spacer
spacer

PDBsum entry 2dp3

Go to PDB code: 
protein ligands links
Isomerase PDB id
2dp3
Jmol
Contents
Protein chain
255 a.a. *
Ligands
SO4 ×4
Waters ×303
* Residue conservation analysis
PDB id:
2dp3
Name: Isomerase
Title: Crystal structure of a double mutant (c202a/a198v) of triose isomerase from giardia lamblia
Structure: Triosephosphate isomerase. Chain: a. Synonym: tim, triose-phosphate isomerase. Engineered: yes. Mutation: yes
Source: Giardia intestinalis. Organism_taxid: 5741. Strain: wb strain. Gene: gltim. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.175     R-free:   0.181
Authors: A.Diaz,H.Reyes-Vivas,G.Lopez-Velazquez
Key ref:
H.Reyes-Vivas et al. (2007). Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity. J Mol Biol, 365, 752-763. PubMed id: 17095008 DOI: 10.1016/j.jmb.2006.10.053
Date:
05-May-06     Release date:   02-Jan-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P36186  (TPI1_GIAIN) -  Triosephosphate isomerase
Seq:
Struc:
257 a.a.
255 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
= 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     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.jmb.2006.10.053 J Mol Biol 365:752-763 (2007)
PubMed id: 17095008  
 
 
Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity.
H.Reyes-Vivas, A.Diaz, J.Peon, G.Mendoza-Hernandez, G.Hernandez-Alcantara, I.De la Mora-De la Mora, S.Enriquez-Flores, L.Dominguez-Ramirez, G.Lopez-Velazquez.
 
  ABSTRACT  
 
Triosephosphate isomerase from the mesophile Giardia lamblia (GlTIM) is the only known TIM with natural disulfide bridges. We previously found that oxidized and reduced thiol states of GlTIM are involved in the interconversion between native dimers and higher oligomeric species, and in the regulation of enzymatic activity. Here, we found that trophozoites and cysts have different oligomeric species of GlTIM and complexes of GlTIM with other proteins. Our data indicate that the internal milieu of G. lamblia is favorable for the formation of disulfide bonds. Enzyme mutants of the three most solvent exposed Cys of GlTIM (C202A, C222A, and C228A) were prepared to ascertain their contribution to oligomerization and activity. The data show that the establishment of a disulfide bridge between two C202 of two dimeric GlTIMs accounts for multimerization. In addition, we found that the establishment of an intramonomeric disulfide bond between C222 and C228 abolishes catalysis. Multimerization and inactivation are both reversed by reducing conditions. The 3D structure of the C202A GlTIM was solved at 2.1 A resolution, showing that the environment of the C202 is prone to hydrophobic interactions. Molecular dynamics of an in silico model of GlTIM when the intramonomeric disulfide bond is formed, showed that S216 is displaced 4.6 A from its original position, causing loss of hydrogen bonds with residues of the active-site loop. This suggests that this change perturb the conformational state that aligns the catalytic center with the substrate, inducing enzyme inactivation.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. In situ distribution of GlTIM. Immunofluorescence image of GlTIM distribution in (a) trophozoites, and (b) cysts. The scale bar represents 2 μm. Figure 2. In situ distribution of GlTIM. Immunofluorescence image of GlTIM distribution in (a) trophozoites, and (b) cysts. The scale bar represents 2 μm.
Figure 5.
Figure 5. Topology of the residues C202 in the homodimeric GlTIM and their role in the oligomerization. (a) Top view of the homodimeric GlTIM. The C202 residues added in silico are shown as a CPK model. (b) A representation of the linking mechanism in homodimeric GlTIM. a, Side-view of two homodimers with their C202 aligned to form the disulfide bond. b, Upon disulfide formation, the tetramer produced can react with the C202 of another dimer. c, The reaction among several homodimers produces multimers of GlTIM; oligomerization can be reverted under reducing conditions. Figure 5. Topology of the residues C202 in the homodimeric GlTIM and their role in the oligomerization. (a) Top view of the homodimeric GlTIM. The C202 residues added in silico are shown as a CPK model. (b) A representation of the linking mechanism in homodimeric GlTIM. a, Side-view of two homodimers with their C202 aligned to form the disulfide bond. b, Upon disulfide formation, the tetramer produced can react with the C202 of another dimer. c, The reaction among several homodimers produces multimers of GlTIM; oligomerization can be reverted under reducing conditions. Figures were generated with VMD.[3]^72
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 365, 752-763) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21396445 J.Moraes, R.Arreola, N.Cabrera, L.Saramago, D.Freitas, A.Masuda, I.da Silva Vaz, M.Tuena de Gomez-Puyou, R.Perez-Montfort, A.Gomez-Puyou, and C.Logullo (2011).
Structural and biochemical characterization of a recombinant triosephosphate isomerase from Rhipicephalus (Boophilus) microplus.
  Insect Biochem Mol Biol, 41, 400-409.
PDB code: 3th6
19583769 M.Banerjee, H.Balaram, and P.Balaram (2009).
Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase. The role of conserved residues and complementary mutations.
  FEBS J, 276, 4169-4183.  
19225662 S.R.Devenish, and J.A.Gerrard (2009).
The role of quaternary structure in (beta/alpha)(8)-barrel proteins: evolutionary happenstance or a higher level of structure-function relationships?
  Org Biomol Chem, 7, 833-839.  
18632730 S.Barranco-Medina, T.Krell, L.Bernier-Villamor, F.Sevilla, J.J.Lázaro, and K.J.Dietz (2008).
Hexameric oligomerization of mitochondrial peroxiredoxin PrxIIF and formation of an ultrahigh affinity complex with its electron donor thioredoxin Trx-o.
  J Exp Bot, 59, 3259-3269.  
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 code is shown on the right.