PDBsum entry 1e77

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Oxidoreductase PDB id
Jmol PyMol
Protein chain
485 a.a. *
Waters ×108
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Complex of active mutant (q365->c) of glucose 6-phosphate dehydrogenase from leuconostoc mesenteroides with substrate
Structure: Glucose 6-phosphate 1-dehydrogenase. Chain: a. Synonym: g6pd. Engineered: yes. Mutation: yes
Source: Leuconostoc mesenteroides. Organism_taxid: 1245. Strain: su294. Plasmid: plmz. Gene: g6pd. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: site directed mutagenesis
Biol. unit: Homo-Dimer (from PDB file)
2.69Å     R-factor:   0.180     R-free:   0.285
Authors: M.J.Adams,L.Vandeputte-Rutten,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
24-Aug-00     Release date:   11-Dec-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P11411  (G6PD_LEUME) -  Glucose-6-phosphate 1-dehydrogenase
486 a.a.
485 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Glucose-6-phosphate dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Pentose Phosphate Pathway (early stages)
      Reaction: D-glucose 6-phosphate + NADP+ = 6-phospho-D-glucono-1,5-lactone + NADPH
D-glucose 6-phosphate
Bound ligand (Het Group name = BG6)
corresponds exactly
+ NADP(+)
= 6-phospho-D-glucono-1,5-lactone
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     3 terms  


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.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
16326697 S.Watanabe, T.Kodaki, T.Kodak, and K.Makino (2006).
Cloning, expression, and characterization of bacterial L-arabinose 1-dehydrogenase involved in an alternative pathway of L-arabinose metabolism.
  J Biol Chem, 281, 2612-2623.  
15843172 E.Ganea, and J.J.Harding (2005).
Trehalose and 6-aminohexanoic acid stabilize and renature glucose-6-phosphate dehydrogenase inactivated by glycation and by guanidinium hydrochloride.
  Biol Chem, 386, 269-278.  
16193512 J.Merritt, J.A.Butz, B.A.Ogunnaike, and J.S.Edwards (2005).
Parallel analysis of mutant human glucose 6-phosphate dehydrogenase in yeast using PCR colonies.
  Biotechnol Bioeng, 92, 519-531.  
15858258 M.Kotaka, S.Gover, L.Vandeputte-Rutten, S.W.Au, V.M.Lam, and M.J.Adams (2005).
Structural studies of glucose-6-phosphate and NADP+ binding to human glucose-6-phosphate dehydrogenase.
  Acta Crystallogr D Biol Crystallogr, 61, 495-504.
PDB codes: 2bh9 2bhl
11841213 J.L.Brosius, and R.F.Colman (2002).
Three subunits contribute amino acids to the active site of tetrameric adenylosuccinate lyase: Lys268 and Glu275 are required.
  Biochemistry, 41, 2217-2226.  
11320304 C.E.Naylor, S.Gover, A.K.Basak, M.S.Cosgrove, H.R.Levy, and M.J.Adams (2001).
NADP+ and NAD+ binding to the dual coenzyme specific enzyme Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase: different interdomain hinge angles are seen in different binary and ternary complexes.
  Acta Crystallogr D Biol Crystallogr, 57, 635-648.
PDB codes: 1h93 1h94 1h9a 1h9b
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