1N1E

Crystal structure of Leishmania mexicana Glycerol-3-phosphate dehydrogenase complexed with DHAP and NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Leishmania mexicana Glycerol-3-phosphate Dehydrogenase Showed Conformational Changes Upon Binding a Bi-substrate Adduct

Choe, J.Guerra, D.Michels, P.A.M.Hol, W.G.J.

(2003) J.Mol.Biol. 320: 335-349


  • PubMed Abstract: 
  • Certain pathogenic trypanosomatids are highly dependent on glycolysis for ATP production, and hence their glycolytic enzymes, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. The ternary complex structure o ...

    Certain pathogenic trypanosomatids are highly dependent on glycolysis for ATP production, and hence their glycolytic enzymes, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. The ternary complex structure of Leishmania mexicana GPDH (LmGPDH) with dihydroxyacetone phosphate (DHAP) and NAD(+) was determined to 1.9A resolution as a further step towards understanding this enzyme's mode of action. When compared with the apo and binary complex structures, the ternary complex structure shows an 11 degrees hinge-bending motion of the C-terminal domain with respect to the N-terminal domain. In addition, residues in the C-terminal domain involved in catalysis or substrates binding show significant movements and a previously invisible five-residue loop region becomes well ordered and participates in NAD(+) binding. Unexpectedly, DHAP and NAD(+) appear to form a covalent bond, producing an adduct in the active site of LmGPDH. Modeling a ternary complex glycerol 3-phosphate (G3P) and NAD(+) with LmGPDH identified ten active site residues that are highly conserved among all GPDHs. Two lysine residues, Lys125 and Lys210, that are presumed to be critical in catalysis, were mutated resulting in greatly reduced catalytic activity. Comparison with other structurally related enzymes found by the program DALI suggested Lys210 as a key catalytic residue, which is located on a structurally conserved alpha-helix. From the results of site-directed mutagenesis, molecular modeling and comparison with related dehydrogenases, a catalytic mechanism of LmGPDH and a possible evolutionary scenario of this group of dehydrogenases are proposed.


    Organizational Affiliation

    Department of Biochemistry, Biomolecular Structure and Design program, University of Washington, Seattle 98195-7742, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glycerol-3-phosphate dehydrogenase
A, B
366Leishmania mexicanaMutation(s): 0 
Gene Names: GPD
EC: 1.1.1.8
Find proteins for P90551 (Leishmania mexicana)
Go to UniProtKB:  P90551
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDE
Query on NDE

Download SDF File 
Download CCD File 
A, B
ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) P'-5'-ESTER WITH 3-(AMINOCARBONYL)-4-(1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPYL)-1-BETA-D-RIBOFURANOSYLPYRIDINIUM INNER SALT
NAD WITH (1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPANE)
C24 H32 N7 O20 P3
IVZPTIKSOMOSEU-WPIGAQFXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 77.745α = 90.00
b = 77.745β = 90.00
c = 266.631γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-10-17 
  • Released Date: 2003-05-27 
  • Deposition Author(s): Choe, J., Hol, W.G.J.

Revision History 

  • Version 1.0: 2003-05-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance