spacer
spacer

PDBsum entry 1tre

Go to PDB code: 
protein Protein-protein interface(s) links
Intramolecular oxidoreductase PDB id
1tre
Jmol
Contents
Protein chains
255 a.a. *
Waters ×172
* Residue conservation analysis
PDB id:
1tre
Name: Intramolecular oxidoreductase
Title: The structure of triosephosphate isomerase from escherichia coli determined at 2.6 angstrom resolution
Structure: Triosephosphate isomerase. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.119    
Authors: M.E.M.Noble,R.K.Wierenga
Key ref:
M.E.Noble et al. (1993). Structure of triosephosphate isomerase from Escherichia coli determined at 2.6 A resolution. Acta Crystallogr D Biol Crystallogr, 49, 403-417. PubMed id: 15299515 DOI: 10.1107/S0907444993002628
Date:
12-Oct-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A858  (TPIS_ECOLI) -  Triosephosphate isomerase
Seq:
Struc:
255 a.a.
255 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.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     membrane   3 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444993002628 Acta Crystallogr D Biol Crystallogr 49:403-417 (1993)
PubMed id: 15299515  
 
 
Structure of triosephosphate isomerase from Escherichia coli determined at 2.6 A resolution.
M.E.Noble, J.P.Zeelen, R.K.Wierenga, V.Mainfroid, K.Goraj, A.C.Gohimont, J.A.Martial.
 
  ABSTRACT  
 
The structure of triosephosphate isomerase (TIM) from the organism Escherichia coli has been determined at a resolution of 2.6 A. The structure was solved by the molecular replacement method, first at 2.8 A resolution with a crystal grown by the technique of hanging-drop crystallization from a mother liquor containing the transition-state analogue 2-phosphoglycolate (2PG). As a search model in the molecular replacement calculations, the refined structure of TIM from Trypanosoma brucei, which has a sequence identity of 46% compared to the enzyme from E. coli, was used. An E. coli TIM crystal grown in the absence of 2PG, diffracting to 2.6 A resolution, was later obtained by application of the technique of macro-seeding using a seed crystal grown from a mother liquor without 2PG. The final 2.6 A model has a crystallographic R factor of 11.9%, and agrees well with standard stereochemical parameters. The structure of E. coli TIM suggests the importance of residues which favour helix initiation for the formation of the TIM fold. In addition, TIM from E. coli shows peculiarities in its dimer interface, and in the packing of core residues within the beta-barrel.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The reaction catalysed by triosephosphate isomerase. Stereospecific interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde-3-phosphate (GAP) proceeds via a cis enediol(ate) intermediate. Atomic labels are given for DHAP atoms.
Figure 2.
Fig. 2. Cartoon representation of one monomer of triosephos- phate isomerase (trypanosomal TIM numbering). The eightfold repeat of a (loop-fl-loop-a) motif is viewed along the barrel axis from the C-terminal end of the fl-strands. The explicitly drawn and labelled residues (Asnl 1, Lysl3, His95 and Glu167) all form hydrogen bonds with bound substrate analogues. Also labelled are loops 5 (residues 129-139), 6 (residues 167-180) and 7 (residues 210-214). These loops, which are known to undergo conformational changes upon ligand binding, are depicted in their 'closed' conformation. The last labelled loop (loop 3, residues 70-80) is responsible for many of the contacts between monomers of the dimeric enzyme. This picture was generated using the program XRENDER (Noble, unpublished work).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 403-417) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19649324 P.V.Afonine, R.W.Grosse-Kunstleve, A.Urzhumtsev, and P.D.Adams (2009).
Automatic multiple-zone rigid-body refinement with a large convergence radius.
  J Appl Crystallogr, 42, 607-615.  
19261703 S.S.Thakur, P.D.Deepalakshmi, P.Gayathri, M.Banerjee, M.R.Murthy, and P.Balaram (2009).
Detection of the protein dimers, multiple monomeric states and hydrated forms of Plasmodium falciparum triosephosphate isomerase in the gas phase.
  Protein Eng Des Sel, 22, 289-304.  
16980388 A.M.Celotto, A.C.Frank, J.L.Seigle, and M.J.Palladino (2006).
Drosophila model of human inherited triosephosphate isomerase deficiency glycolytic enzymopathy.
  Genetics, 174, 1237-1246.  
12112681 H.Reyes-Vivas, E.Martínez-Martínez, G.Mendoza-Hernández, G.López-Velázquez, R.Pérez-Montfort, M.Tuena de Gómez-Puyou, and A.Gómez-Puyou (2002).
Susceptibility to proteolysis of triosephosphate isomerase from two pathogenic parasites: characterization of an enzyme with an intact and a nicked monomer.
  Proteins, 48, 580-590.  
10785370 A.M.Lambeir, J.Backmann, J.Ruiz-Sanz, V.Filimonov, J.E.Nielsen, I.Kursula, B.V.Norledge, and R.K.Wierenga (2000).
The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase.
  Eur J Biochem, 267, 2516-2524.
PDB code: 1qds
10468562 X.G.Gao, E.Maldonado, R.Pérez-Montfort, G.Garza-Ramos, M.T.de Gómez-Puyou, A.Gómez-Puyou, and A.Rodríguez-Romero (1999).
Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane.
  Proc Natl Acad Sci U S A, 96, 10062-10067.
PDB code: 1ci1
10545327 Y.Modis, and R.K.Wierenga (1999).
A biosynthetic thiolase in complex with a reaction intermediate: the crystal structure provides new insights into the catalytic mechanism.
  Structure, 7, 1279-1290.
PDB code: 1qfl
9739087 Y.Modis, S.A.Filppula, D.K.Novikov, B.Norledge, J.K.Hiltunen, and R.K.Wierenga (1998).
The crystal structure of dienoyl-CoA isomerase at 1.5 A resolution reveals the importance of aspartate and glutamate sidechains for catalysis.
  Structure, 6, 957-970.
PDB code: 1dci
9249046 A.Landa, A.Rojo-Domínguez, L.Jiménez, and D.A.Fernández-Velasco (1997).
Sequencing, expression and properties of triosephosphate isomerase from Entamoeba histolytica.
  Eur J Biochem, 247, 348-355.  
  9336838 N.Beaucamp, A.Hofmann, B.Kellerer, and R.Jaenicke (1997).
Dissection of the gene of the bifunctional PGK-TIM fusion protein from the hyperthermophilic bacterium Thermotoga maritima: design and characterization of the separate triosephosphate isomerase.
  Protein Sci, 6, 2159-2165.  
9261072 S.S.Velanker, S.S.Ray, R.S.Gokhale, S.Suma, H.Balaram, P.Balaram, and M.R.Murthy (1997).
Triosephosphate isomerase from Plasmodium falciparum: the crystal structure provides insights into antimalarial drug design.
  Structure, 5, 751-761.
PDB code: 1ydv
9370435 X.Raquet, V.Lounnas, J.Lamotte-Brasseur, J.M.Frère, and R.C.Wade (1997).
pKa calculations for class A beta-lactamases: methodological and mechanistic implications.
  Biophys J, 73, 2416-2426.  
  8895557 C.K.Engel, M.Mathieu, J.P.Zeelen, J.K.Hiltunen, and R.K.Wierenga (1996).
Crystal structure of enoyl-coenzyme A (CoA) hydratase at 2.5 angstroms resolution: a spiral fold defines the CoA-binding pocket.
  EMBO J, 15, 5135-5145.
PDB code: 1dub
8898895 G.Garza-Ramos, R.Pérez-Montfort, A.Rojo-Domínguez, M.T.de Gómez-Puyou, and A.Gómez-Puyou (1996).
Species-specific inhibition of homologous enzymes by modification of nonconserved amino acids residues. The cysteine residues of triosephosphate isomerase.
  Eur J Biochem, 241, 114-120.  
8807818 A.Gómez-Puyou, E.Saavedra-Lira, I.Becker, R.A.Zubillaga, A.Rojo-Domínguez, and R.Pérez-Montfort (1995).
Using evolutionary changes to achieve species-specific inhibition of enzyme action--studies with triosephosphate isomerase.
  Chem Biol, 2, 847-855.  
  8580851 L.F.Delboni, S.C.Mande, F.Rentier-Delrue, V.Mainfroid, S.Turley, F.M.Vellieux, J.A.Martial, and W.G.Hol (1995).
Crystal structure of recombinant triosephosphate isomerase from Bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three-dimensional structures points to the importance of hydrophobic interactions.
  Protein Sci, 4, 2594-2604.
PDB code: 1btm
8591044 T.V.Borchert, K.V.Kishan, J.P.Zeelen, W.Schliebs, N.Thanki, R.Abagyan, R.Jaenicke, and R.K.Wierenga (1995).
Three new crystal structures of point mutation variants of monoTIM: conformational flexibility of loop-1, loop-4 and loop-8.
  Structure, 3, 669-679.
PDB codes: 1mss 1tti 1ttj
  8061607 K.V.Kishan, J.P.Zeelen, M.E.Noble, T.V.Borchert, and R.K.Wierenga (1994).
Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms.
  Protein Sci, 3, 779-787.
PDB codes: 1tpe 1tpf
8125090 L.Kohl, M.Callens, R.K.Wierenga, F.R.Opperdoes, and P.A.Michels (1994).
Triose-phosphate isomerase of Leishmania mexicana mexicana. Cloning and characterization of the gene, overexpression in Escherichia coli and analysis of the protein.
  Eur J Biochem, 220, 331-338.  
7812714 M.Mathieu, J.P.Zeelen, R.A.Pauptit, R.Erdmann, W.H.Kunau, and R.K.Wierenga (1994).
The 2.8 A crystal structure of peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: a five-layered alpha beta alpha beta alpha structure constructed from two core domains of identical topology.
  Structure, 2, 797-808.
PDB code: 1pxt
  8061610 S.C.Mande, V.Mainfroid, K.H.Kalk, K.Goraj, J.A.Martial, and W.G.Hol (1994).
Crystal structure of recombinant human triosephosphate isomerase at 2.8 A resolution. Triosephosphate isomerase-related human genetic disorders and comparison with the trypanosomal enzyme.
  Protein Sci, 3, 810-821.
PDB code: 1hti
16100954 T.V.Borchert, R.Abagyan, K.V.Kishan, J.P.Zeelen, and R.K.Wierenga (1993).
The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop.
  Structure, 1, 205-213.
PDB code: 1tri
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.