PDBsum entry 1ii2

Lyase

PDB id: 1ii2

Contents

Protein chains

522 a.a. *

Ligands

SO4 ×2

Waters ×827

* Residue conservation analysis

PDB id:

1ii2

Name:

Lyase

Title:

Crystal structure of phosphoenolpyruvate carboxykinase (pepck) from trypanosoma cruzi

Structure:

Phosphoenolpyruvate carboxykinase. Chain: a, b. Engineered: yes

Source:

Trypanosoma cruzi. Organism_taxid: 5693. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.195 R-free: 0.220

Authors:

S.Trapani,J.Linss,S.Goldenberg,H.Fischer,A.F.Craievich,G.Oliva

Key ref:

S.Trapani et al. (2001). Crystal structure of the dimeric phosphoenolpyruvate carboxykinase (PEPCK) from Trypanosoma cruzi at 2 A resolution. J Mol Biol, 313, 1059-1072. PubMed id: 11700062 DOI: 10.1006/jmbi.2001.5093

Date:

20-Apr-01 Release date: 21-Nov-01

Protein chains

P51058  (PCKA_TRYCR) -  Phosphoenolpyruvate carboxykinase (ATP), glycosomal from Trypanosoma cruzi

Seq: 472 a.a.

Struc: 522 a.a.*

* PDB and UniProt seqs differ at 14 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.1.1.49 - phosphoenolpyruvate carboxykinase (ATP).
• Reaction: oxaloacetate + ATP = phosphoenolpyruvate + ADP + CO2

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

reference

DOI no: 10.1006/jmbi.2001.5093

J Mol Biol 313:1059-1072 (2001)

PubMed id: 11700062

Crystal structure of the dimeric phosphoenolpyruvate carboxykinase (PEPCK) from Trypanosoma cruzi at 2 A resolution.

S.Trapani, J.Linss, S.Goldenberg, H.Fischer, A.F.Craievich, G.Oliva.

ABSTRACT

ATP-dependent phosphoenolpyruvate carboxykinase (PEPCK) (ATP: oxaloacetate carboxylyase (transphosphorylating), EC 4.1.1.49) is a key enzyme involved in the catabolism of glucose and amino acids in the parasite Trypanosoma cruzi, the causative agent of Chagas' disease. Due to the significant differences in the amino acid sequence and substrate specificity of the human enzyme (PEPCK (GTP-dependent), EC 4.1.1.32), the parasite enzyme has been considered a good target for the development of new anti-chagasic drugs. We have solved the crystal structure of the recombinant PEPCK of T. cruzi up to 2.0 A resolution, characterised the dimeric organisation of the enzyme by solution small angle X-ray scattering (SAXS) and compared the enzyme structure with the known crystal structure of the monomeric PEPCK from Escherichia coli. The dimeric structure possesses 2-fold symmetry, with each monomer sharing a high degree of structural similarity with the monomeric structure of the E. coli PEPCK. Each monomer folds into two complex mixed alpha/beta domains, with the active site located in a deep cleft between the domains. The two active sites in the dimer are far apart from each other, in an arrangement that seems to permit an independent access of the substrates to the two active sites. All residues of the E. coli PEPCK structure that had been found to interact with substrates and metal cofactors have been found conserved and in a substantially equivalent spatial disposition in the T. cruzi PEPCK structure. No substrate or metal ion was present in the crystal structure. A sulphate ion from the crystallisation medium has been found bound to the active site. Solution SAXS data suggest that, in solutions with lower sulphate concentration than that used for the crystallisation experiments, the actual enzyme conformation may be slightly different from its conformation in the crystal structure. This could be due to a conformational transition upon sulphate binding, similar to the ATP-induced transition observed in the E. coli PEPCK, or to crystal packing effects. The present structure of the T. cruzi PEPCK will provide a good basis for the modelling of new anti-chagasic drug leads.

Selected figure(s)

Figure 1.
Figure 1. T. cruzi PEPCK stick model and (3m|F[o]| -2D|F[c]|) difference Fourier map contoured at 1s level around: (a) the sulphate ion in the phosphate-binding site; (b) residues 360-379, containing the disordered loop 366-373; the (incomplete) C^a trace of the corresponding region of the E. coli PEPCK is shown in green; a discontinuity in the drawing is due to missing residues in the deposited atomic coordinates of the E. coli PEPCK. The Figure was drawn using O.[65]

Figure 7.
Figure 7. The dimeric arrangement of the T. cruzi PEPCK. N-terminal domains are shown in blue, C-terminal domains in magenta. The monomer-monomer interface residues are highlighted.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 313, 1059-1072) copyright 2001.

Figures were selected by an automated process.