2X0N

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


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 U S A 90: 2355

  • DOI: https://doi.org/10.1073/pnas.90.6.2355
  • Primary Citation of Related Structures:  
    2X0N

  • 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 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 [Skarzyński, 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL359Trypanosoma brucei bruceiMutation(s): 0 
EC: 1.2.1.12
UniProt
Find proteins for P22512 (Trypanosoma brucei brucei)
Explore P22512 
Go to UniProtKB:  P22512
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22512
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O
R [auth P]
U [auth Q]
I [auth A],
L [auth B],
O,
R [auth P],
U [auth Q],
X [auth R]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
J [auth B]
K [auth B]
M [auth O]
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth O],
N [auth O],
P,
Q [auth P],
S [auth Q],
T [auth Q],
V [auth R],
W [auth R]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.52α = 90
b = 256.27β = 90
c = 114.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DARESBURYdata reduction
DARESBURYdata scaling
MERLOTphasing
BIOMOLphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Data collection
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description