PDBsum entry 2vom

Go to PDB code: 
protein Protein-protein interface(s) links
Isomerase PDB id
Protein chain
245 a.a. *
Waters ×611
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Structural basis of human triosephosphate isomerase deficiency. Mutation e104d and correlation to solvent perturbation.
Structure: Triosephosphate isomerase. Chain: a, b, c, d. Fragment: residues 2-249. Synonym: tim. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693.
1.85Å     R-factor:   0.219     R-free:   0.252
Authors: C.Rodriguez-Almazan,R.Arreola-Alemon,D.Rodriguez-Larrea, B.Aguirre-Lopez,M.T.De Gomez-Puyou,R.Perez-Montfort, M.Costas,A.Gomez-Puyou,A.Torres-Larios
Key ref:
C.Rodríguez-Almazán et al. (2008). Structural basis of human triosephosphate isomerase deficiency: mutation E104D is related to alterations of a conserved water network at the dimer interface. J Biol Chem, 283, 23254-23263. PubMed id: 18562316 DOI: 10.1074/jbc.M802145200
19-Feb-08     Release date:   17-Jun-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P60174  (TPIS_HUMAN) -  Triosephosphate isomerase
286 a.a.
245 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - 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   2 terms 
  Biochemical function     catalytic activity     2 terms  


    Added reference    
DOI no: 10.1074/jbc.M802145200 J Biol Chem 283:23254-23263 (2008)
PubMed id: 18562316  
Structural basis of human triosephosphate isomerase deficiency: mutation E104D is related to alterations of a conserved water network at the dimer interface.
C.Rodríguez-Almazán, R.Arreola, D.Rodríguez-Larrea, B.Aguirre-López, Gómez-Puyou, R.Pérez-Montfort, M.Costas, A.Gómez-Puyou, A.Torres-Larios.
Human triosephosphate isomerase deficiency is a rare autosomal disease that causes premature death of homozygous individuals. The most frequent mutation that leads to this illness is in position 104, which involves a conservative change of a Glu for Asp. Despite the extensive work that has been carried out on the E104D mutant enzyme in hemolysates and whole cells, the molecular basis of this disease is poorly understood. Here, we show that the purified, recombinant mutant enzyme E104D, while exhibiting normal catalytic activity, shows impairments in the formation of active dimers and low thermostability and monomerizes under conditions in which the wild type retains its dimeric form. The crystal structure of the E104D mutant at 1.85 A resolution showed that its global structure was similar to that of the wild type; however, residue 104 is part of a conserved cluster of 10 residues, five from each subunit. An analysis of the available high resolution structures of TIM dimers revealed that this cluster forms a cavity that possesses an elaborate conserved network of buried water molecules that bridge the two subunits. In the E104D mutant, a disruption of contacts of the amino acid side chains in the conserved cluster leads to a perturbation of the water network in which the water-protein and water-water interactions that join the two monomers are significantly weakened and diminished. Thus, the disruption of this solvent system would stand as the underlying cause of the deficiency.
  Selected figure(s)  
Figure 4.
Overall structure of HsTIM E104D. A, stereo view of a double difference (2F[o] - F[c]) electron density map contoured at 1.5σ (blue) and a difference (F[o] - F[c]) electron density map contoured at 3σ (red). The maps were contoured at 10 Å around residue 104. The maps were obtained following the first refinement cycle made after molecular replacement on the structure of wild type HsTIM. Additional maps for the other three monomers of the asymmetric unit and omit maps around this region where the density for the solvent molecules can be seen are shown in Fig. S4. B, the conserved core of residues in the region of residue 104 mapped on the crystal structure of the mutant E104D. The two monomers are represented in cyan and green. The cluster of conserved residues is depicted in yellow sticks. C, conserved solvent molecules on the whole TIM structure. The 17 conserved water molecules detected in the mutant E104D were also observed in the presence or absence of ligands in a set of 15 different TIM crystal structures from 13 species; they are shown as red spheres.
Figure 5.
Mutation E104D perturbs both the conserved cluster of residues and the conserved water network. Shown is a comparison between wild type HsTIM (A) and the mutant E104D HsTIM (B). The dashes represent polar interactions in the region using a cut-off of 3.5 Å. Conserved water molecules in this region are shown as yellow spheres. Values in parentheses in B indicate the number of the equivalent water molecules on the wild type enzyme (see Table SII). Nonconserved water molecules are represented as red spheres. The pairs of conserved water molecules that are related by symmetry of the dimer as numbered in the Protein Data Bank are as follows: 1wyi, 1–152, 3–222, 35–151, 40–162 and 149–163. Residues of the two different monomers are represented in cyan and green.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 23254-23263) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20546019 F.Orosz, J.Oláh, and J.Ovádi (2011).
Reappraisal of triosephosphate isomerase deficiency.
  Eur J Haematol, 86, 265-267.  
  21469159 S.Y.Lu, Y.J.Jiang, J.Lv, J.W.Zou, and T.X.Wu (2011).
Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.
  J Comput Chem, 32, 1907-1918.  
20694739 R.K.Wierenga, E.G.Kapetaniou, and R.Venkatesan (2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
  Cell Mol Life Sci, 67, 3961-3982.  
19425109 J.D.Knight, D.Hamelberg, J.A.McCammon, and R.Kothary (2009).
The role of conserved water molecules in the catalytic domain of protein kinases.
  Proteins, 76, 527-535.  
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.  
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
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.