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PDBsum entry 1ci1

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protein ligands Protein-protein interface(s) links
Triosephosphate isomerase PDB id
1ci1
Jmol
Contents
Protein chains
248 a.a. *
Ligands
HEX ×3
Waters ×236
* Residue conservation analysis
PDB id:
1ci1
Name: Triosephosphate isomerase
Title: Crystal structure of triosephosphate isomerase from trypanos in hexane
Structure: Protein (triosephosphate isomerase). Chain: a, b. Synonym: tim. Engineered: yes
Source: Trypanosoma cruzi. Organism_taxid: 5693. Strain: mexican ninoa strain. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.181     R-free:   0.239
Authors: X.-G.Gao,E.Maldondo,R.Perez-Montfort,M.T.De Gomez-Puyou,A.Go Puyou,A.Rodriguez-Romero
Key ref:
X.G.Gao et al. (1999). Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane. Proc Natl Acad Sci U S A, 96, 10062-10067. PubMed id: 10468562 DOI: 10.1073/pnas.96.18.10062
Date:
06-Apr-99     Release date:   01-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P52270  (TPIS_TRYCR) -  Triosephosphate isomerase, glycosomal
Seq:
Struc:
251 a.a.
248 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     glycosome   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.96.18.10062 Proc Natl Acad Sci U S A 96:10062-10067 (1999)
PubMed id: 10468562  
 
 
Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane.
X.G.Gao, E.Maldonado, R.Pérez-Montfort, G.Garza-Ramos, M.T.de Gómez-Puyou, A.Gómez-Puyou, A.Rodríguez-Romero.
 
  ABSTRACT  
 
To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2-A resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 A from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Stereoview of the (2F[o] F[c]) map contoured at 1 of H2, H3, and surrounding residues. The residues of subunits A and B are shown in green and orange, respectively. H2 and H3 are in purple, and waters are in red.
Figure 5.
Fig. 5. Stereoview of the C trace of the interface region near H2 and H3 in the hexane and native structures. All atoms of the indicated residues are shown. Colors are as in Fig. 1. Note that the numbering of the residues in subunit A is from 1 to 251, and in subunit B from 301 to 551.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19622869 P.Gayathri, M.Banerjee, A.Vijayalakshmi, H.Balaram, P.Balaram, and M.R.Murthy (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.
PDB codes: 2vfd 2vfe 2vff 2vfg 2vfh 2vfi
12609866 C.M.Soares, V.H.Teixeira, and A.M.Baptista (2003).
Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies.
  Biophys J, 84, 1628-1641.  
7015072 E.H.Leiter, D.L.Coleman, A.B.Eisenstein, and I.Strack (1981).
Dietary control of pathogenesis in C57BL/KsJ db/db diabetes mice.
  Metabolism, 30, 554-562.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.