1H9A

COMPLEX OF ACTIVE MUTANT (Q365->C) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM L. MESENTEROIDES WITH COENZYME NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.5 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 D Biol Crystallogr 57: 635

  • DOI: 10.1107/s0907444901003420
  • Primary Citation of Related Structures:  
    1H94, 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 6-phosphate dehydrogenase (G6PD) from Leuconostoc mesenteroides is rare in being functionally dual specific ...

    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: 
    • 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
    • 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
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASEA485Leuconostoc mesenteroidesMutation(s): 1 
Gene Names: G6PDzwf
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • 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-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-03
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-10-24
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-05-22
    Changes: Data collection, Refinement description