1PGJ

X-RAY STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE FROM THE PROTOZOAN PARASITE T. BRUCEI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A 2.8 A resolution structure of 6-phosphogluconate dehydrogenase from the protozoan parasite Trypanosoma brucei: comparison with the sheep enzyme accounts for differences in activity with coenzyme and substrate analogues.

Phillips, C.Dohnalek, J.Gover, S.Barrett, M.P.Adams, M.J.

(1998) J.Mol.Biol. 282: 667-681

  • DOI: 10.1006/jmbi.1998.2059

  • PubMed Abstract: 
  • The three-dimensional structure of 6-phosphogluconate dehydrogenase (6PGDH) from the parasitic protozoan Trypanosoma brucei has been solved at 2.8 A resolution. This pentose phosphate pathway enzyme is NADP-dependent; NADPH generated in the reaction ...

    The three-dimensional structure of 6-phosphogluconate dehydrogenase (6PGDH) from the parasitic protozoan Trypanosoma brucei has been solved at 2.8 A resolution. This pentose phosphate pathway enzyme is NADP-dependent; NADPH generated in the reaction protects against oxidative stress. The enzyme crystallises in the space-group P3121 with a dimer in the asymmetric unit and cell dimensions a=b=135.13 A, c=116.74 A, alpha=beta=90 degrees, gamma=120 degrees. The structure has refined to R=18.6% (Rfree=27.3%) with good geometry. The amino acid sequence of T. brucei 6PGDH is only 35% identical to that of the sheep liver enzyme and significant activity differences have been observed. The active dimer assembles with the C-terminal tail of one subunit threaded through the other, forming part of the substrate binding site. The tail of T. brucei 6PGDH is shorter than that of the sheep enzyme and its terminal residues associate tightly with the second monomer. The three-dimensional structure shows this generates additional interactions between the subunits close to the active site; the coenzyme binding domain is thereby associated more tightly with the helical domain. Three residues, conserved in all other known sequences, are important in creating a salt bridge between monomers close to the substrate binding site. The differences could explain the 200-fold enhanced affinity observed for the substrate analogue 6-phospho-2-deoxy-D-gluconate and suggest targets for anti-parasite drug design. The coenzyme binding domain of 6PGDH has a beta-alpha-beta fold; while in most species the "fingerprint" sequence is GxAxxG, in the T. brucei enzyme it is GxGxxG. Additional interactions between the enzyme and the coenzyme bis-phosphate are likely in the parasite 6PGDH, accounting for greater inhibition (40-fold) of 2'5'-ADP. While the core of the T. brucei dimer was restrained during refinement, several conformational differences have been found between the monomers; those at the coenzyme binding site suggest the molecule could be asymmetric during the enzyme reaction.


    Related Citations: 
    • Preliminary Crystallographic Study of 6-Phosphogluconate Dehydrogenase from Trypanosoma Brucei
      Phillips, C.,Barrett, M.P.,Gover, S.,Le Page, R.W.,Adams, M.J.
      (1993) J.Mol.Biol. 233: 317
    • Overexpression in Escherichia Coli and Purification of the 6-Phosphogluconate Dehydrogenase of Trypanosoma Brucei
      Barrett, M.P.,Phillips, C.,Adams, M.J.,Le Page, R.W.
      (1994) Protein Expr.Purif. 5: 44
    • Crystallographic Study of Coenzyme, Coenzyme Analogue and Substrate Binding in 6-Phosphogluconate Dehydrogenase: Implications for Nadp Specificity and the Enzyme Mechanism
      Adams, M.J.,Ellis, G.H.,Gover, S.,Naylor, C.E.,Phillips, C.
      (1994) Structure 2: 651
    • Erratum. Crystallographic Study of Coenzyme, Coenzyme Analogue and Substrate Binding in 6-Phosphogluconate Dehydrogenase: Implications for Nadp Specificity and the Enzyme Mechanism
      Adams, M.J.,Ellis, G.H.,Gover, S.,Naylor, C.E.,Phillips, C.
      (1994) Structure 2: 784


    Organizational Affiliation

    Department of Biochemistry, Oxford University, Rex Richards Building, Oxford, OX1 3QU, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-PHOSPHOGLUCONATE DEHYDROGENASE
A, B
478Trypanosoma brucei bruceiGene Names: GND
EC: 1.1.1.44
Find proteins for P31072 (Trypanosoma brucei brucei)
Go to UniProtKB:  P31072
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.130α = 90.00
b = 135.130β = 90.00
c = 116.740γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
SSMdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other