PDBsum entry 1amk

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Gluconeogenesis PDB id
Protein chain
250 a.a. *
Waters ×112
* Residue conservation analysis
PDB id:
Name: Gluconeogenesis
Title: Leishmania mexicana triose phosphate isomerase
Structure: Triose phosphate isomerase. Chain: a. Engineered: yes
Source: Leishmania mexicana. Organism_taxid: 5665
Biol. unit: Homo-Dimer (from PDB file)
1.83Å     R-factor:   0.107    
Authors: J.C.Williams,R.Wierenga
Key ref: J.C.Williams et al. (1999). Structural and mutagenesis studies of leishmania triosephosphate isomerase: a point mutation can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power. Protein Eng, 12, 243-250. PubMed id: 10235625
17-Jun-97     Release date:   17-Dec-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P48499  (TPIS_LEIME) -  Triosephosphate isomerase
251 a.a.
250 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = PGA)
matches with 72.73% similarity
= 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    
Protein Eng 12:243-250 (1999)
PubMed id: 10235625  
Structural and mutagenesis studies of leishmania triosephosphate isomerase: a point mutation can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power.
J.C.Williams, J.P.Zeelen, G.Neubauer, G.Vriend, J.Backmann, P.A.Michels, A.M.Lambeir, R.K.Wierenga.
The dimeric enzyme triosephosphate isomerase (TIM) has a very tight and rigid dimer interface. At this interface a critical hydrogen bond is formed between the main chain oxygen atom of the catalytic residue Lys13 and the completely buried side chain of Gln65 (of the same subunit). The sequence of Leishmania mexicana TIM, closely related to Trypanosoma brucei TIM (68% sequence identity), shows that this highly conserved glutamine has been replaced by a glutamate. Therefore, the 1.8 A crystal structure of leishmania TIM (at pH 5.9) was determined. The comparison with the structure of trypanosomal TIM shows no rearrangements in the vicinity of Glu65, suggesting that its side chain is protonated and is hydrogen bonded to the main chain oxygen of Lys13. Ionization of this glutamic acid side chain causes a pH-dependent decrease in the thermal stability of leishmania TIM. The presence of this glutamate, also in its protonated state, disrupts to some extent the conserved hydrogen bond network, as seen in all other TIMs. Restoration of the hydrogen bonding network by its mutation to glutamine in the E65Q variant of leishmania TIM results in much higher stability; for example, at pH 7, the apparent melting temperature increases by 26 degrees C (57 degrees C for leishmania TIM to 83 degrees C for the E65Q variant). This mutation does not affect the kinetic properties, showing that even point mutations can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power at the mesophilic temperature.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20694739 R.K.Wierenga, E.G.Kapetaniou, and R.Venkatesan (2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
  Cell Mol Life Sci, 67, 3961-3982.  
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.  
18219118 M.Alahuhta, M.G.Casteleijn, P.Neubauer, and R.K.Wierenga (2008).
Structural studies show that the A178L mutation in the C-terminal hinge of the catalytic loop-6 of triosephosphate isomerase (TIM) induces a closed-like conformation in dimeric and monomeric TIM.
  Acta Crystallogr D Biol Crystallogr, 64, 178-188.
PDB codes: 2v0t 2v2c 2v2d 2v2h
17404726 M.Leisola, and O.Turunen (2007).
Protein engineering: opportunities and challenges.
  Appl Microbiol Biotechnol, 75, 1225-1232.  
17242514 P.Gayathri, M.Banerjee, A.Vijayalakshmi, S.Azeez, H.Balaram, P.Balaram, and M.R.Murthy (2007).
Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii.
  Acta Crystallogr D Biol Crystallogr, 63, 206-220.
PDB code: 2h6r
17919319 R.R.Gabdoulline, M.Stein, and R.C.Wade (2007).
qPIPSA: relating enzymatic kinetic parameters and interaction fields.
  BMC Bioinformatics, 8, 373.  
17989778 V.Olivares-Illana, A.Rodríguez-Romero, I.Becker, M.Berzunza, J.García, R.Pérez-Montfort, N.Cabrera, F.López-Calahorra, Gómez-Puyou, and A.Gómez-Puyou (2007).
Perturbation of the Dimer Interface of Triosephosphate Isomerase and its Effect on Trypanosoma cruzi.
  PLoS Negl Trop Dis, 1, e1.
PDB code: 2oma
15857781 B.Höcker (2005).
Directed evolution of (betaalpha)(8)-barrel enzymes.
  Biomol Eng, 22, 31-38.  
15857780 V.G.Eijsink, S.Gåseidnes, T.V.Borchert, and B.van den Burg (2005).
Directed evolution of enzyme stability.
  Biomol Eng, 22, 21-30.  
12323355 B.van den Burg, and V.G.Eijsink (2002).
Selection of mutations for increased protein stability.
  Curr Opin Biotechnol, 13, 333-337.  
12223057 K.A.Werbovetz (2002).
Promising therapeutic targets for antileishmanial drugs.
  Expert Opin Ther Targets, 6, 407-422.  
11551466 B.Höcker, C.Jürgens, M.Wilmanns, and R.Sterner (2001).
Stability, catalytic versatility and evolution of the (beta alpha)(8)-barrel fold.
  Curr Opin Biotechnol, 12, 376-381.  
11512153 C.L.Verlinde, V.Hannaert, C.Blonski, M.Willson, J.J.Périé, L.A.Fothergill-Gilmore, F.R.Opperdoes, M.H.Gelb, W.G.Hol, and P.A.Michels (2001).
Glycolysis as a target for the design of new anti-trypanosome drugs.
  Drug Resist Updat, 4, 50-65.  
11166567 F.H.Arnold, P.L.Wintrode, K.Miyazaki, and A.Gershenson (2001).
How enzymes adapt: lessons from directed evolution.
  Trends Biochem Sci, 26, 100-106.  
11589711 I.Kursula, S.Partanen, A.M.Lambeir, D.M.Antonov, K.Augustyns, and R.K.Wierenga (2001).
Structural determinants for ligand binding and catalysis of triosephosphate isomerase.
  Eur J Biochem, 268, 5189-5196.
PDB code: 1if2
11093265 W.S.Valdar, and J.M.Thornton (2001).
Protein-protein interfaces: analysis of amino acid conservation in homodimers.
  Proteins, 42, 108-124.  
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
11080642 T.Kajander, P.C.Kahn, S.H.Passila, D.C.Cohen, L.Lehtiö, W.Adolfsen, J.Warwicker, U.Schell, and A.Goldman (2000).
Buried charged surface in proteins.
  Structure, 8, 1203-1214.
PDB code: 1f9c
10591103 D.Maes, J.P.Zeelen, N.Thanki, N.Beaucamp, M.Alvarez, M.H.Thi, J.Backmann, J.A.Martial, L.Wyns, R.Jaenicke, and R.K.Wierenga (1999).
The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
  Proteins, 37, 441-453.
PDB code: 1b9b
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.