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PDBsum entry 1e7m

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Oxidoreductase PDB id
1e7m
Jmol
Contents
Protein chain
485 a.a. *
Metals
_CA
Waters ×68
* Residue conservation analysis
PDB id:
1e7m
Name: Oxidoreductase
Title: Active site mutant (d177->n) of glucose 6-phosphate dehydrogenase from leuconostoc mesenteroides
Structure: Glucose 6-phosphate 1-dehydrogenase. Chain: a. Synonym: g6pd. Engineered: yes. Mutation: yes
Source: Leuconostoc mesenteroides. Organism_taxid: 1245. Strain: su294. Plasmid: puc-19/asp177asnplmz. Gene: plmz/d177n. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: site directed mutagenesis
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.54Å     R-factor:   0.222     R-free:   0.299
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:
30-Aug-00     Release date:   11-Dec-00    
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(+)
= 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/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.
 

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
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.