PDBsum entry 2x0s

Transferase

PDB id: 2x0s

Contents

Protein chain

899 a.a. *

Waters ×36

* Residue conservation analysis

PDB id:

2x0s

Name:

Transferase

Title:

3.0 a resolution crystal structure of glycosomal pyruvate phosphate dikinase from trypanosoma brucei

Structure:

Pyruvate phosphate dikinase. Chain: a. Engineered: yes

Source:

Trypanosoma brucei. Organism_taxid: 5691. Strain: antat1. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

3.00Å R-factor: 0.169 R-free: 0.242

Authors:

L.W.Cosenza,F.Bringaud,T.Baltz,F.M.D.Vellieux

Key ref:

L.W.Cosenza et al. (2002). The 3.0 A resolution crystal structure of glycosomal pyruvate phosphate dikinase from Trypanosoma brucei. J Mol Biol, 318, 1417-1432. PubMed id: 12083528 DOI: 10.1016/S0022-2836(02)00113-4

Date:

17-Dec-09 Release date: 29-Dec-09

Supersedes:

1h6z

Protein chain

O76283  (O76283_9TRYP) -  Pyruvate, phosphate dikinase from Trypanosoma brucei

Seq: 913 a.a.

Struc: 899 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.9.1 - pyruvate, phosphate dikinase.
• Reaction: pyruvate + phosphate + ATP = phosphoenolpyruvate + AMP + diphosphate + H⁺

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

reference

DOI no: 10.1016/S0022-2836(02)00113-4

J Mol Biol 318:1417-1432 (2002)

PubMed id: 12083528

The 3.0 A resolution crystal structure of glycosomal pyruvate phosphate dikinase from Trypanosoma brucei.

L.W.Cosenza, F.Bringaud, T.Baltz, F.M.Vellieux.

ABSTRACT

The crystal structure of the glycosomal enzyme pyruvate phosphate dikinase from the African protozoan parasite Trypanosoma brucei has been solved to 3.0 A resolution by molecular replacement. The search model was the 2.3 A resolution structure of the Clostridium symbiosum enzyme. Due to different relative orientations of the domains and sub-domains in the two structures, molecular replacement could be achieved only by positioning these elements (four bodies altogether) sequentially in the asymmetric unit of the P2(1)2(1)2 crystal, which contains one pyruvate phosphate dikinase (PPDK) subunit. The refined model, comprising 898 residues and 188 solvent molecules per subunit, has a crystallographic residual index Rf = 0.245 (cross-validation residual index Rfree = 0.291) and displays satisfactory stereochemistry. Eight regions, comprising a total of 69 amino acid residues at the surface of the molecule, are disordered in this crystal form. The PPDK subunits are arranged around the crystallographic 2-fold axis as a dimer, analogous to that observed in the C. symbiosum enzyme. Comparison of the two structures was carried out by superposition of the models. Although the fold of each domain or sub-domain is similar, the relative orientations of these constitutive elements are different in the two structures. The trypanosome enzyme is more "bent" than the bacterial enzyme, with bending increasing from the center of the molecule (close to the molecular 2-fold axis) towards the periphery where the N-terminal domain is located. As a consequence of this increased bending and of the differences in relative positions of subdomains, the nucleotide-binding cleft in the amino-terminal domain is wider in T. brucei PPDK: the N-terminal fragment of the amino-terminal domain is distant from the catalytic, phospho-transfer competent histidine 482 (ca 10 A away). Our observations suggest that the requirements of domain motion during enzyme catalysis might include widening of the nucleotide-binding cleft to allow access and departure of the AMP or ATP ligand.

Selected figure(s)

Figure 6.
Figure 6. A GRASP representation of the electrostatic potential at the surface of the glycosomal PPDK molecule. This Figure shows the PPDK dimer viewed from opposite sides (related by a 180° rotation). The separation between the two monomers is indicated by a thick line. The entire surface of the molecule is covered by basic residues, giving a blue surface. The only area where acidic residues are in excess (red area) is located in the inter-domain depression where the central domain is situated.

Figure 7.
Figure 7. Superimposed subunits of T. brucei and C. symbiosum PPDK. The superposition operation was carried out using only the C-terminal domains. The C^a tracings of the superimposed subunits are shown, with T. brucei PPDK in black and bacterial PPDK in gray. For easier understanding, the equivalent domains and sub-domains in the two subunits are also represented by vectors between corresponding residues in the two structures (shown as thick lines).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 1417-1432) copyright 2002.

Figures were selected by the author.