2DPG

COMPLEX OF INACTIVE MUTANT (H240->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES WITH NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

On the mechanism of the reaction catalyzed by glucose 6-phosphate dehydrogenase.

Cosgrove, M.S.Naylor, C.Paludan, S.Adams, M.J.Levy, H.R.

(1998) Biochemistry 37: 2759-2767

  • DOI: 10.1021/bi972069y
  • Primary Citation of Related Structures:  
    2DPG

  • PubMed 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 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.


    Related Citations: 
    • The Three-Dimensional Structure of Glucose 6-Phosphate Dehydrogenase from Leuconostoc Mesenteroides Refined at 2.0 A Resolution
      Rowland, P., Basak, A.K., Gover, S., Levy, H.R., Adams, M.J.
      (1994) Structure 2: 1073
    • Site-Directed Mutagenesis to Facilitate X-Ray Structural Studies of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase
      Adams, M.J., Basak, A.K., Gover, S., Rowland, P., Levy, H.R.
      (1993) Protein Sci 2: 859

    Organizational Affiliation

    Department of Biology, Syracuse University, Syracuse, New York 13244, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSE 6-PHOSPHATE DEHYDROGENASEA485Leuconostoc mesenteroidesMutation(s): 1 
Gene Names: PLMZ/H240Nzwf
EC: 1.1.1.49 (PDB Primary Data), 1.1.1.363 (UniProt)
UniProt
Find proteins for P11411 (Leuconostoc mesenteroides)
Explore P11411 
Go to UniProtKB:  P11411
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.7α = 90
b = 136.7β = 90
c = 121.2γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-07-15
    Type: Initial release
  • Version 1.1: 2008-03-05
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance