2B4R

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 Angstrom Resolution reveals intriguing extra electron density in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 A resolution reveals intriguing extra electron density in the active site

Robien, M.A.Bosch, J.Buckner, F.S.Van Voorhis, W.C.Worthey, E.A.Myler, P.Mehlin, C.Boni, E.E.Kalyuzhniy, O.Anderson, L.Lauricella, A.Gulde, S.Luft, J.R.Detitta, G.Caruthers, J.M.Hodgson, K.O.Soltis, M.Zucker, F.Verlinde, C.L.Merritt, E.A.Schoenfeld, L.W.Hol, W.G.

(2006) Proteins 62: 570-577

  • DOI: 10.1002/prot.20801
  • Primary Citation of Related Structures:  
    2B4T, 2B4R

  • PubMed Abstract: 
  • The crystal structure of D-glyceraldehyde-3-phosphate dehydrogenase (PfGAPDH) from the major malaria parasite Plasmodium falciparum is solved at 2.25 A resolution. The structure of PfGAPDH is of interest due to the dependence of the malaria parasite in infected human erythrocytes on the glycolytic pathway for its energy generation ...

    The crystal structure of D-glyceraldehyde-3-phosphate dehydrogenase (PfGAPDH) from the major malaria parasite Plasmodium falciparum is solved at 2.25 A resolution. The structure of PfGAPDH is of interest due to the dependence of the malaria parasite in infected human erythrocytes on the glycolytic pathway for its energy generation. Recent evidence suggests that PfGAPDH may also be required for other critical activities such as apical complex formation. The cofactor NAD(+) is bound to all four subunits of the tetrameric enzyme displaying excellent electron densities. In addition, in all four subunits a completely unexpected large island of extra electron density in the active site is observed, approaching closely the nicotinamide ribose of the NAD(+). This density is most likely the protease inhibitor AEBSF, found in maps from two different crystals. This putative AEBSF molecule is positioned in a crucial location and hence our structure, with expected and unexpected ligands bound, can be of assistance in lead development and design of novel antimalarials.


    Organizational Affiliation

    Structural Genomics of Pathogenic Protozoa (SGPP), Department of Biochemistry, University of Washington, Seattle 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glyceraldehyde-3-phosphate dehydrogenase OPQR345Plasmodium falciparumMutation(s): 3 
Gene Names: PF14_0598
EC: 1.2.1.12
Find proteins for Q8T6B1 (Plasmodium falciparum)
Explore Q8T6B1 
Go to UniProtKB:  Q8T6B1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.327α = 90
b = 104.585β = 107.35
c = 90.838γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance