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PDBsum entry 2vfg

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
2vfg
Jmol
Contents
Protein chains
247 a.a. *
Ligands
3PG ×4
Waters ×677
* Residue conservation analysis
PDB id:
2vfg
Name: Isomerase
Title: Crystal structure of the f96h mutant of plasmodium falciparum triosephosphate isomerase with 3- phosphoglycerate bound at the dimer interface
Structure: Triosephosphate isomerase. Chain: a, b, c, d. Synonym: tim, triose-phosphate isomerase. Engineered: yes. Mutation: yes
Source: Plasmodium falciparum. Malarial parasite. Organism_taxid: 5833. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.95Å     R-factor:   0.210     R-free:   0.248
Authors: P.Gayathri,M.Banerjee,A.Vijayalakshmi,H.Balaram,P.Balaram, M.R.N.Murthy
Key ref:
P.Gayathri et al. (2009). Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site. Acta Crystallogr D Biol Crystallogr, 65, 847-857. PubMed id: 19622869 DOI: 10.1107/S0907444909018666
Date:
04-Nov-07     Release date:   09-Dec-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q07412  (TPIS_PLAFA) -  Triosephosphate isomerase
Seq:
Struc:
248 a.a.
247 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.1  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = 3PG)
matches with 90.00% similarity
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444909018666 Acta Crystallogr D Biol Crystallogr 65:847-857 (2009)
PubMed id: 19622869  
 
 
Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site.
P.Gayathri, M.Banerjee, A.Vijayalakshmi, H.Balaram, P.Balaram, M.R.Murthy.
 
  ABSTRACT  
 
Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K(m) values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant; (1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Superposition of the active site showing the residue conformations of F96S (pink), F96H (cyan) and wild-type PfTIM (green; PDB code 1ydv ) in the unliganded structures. This figure was prepared in wall-eyed stereo using PyMOL (DeLano, 2002[DeLano, W. L. (2002). The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, California, USA.]).
Figure 5.
Figure 5 Changes in the water structure at the active site accompanying ligand binding and loop closure. Loop 6 is shown in cartoon representation, while the active-site residues are shown in ball-and-stick representation. The respective water molecules are shown as spheres in the corresponding colours. The water molecules in the neighbourhood (<4 Å) of the loop residues are shown in a lighter shade compared with the water molecules within 4 Å of the bound ligand at the active site. All the water molecules shown in the figure have been included during structure solution on observation of electron density corresponding to 2F[o] - F[c] at the 1 level or F[o] - F[c] at the 3 level following refinement. The figures were prepared in wall-eyed stereo using PyMOL (DeLano, 2002[DeLano, W. L. (2002). The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, California, USA.]). (a) Superposition of the unliganded wild-type PfTIM structure (magenta; PDB code 1ydv ; 2.2 Å resolution) and the wild-type PfTIM-3PG complex with loop open (green; PDB code 1m7o ; 2.4 Å resolution). (b) Superposition of the wild-type PfTIM 3PG-bound structures with loop open (green; PDB code 1m7o ; 2.4 Å resolution) and loop closed (blue; PDB code 2vfi ; 2.25 Å resolution).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 847-857) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20694739 R.K.Wierenga, E.G.Kapetaniou, and R.Venkatesan (2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
  Cell Mol Life Sci, 67, 3961-3982.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.