Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 113867.35 
• Atom Count: 7822 
• Residue Count: 978 
• Unique protein chains: 1

2BHL

X-RAY STRUCTURE OF HUMAN GLUCOSE-6-PHOSPHATE DEHYDROGENASE (DELETION VARIANT) COMPLEXED WITH GLUCOSE-6-PHOSPHATE

• DOI: 10.2210/pdb2BHL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2005-01-13 Released: 2005-04-25 
• Deposition Author(s): Kotaka, M., Gover, S., Lam, V.M.S., Adams, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.261 
• R-Value Work: 0.212 

Literature

Structural Studies of Glucose-6-Phosphate and Nadp+ Binding to Human Glucose-6-Phosphate Dehydrogenase

Kotaka, M., Gover, S., Vandeputte-Rutten, L., Au, S.W.N., Lam, V.M.S., Adams, M.J.

(2005) Acta Crystallogr.,Sect.D 61: 495

• PubMed: 15858258 
• DOI: 10.1107/S0907444905002350
• Primary Citation of Related Structures:  
  2BH9


• PubMed Abstract: 
  

Human glucose-6-phosphate dehydrogenase (G6PD) is NADP(+)-dependent and catalyses the first and rate-limiting step of the pentose phosphate shunt. Binary complexes of the human deletion mutant, DeltaG6PD, with glucose-6-phosphate and NADP(+) have been crystallized and their structures solved to 2.9 and 2.5 A, respectively. The structures are compared with the previously determined structure of the Canton variant of human G6PD (G6PD(Canton)) in which NADP(+) is bound at the structural site. Substrate binding in DeltaG6PD is shown to be very similar to that described previously in Leuconostoc mesenteroides G6PD. NADP(+) binding at the coenzyme site is seen to be comparable to NADP(+) binding in L. mesenteroides G6PD, although some differences arise as a result of sequence changes. The tetramer interface varies slightly among the human G6PD complexes, suggesting flexibility in the predominantly hydrophilic dimer-dimer interactions. In both complexes, Pro172 of the conserved peptide EKPxG is in the cis conformation; it is seen to be crucial for close approach of the substrate and coenzyme during the enzymatic reaction. Structural NADP(+) binds in a very similar way in the DeltaG6PD-NADP(+) complex and in G6PD(Canton), while in the substrate complex the structural NADP(+) has low occupancy and the C-terminal tail at the structural NADP(+) site is disordered. The implications of possible interaction between the structural NADP(+) and G6P are considered.

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Related Citations: 

• Solution of the Structure of Tetrameric Human Glucose 6-Phosphate Dehydrogenase by Molecular Replacement
  Au, S.W.N.,Naylor, C.E.,Gover, S.,Vandeputte-Rutten, L.,Scopes, D.A.,Mason, P.J.,Luzzatto, L.,Lam, V.M.S.,Adams, M.J.
  (1999) Acta Crystallogr.,Sect.D 55: 826
• Human Glucose-6-Phosphate Dehydrogenase: The Crystal Structure Reveals a Structural Nadp Molecule and Provides Insights Into Enzyme Deficiency
  Au, S.W.N.,Gover, S.,Lam, V.M.S.,Adams, M.J.
  (2000) Structure 8: 293




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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE	A, B	489	Homo sapiens	Mutation(s): 0  Gene Names: G6PD EC: 1.1.1.49
Find proteins for P11413 (Homo sapiens) Go to Gene View: G6PD Go to UniProtKB:  P11413

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BG6	A, B	BETA-D-GLUCOSE-6-PHOSPHATE C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.261 
• R-Value Work: 0.212 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 117.552	α = 90.00
b = 179.527	β = 90.00
c = 137.938	γ = 90.00

Software Package:

Software Name	Purpose
TNT	refinement
SCALA	data scaling
MOLREP	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-13 
• Released Date: 2005-04-25 
• Deposition Author(s): Kotaka, M., Gover, S., Lam, V.M.S., Adams, M.J.

Revision History 

• Version 1.0: 2005-04-25
  Type: Initial release
• Version 1.1: 2014-02-05
  Type: Other, Refinement description, Structure summary, Version format compliance