PDBsum entry 2b4t

Oxidoreductase

PDB id: 2b4t

Contents

Protein chains

333 a.a. *

Ligands

NAD ×4

AES ×3

Waters ×232

* Residue conservation analysis

PDB id:

2b4t

Name:

Oxidoreductase

Title:

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

Structure:

Glyceraldehyde-3-phosphate dehydrogenase. Chain: o, p, q, r. Engineered: yes. Mutation: yes

Source:

Plasmodium falciparum. Malaria parasite p. Falciparum. Organism_taxid: 5833. Gene: pf14_0598. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.176 R-free: 0.217

Authors:

M.A.Robien,J.Bosch,W.G.J.Hol,Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)

Key ref:

M.A.Robien et al. (2006). Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 A resolution reveals intriguing extra electron density in the active site. Proteins, 62, 570-577. PubMed id: 16345073 DOI: 10.1002/prot.20801

Date:

26-Sep-05 Release date: 04-Oct-05

Protein chains

Q8T6B1  (Q8T6B1_PLAFA) -  Glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum

Seq: 337 a.a.

Struc: 333 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.2.1.12 - glyceraldehyde-3-phosphate dehydrogenase (phosphorylating).
• Pathway: Glyceraldehyde-3-phosphate Dehydrogenase (phosphorylating)
• Reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD⁺ = (2R)-3-phospho- glyceroyl phosphate + NADH + H⁺

D-glyceraldehyde 3-phosphate + phosphate (Bound ligand (Het Group name = NAD) corresponds exactly) + NAD(+) = (2R)-3-phospho- glyceroyl phosphate + NADH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1002/prot.20801

Proteins 62:570-577 (2006)

PubMed id: 16345073

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

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

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. 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.

Selected figure(s)

Figure 1.
Figure 1. (A) The PfGAPDH monomer. The NAD^+-binding domain is shown in blue, the meandering S-loop in red, and the remainder of the catalytic domain in green. NAD^+ is shown as a ball-and-stick model, together with two strictly conserved catalytic residues, Cys153 and His180 (where carbon is gold, nitrogen is blue, oxygen is red, phosphate is purple, and sulphur is green). In simple black stick model are represented: Met38 and Lys194-Gly195, identified as potentially significant based on a previous analysis of differences between the experimental rabbit structure and a PfGAPDH homology model.[8] In purple is depicted the position of AEBSF which has been modeled into the islands of extra density (See Fig. 2). (B) The PfGAPDH tetramer. The PfGAPDH tetramer shows the deep grooves between the O-R and the P-Q NAD^+-binding sites. The S-loops are colored red, showing the raised plateau these loops form between adjacent pairs of the NAD^+-binding sites. The secondary structure elements of the C-terminal domain are depicted with thinner helices and strands than in the catalytic domain to help distinguish the two domains. The O and P subunits are shown in lighter colors for contrast with the Q and R subunits. NAD^+ is shown in CPK representation. The additional unknown compound is shown as a smaller ball-and-stick model in purple, labeled ligand. (C) Electrostatic environment of the NAD^+ binding groove. Comparison of the electrostatic surface[43-45] representation of the NAD^+ binding groove: PfGAPDH versus HumanGAPDH. In PfGAPDH, the walls and the roof of the NAD^+-binding cavity are more closed and there is a small bulge due to the - KG - insertion.

Figure 2.
Figure 2. The extra density found near active site of PfGAPDH. The stereo view of the additional electron density shows the excellent correspondence between the difference density (green, contour level +3 sigma) prior to refinement with the AEBSF and the Sigma-A weighted electron density after placement and refinement with AEBSF (blue, contour level +1 sigma). PfGAPDH, the associated NAD^+, and the AEBSF are shown with carbon in gold, oxygen in red, nitrogen in blue, phosphorous in magenta, and sulfur in green. A superimposed region of the human GAPDH structure (PDB: 1ZNQ, shown in gray) shows the structural similarity of the active site, with the exception of a threonine found at the site corresponding to PfGAPDH Asn185. Hydrogen bonds or other favorable electronstatic interactions between the PfGAPDH and the AEBSF, or the NAD^+ and the AEBSF are shown in dashed lines.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 62, 570-577) copyright 2006.

Figures were selected by an automated process.