1H94

COMPLEX OF ACTIVE MUTANT (S215->C) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM L.MESENTEROIDES WITH COENZYME NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Naylor, C.E.Gover, S.Basak, A.K.Cosgrove, M.S.Levy, H.R.Adams, M.J.

(2001) Acta Crystallogr.,Sect.D 57: 635

  • Primary Citation of Related Structures:  1H93, 1H9A, 1H9B

  • PubMed Abstract: 
  • The reduced coenzymes NADH and NADPH only differ by one phosphate, but in the cell NADH provides reducing power for catabolism while NADPH is utilized in biosynthetic pathways. Enzymes almost invariably discriminate between the coenzymes, but glucose ...

    The reduced coenzymes NADH and NADPH only differ by one phosphate, but in the cell NADH provides reducing power for catabolism while NADPH is utilized in biosynthetic pathways. Enzymes almost invariably discriminate between the coenzymes, but glucose 6-phosphate dehydrogenase (G6PD) from Leuconostoc mesenteroides is rare in being functionally dual specific. In order to elucidate the coenzyme selectivity, the structures of NADP(+)- and NAD(+)-complexed L. mesenteroides G6PD have been determined including data to 2.2 and 2.5 A resolution, respectively, and compared with unliganded G6PD crystallized in the same space groups. Coenzyme binding is also compared with that in a ternary complex of a mutant in which Asp177 in the active site has been mutated to asparagine. There are no gross structural differences between the complexes. In both binary complexes, the enzyme interdomain hinge angle has opened. NADP(+) binds to the furthest open form; of the residues within the coenzyme domain, only Arg46 moves, interacting with the 2'-phosphate and adenine. NAD(+) is less well defined in the binding site; smaller hinge opening is seen but larger local changes: Arg46 is displaced, Thr14 bonds the 3'-hydroxyl and Gln47 bonds the 2'-hydroxyl. In the ternary complex, the hinge angle has closed; only the adenine nucleotide is ordered in the binding site. Arg46 again provides most binding interactions.


    Related Citations: 
    • The Three-Dimensional Structure of Glucose 6-Phosphate Dehydrogenase from Leuconostoc Mesenteroides Refined at 2 Angstroms Resolution
      Rowland, P.,Basak, A.K.,Gover, S.,Levy, H.R.,Adams, M.J.
      (1994) Structure 2: 1073
    • 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
      Cosgrove, M.S.,Gover, S.,Naylor, C.E.,Vandeputte-Rutten, L.,Adams, M.J.,Levy, H.R.
      (2000) Biochemistry 39: 15002
    • 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

    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Rex Richards Building, South Parks Road, Oxford OX1 3QU, England, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
A
485Leuconostoc mesenteroidesGene Names: zwf
EC: 1.1.1.49
Find proteins for P11411 (Leuconostoc mesenteroides)
Go to UniProtKB:  P11411
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.900α = 90.00
b = 45.200β = 107.10
c = 93.500γ = 90.00
Software Package:
Software NamePurpose
TFFCphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-03
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance