2X0N

Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


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Literature

Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma Brucei Determined from Laue Data.

Vellieux, F.M.D.Hajdu, J.Verlinde, C.L.Groendijk, H.Read, R.J.Greenhough, T.J.Campbell, J.W.Kalk, K.H.Littlechild, J.A.Watson, H.C.

(1993) Proc.Natl.Acad.Sci.USA 90: 2355

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating), EC 1.12.1.12] from the sleeping-sickness parasite Trypanosoma brucei was solved by molecular r ...

    The three-dimensional structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating), EC 1.12.1.12] from the sleeping-sickness parasite Trypanosoma brucei was solved by molecular replacement at 3.2-A resolution with an x-ray data set collected by the Laue method. For data collection, three crystals were exposed to the polychromatic synchrotron x-ray beam for a total of 20.5 sec. The structure was solved by using the Bacillus stearothermophilus enzyme model [SkarzyƄski, T., Moody, P. C. E. & Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187] with a partial data set which was 37% complete. The crystals contain six subunits per asymmetric unit, which allowed us to overcome the absence of > 60% of the reflections by 6-fold density averaging. After molecular dynamics refinement, the current molecular model has an R factor of 17.6%. Comparing the structure of the trypanosome enzyme with that of the homologous human muscle enzyme, which was determined at 2.4-A resolution, reveals important structural differences in the NAD binding region. These are of great interest for the design of specific inhibitors of the parasite enzyme.


    Related Citations: 
    • Two Tandemly Linked Identical Genes Code for the Glycosomal Glyceraldehyde-Phosphate Dehydrogenase in Trypanosoma Brucei.
      Michels, P.A.,Poliszczak, A.,Osinga, K.A.,Misset, O.,Van Beeumen, J.,Wierenga, R.K.,Borst, P.,Opperdoes, F.R.
      (1986) Embo J. 5: 1049
    • Refined 3.2 A Structure of Glycosomal Holo Glyceraldehyde Phosphate Dehydrogenase from Trypanosoma Brucei Brucei.
      Vellieux, F.M.D.,Hajdu, J.,Hol, W.G.
      (1995) Acta Crystallogr.,Sect.D 51: 575
    • Preliminary Crystallographic Studies of Glycosomal Glyceraldehyde Phosphate Dehydrogenase from Trypanosoma Brucei Brucei.
      Read, R.J.,Wierenga, R.K.,Groendijk, H.,Hol, W.G.,Lambeir, A.,Opperdoes, F.R.
      (1987) J.Mol.Biol. 194: 573


    Organizational Affiliation

    Department of Chemistry, BIOSON Research Institute, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL
A, B, O, P, Q, R
359Trypanosoma brucei bruceiMutation(s): 0 
EC: 1.2.1.12
Find proteins for P22512 (Trypanosoma brucei brucei)
Go to UniProtKB:  P22512
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, O, P, Q, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, O, P, Q, R
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.520α = 90.00
b = 256.270β = 90.00
c = 114.910γ = 90.00
Software Package:
Software NamePurpose
BIOMOLphasing
MERLOTphasing
PHENIXrefinement
DARESBURYdata reduction
DARESBURYdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Data collection