PDBsum entry 2btm

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Isomerase PDB id
Protein chains
251 a.a. *
PGA ×2
Waters ×121
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Does the his12-lys13 pair play a role in the adaptation of thermophilic tims to high temperatures?
Structure: Protein (triosephosphate isomerase). Chain: a, b. Synonym: tim. Engineered: yes. Mutation: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
2.40Å     R-factor:   0.176     R-free:   0.220
Authors: L.F.Delboni,S.C.Mande,W.G.J.Hol
Key ref:
M.Alvarez et al. (1999). Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures. J Biol Chem, 274, 19181-19187. PubMed id: 10383424 DOI: 10.1074/jbc.274.27.19181
04-Jan-99     Release date:   13-Jan-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00943  (TPIS_GEOSE) -  Triosephosphate isomerase
253 a.a.
251 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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 72.00% 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   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  


    Added reference    
DOI no: 10.1074/jbc.274.27.19181 J Biol Chem 274:19181-19187 (1999)
PubMed id: 10383424  
Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures.
M.Alvarez, J.Wouters, D.Maes, V.Mainfroid, F.Rentier-Delrue, L.Wyns, E.Depiereux, J.A.Martial.
The thermophilic triose-phosphate isomerases (TIMs) of Bacillus stearothermophilus (bTIM) and Thermotoga maritima (tTIM) have been found to possess a His12-Lys13 pair instead of the Asn12-Gly13 pair normally present in mesophilic TIMs. His12 in bTIM was proposed to prevent deamidation at high temperature, while the precise role of Lys13 is unknown. To investigate the role of the His12 and Lys13 pair in the enzyme's thermoadaptation, we reintroduced the "mesophilic residues" Asn and Gly into both thermophilic TIMs. Neither double mutant displayed diminished structural stability, but the bTIM double mutant showed drastically reduced catalytic activity. No similar behavior was observed with the tTIM double mutant, suggesting that the presence of the His12 and Lys13 cannot be systematically correlated to thermoadaptation in TIMs. We determined the crystal structure of the bTIM double mutant complexed with 2-phosphoglycolate to 2.4-A resolution. A molecular dynamics simulation showed that upon substitution of Lys13 to Gly an increase of the flexibility of loop 1 is observed, causing an incorrect orientation of the catalytic Lys10. This suggests that Lys13 in bTIM plays a crucial role in the functional adaptation of this enzyme to high temperature. Analysis of bTIM single mutants supports this assumption.
  Selected figure(s)  
Figure 2.
Fig. 2. X-ray structure of H12N/K13G bTIM. The C trace of each subunit is represented (green, subunit A; blue, subunit B). One molecule of 2-phosphoglycolate (yellow) occupies the active site of each subunit. The mutated region is represented in red.
Figure 4.
Fig. 4. Molecular geometries of loop 1 generated by molecular dynamics simulation. Residues 9-13 from loop 1 as well as Leu^237 and 2-phosphoglycolate (2-PG) are shown. 20 geometries obtained for bTIM (A), H12N/K13G bTIM (B), H12N bTIM (C), K13G bTIM (D), and tTIM (E) are represented.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 19181-19187) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19342791 S.Mukherjee, D.Dutta, B.Saha, and A.K.Das (2009).
Expression, purification, crystallization and preliminary X-ray diffraction studies of triosephosphate isomerase from methicillin-resistant Staphylococcus aureus (MRSA252).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 398-401.  
15175111 S.Mahato, D.De, D.Dutta, M.Kundu, S.Bhattacharya, M.T.Schiavone, and S.K.Bhattacharya (2004).
Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate.
  Microb Cell Fact, 3, 7.  
10957646 J.Wouters, and D.Maes (2000).
Identification of a potential metal cation-pi binding site in the structure of a thermophilic Bacillus stearothermophilus triosephosphate isomerase mutant.
  Acta Crystallogr D Biol Crystallogr, 56, 1201-1203.  
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.