PDBsum entry 1h6z

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protein links
Transferase PDB id
Protein chain
898 a.a. *
Waters ×177
* Residue conservation analysis
Superseded by: 2x0s
PDB id:
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. Other_details: glycosome
Biol. unit: Dimer (from PDB file)
3.00Å     R-factor:   0.245     R-free:   0.291
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
29-Jun-01     Release date:   05-Jun-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O76283  (O76283_9TRYP) -  Pyruvate phosphate dikinase
913 a.a.
898 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Pyruvate, phosphate dikinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate
+ pyruvate
+ phosphate
+ phosphoenolpyruvate
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17053069 A.Teplyakov, K.Lim, P.P.Zhu, G.Kapadia, C.C.Chen, J.Schwartz, A.Howard, P.T.Reddy, A.Peterkofsky, and O.Herzberg (2006).
Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein.
  Proc Natl Acad Sci U S A, 103, 16218-16223.
PDB code: 2hwg
15130474 D.Das, and M.M.Georgiadis (2004).
The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus.
  Structure, 12, 819-829.
PDB code: 1rw3
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