PDBsum entry 2dpg

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protein ligands links
Oxidoreductase PDB id
Protein chain
485 a.a. *
Waters ×74
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Complex of inactive mutant (h240->n) of glucose 6-phosphate dehydrogenase from leuconostoc mesenteroides with NADP+
Structure: Glucose 6-phosphate dehydrogenase. Chain: a. Synonym: g6pd. Engineered: yes. Mutation: yes. Other_details: the mutant is inactive, lacking the catalyti the structure contains a partial NADP bound to nucleotide b domain.
Source: Leuconostoc mesenteroides. Organism_taxid: 1245. Gene: plmz/h240n. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.50Å     R-factor:   0.173     R-free:   0.232
Authors: M.J.Adams,C.E.Naylor,S.Paludin,S.Gover
Key ref:
M.S.Cosgrove et al. (1998). On the mechanism of the reaction catalyzed by glucose 6-phosphate dehydrogenase. Biochemistry, 37, 2759-2767. PubMed id: 9485426 DOI: 10.1021/bi972069y
17-Apr-98     Release date:   15-Jul-98    
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 = NAP)
matches with 64.58% similarity
= 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/bi972069y Biochemistry 37:2759-2767 (1998)
PubMed id: 9485426  
On the mechanism of the reaction catalyzed by glucose 6-phosphate dehydrogenase.
M.S.Cosgrove, C.Naylor, S.Paludan, M.J.Adams, H.R.Levy.
The catalytic mechanism of glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides was investigated by replacing three amino acids, His-240, Asp-177, and His 178, with asparagine, using site-directed mutagenesis. Each of the mutant enzymes was purified to homogeneity and characterized by substrate binding studies and steady-state kinetic analyses. The three-dimensional structure of the H240N glucose 6-phosphate dehydrogenase was determined at 2.5 A resolution. The results support a mechanism in which His-240 acts as the general base that abstracts the proton from the C1-hydroxyl group of glucose 6-phosphate, and the carboxylate group of Asp-177 stabilizes the positive charge that forms on His-240 in the transition state. The results also confirm the postulated role of His-178 in binding the phosphate moiety of glucose 6-phosphate.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18616465 A.Andreadeli, D.Platis, V.Tishkov, V.Popov, and N.E.Labrou (2008).
Structure-guided alteration of coenzyme specificity of formate dehydrogenase by saturation mutagenesis to enable efficient utilization of NADP+.
  FEBS J, 275, 3859-3869.  
17666400 S.W.Tuttle, A.Maity, P.R.Oprysko, A.V.Kachur, I.S.Ayene, J.E.Biaglow, and C.J.Koch (2007).
Detection of Reactive Oxygen Species via Endogenous Oxidative Pentose Phosphate Cycle Activity in Response to Oxygen Concentration: IMPLICATIONS FOR THE MECHANISM OF HIF-1{alpha} STABILIZATION UNDER MODERATE HYPOXIA.
  J Biol Chem, 282, 36790-36796.  
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.  
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
12632401 C.O.Rangel-Yagui, H.Lam, D.T.Kamei, D.I.Wang, A.Pessoa, and D.Blankschtein (2003).
Glucose-6-phosphate dehydrogenase partitioning in two-phase aqueous mixed (nonionic/cationic) micellar systems.
  Biotechnol Bioeng, 82, 445-456.  
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.  
12435510 T.Hansen, B.Schlichting, and P.Schönheit (2002).
Glucose-6-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima: expression of the g6pd gene and characterization of an extremely thermophilic enzyme.
  FEMS Microbiol Lett, 216, 249-253.  
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
10745013 S.W.Au, S.Gover, V.M.Lam, and M.J.Adams (2000).
Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency.
  Structure, 8, 293-303.
PDB code: 1qki
10087441 Y.S.Cheng, T.K.Tang, and M.Hwang (1999).
Amino acid conservation and clinical severity of human glucose-6-phosphate dehydrogenase mutations.
  J Biomed Sci, 6, 106-114.  
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