosphate-NADPH ternary complex and appears to be necessary to form this water-binding site.