5UKW

Crystal structure of human Glucose 6-phosphate Dehydrogenase mutant (A277C) complexed with G6P

• PDB DOI: https://doi.org/10.2210/pdb5UKW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-01-23 Released: 2017-04-19 
• Deposition Author(s): Ranzani, A.T., Cordeiro, A.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Mutations in the tetramer interface of human glucose-6-phosphate dehydrogenase reveals kinetic differences between oligomeric states.

Ranzani, A.T., Cordeiro, A.T.

(2017) FEBS Lett 591: 1278-1284

• PubMed: 28370139 
• DOI: https://doi.org/10.1002/1873-3468.12638
• Primary Citation of Related Structures:  
  5UKW


• PubMed Abstract: 
  

  Glucose-6-phosphate dehydrogenase (G6PDH) catalyzes the oxidation of glucose-6-phoshate to 6-phospho-gluconolactone with the concomitant reduction of NADP ⁺ to NADPH. In solution, the recombinant human G6PDH is known to be active as dimers and tetramers. To distinguish between the kinetic properties of dimers and tetramers of the G6PDH is not trivial. Steady-state kinetic experiments are often performed at low enzyme concentrations, which favor the dimeric state. The present work describes two novel human G6PDH mutants, one that creates four disulfide bonds among apposing dimers, resulting in a 'cross-linked' tetramer, and another that prevents the dimer to dimer association. The functional and structural characterizations of such mutants indicate the tetramer as the most active form of human G6PDH.

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Organizational Affiliation: 

Institute of Biology, University of Campinas, Sao Paulo, Brazil.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 56.55 kDa 
• Atom Count: 3,904 
• Modelled Residue Count: 476 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate 1-dehydrogenase	A	488	Homo sapiens	Mutation(s): 1  Gene Names: G6PD EC: 1.1.1.49
UniProt & NIH Common Fund Data Resources
Find proteins for P11413 (Homo sapiens) Explore P11413  Go to UniProtKB:  P11413
PHAROS:  P11413 GTEx:  ENSG00000160211

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BG6	B [auth A]	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.234 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.099	α = 90
b = 177.817	β = 90
c = 216.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Ranzani, A.T., Cordeiro, A.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2012/23682-7

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary