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PDBsum entry 1if2

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Isomerase PDB id
1if2
Jmol
Contents
Protein chain
249 a.a. *
Ligands
129
Waters ×214
* Residue conservation analysis
PDB id:
1if2
Name: Isomerase
Title: X-ray structure of leishmania mexicana triosephosphate isome complexed with ipp
Structure: Triosephosphate isomerase. Chain: a. Synonym: tim. Engineered: yes. Mutation: yes
Source: Leishmania mexicana. Organism_taxid: 5665. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.136     R-free:   0.181
Authors: I.Kursula,S.Partanen,A.-M.Lambeir,D.M.Antonov,K.Augustyns, R.K.Wierenga
Key ref:
I.Kursula et al. (2001). Structural determinants for ligand binding and catalysis of triosephosphate isomerase. Eur J Biochem, 268, 5189-5196. PubMed id: 11589711 DOI: 10.1046/j.0014-2956.2001.02452.x
Date:
12-Apr-01     Release date:   17-Aug-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P48499  (TPIS_LEIME) -  Triosephosphate isomerase
Seq:
Struc:
251 a.a.
249 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     cytoplasm   3 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1046/j.0014-2956.2001.02452.x Eur J Biochem 268:5189-5196 (2001)
PubMed id: 11589711  
 
 
Structural determinants for ligand binding and catalysis of triosephosphate isomerase.
I.Kursula, S.Partanen, A.M.Lambeir, D.M.Antonov, K.Augustyns, R.K.Wierenga.
 
  ABSTRACT  
 
The crystal structure of leishmania triosephosphate isomerase (TIM) complexed with 2-(N-formyl-N-hydroxy)-aminoethyl phosphonate (IPP) highlights the importance of Asn11 for binding and catalysis. IPP is an analogue of the substrate D-glyceraldehyde-3-phosphate, and it is observed to bind with its aldehyde oxygen in an oxyanion hole formed by ND2 of Asn11 and NE2 of His95. Comparison of the mode of binding of IPP and the transition state analogue phosphoglycolohydroxamate (PGH) suggests that the Glu167 side chain, as well as the triose part of the substrate, adopt different conformations as the catalysed reaction proceeds. Comparison of the TIM-IPP and the TIM-PGH structures with other liganded and unliganded structures also highlights the conformational flexibility of the ligand and the active site, as well as the conserved mode of ligand binding.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2 Nomenclature and covalent structure of PGH and IPP.
Figure 4.
Fig. 4 Superposition of the structures of the TIM–IPP complex and the TIM–PGH complex. All residues with atoms within 4.5 Å of the Glu167 carboxylate atoms are included in the image. The water cluster contacting Glu167 (three waters) and the bridging water, near Lys13, are shown as green and purple spheres for the TIM–IPP and the TIM–PGH structures, respectively. In the TIM–IPP complex, the hydroxamate moiety has moved down towards Asn11 and the Glu167 side chain has moved towards the front when compared to the TIM–PGH structure.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2001, 268, 5189-5196) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19857201 M.Klimacek, and B.Nidetzky (2010).
The oxyanion hole of Pseudomonas fluorescens mannitol 2-dehydrogenase: a novel structural motif for electrostatic stabilization in alcohol dehydrogenase active sites.
  Biochem J, 425, 455-463.  
20694739 R.K.Wierenga, E.G.Kapetaniou, and R.Venkatesan (2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
  Cell Mol Life Sci, 67, 3961-3982.  
17696453 M.Gulotta, L.Qiu, R.Desamero, J.Rösgen, D.W.Bolen, and R.Callender (2007).
Effects of cell volume regulating osmolytes on glycerol 3-phosphate binding to triosephosphate isomerase.
  Biochemistry, 46, 10055-10062.  
17444518 R.Sathyapriya, and S.Vishveshwara (2007).
Structure networks of E. coli glutaminyl-tRNA synthetase: effects of ligand binding.
  Proteins, 68, 541-550.  
17444661 T.L.Amyes, and J.P.Richard (2007).
Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion.
  Biochemistry, 46, 5841-5854.  
15890082 D.La, and D.R.Livesay (2005).
Predicting functional sites with an automated algorithm suitable for heterogeneous datasets.
  BMC Bioinformatics, 6, 116.  
15840824 D.R.Livesay, and D.La (2005).
The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins.
  Protein Sci, 14, 1158-1170.  
12509510 G.Jogl, S.Rozovsky, A.E.McDermott, and L.Tong (2003).
Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.
  Proc Natl Acad Sci U S A, 100, 50-55.
PDB codes: 1ney 1nf0
12522213 I.Kursula, and R.K.Wierenga (2003).
Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution.
  J Biol Chem, 278, 9544-9551.
PDB code: 1n55
13679361 K.Hamada, H.Ago, M.Sugahara, Y.Nodake, S.Kuramitsu, and M.Miyano (2003).
Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi).
  J Biol Chem, 278, 49183-49190.
PDB codes: 1uj4 1uj5 1uj6
12581214 P.Pattanaik, G.Ravindra, C.Sengupta, K.Maithal, P.Balaram, and H.Balaram (2003).
Unusual fluorescence of W168 in Plasmodium falciparum triosephosphate isomerase, probed by single-tryptophan mutants.
  Eur J Biochem, 270, 745-756.  
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.