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PDBsum entry 2dpg

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protein ligands links
Oxidoreductase PDB id
2dpg
Jmol
Contents
Protein chain
485 a.a. *
Ligands
NAP
Waters ×74
* Residue conservation analysis
PDB id:
2dpg
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)
Resolution:
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
Date:
17-Apr-98     Release date:   15-Jul-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11411  (G6PD_LEUME) -  Glucose-6-phosphate 1-dehydrogenase
Seq:
Struc:
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.1.1.1.49  - Glucose-6-phosphate dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Pentose Phosphate Pathway (early stages)
      Reaction: D-glucose 6-phosphate + NADP+ = 6-phospho-D-glucono-1,5-lactone + NADPH
D-glucose 6-phosphate
+
NADP(+)
Bound ligand (Het Group name = NAP)
matches with 64.58% similarity
= 6-phospho-D-glucono-1,5-lactone
+ NADPH
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  

 

 
    reference    
 
 
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.
 
  ABSTRACT  
 
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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.