Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.28 kDa 
• Atom Count: 3811 
• Modelled Residue Count: 502 
• Deposited Residue Count: 504 
• Unique protein chains: 1

2BTM

DOES THE HIS12-LYS13 PAIR PLAY A ROLE IN THE ADAPTATION OF THERMOPHILIC TIMS TO HIGH TEMPERATURES?

• PDB DOI: 10.2210/pdb2BTM/pdb

• Classification: ISOMERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-01-04 Released: 1999-01-13 
• Deposition Author(s): Delboni, L.F., Mande, S.C., Hol, W.G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.220 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 

Literature

Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures.

Alvarez, M., Wouters, J., Maes, D., Mainfroid, V., Rentier-Delrue, F., Wyns, L., Depiereux, E., Martial, J.A.

(1999) J Biol Chem 274: 19181-19187

• PubMed: 10383424 
• DOI: 10.1074/jbc.274.27.19181
• Primary Citation of Related Structures:  
  2BTM


• PubMed Abstract: 
  

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.

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Related Citations: 

• Cloning and Overexpression of the Triosephosphate Isomerase Genes from Psychrophilic and Thermophilic Bacteria. Structural Comparison of the Predicted Protein Sequences
  Rentier-Delrue, F., Mande, S.C., Moyens, S., Terpstra, P., Mainfroid, V., Goraj, K., Lion, M., Hol, W.G., Martial, J.A.
  (1993) J Mol Biol 229: 85

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Organizational Affiliation: 

Laboratoire de Biologie Moléculaire et de Génie Génétique, Université de Liège, B6, Sart Tilman, B4000 Liège, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TRIOSEPHOSPHATE ISOMERASE)	A, B	252	Geobacillus stearothermophilus	Mutation(s): 3  Gene Names: tpiA, tpi EC: 5.3.1.1
UniProt
Find proteins for P00943 (Geobacillus stearothermophilus) Explore P00943  Go to UniProtKB:  P00943

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGA	C [auth A], D [auth B]	2-PHOSPHOGLYCOLIC ACID C2 H5 O6 P ASCFNMCAHFUBCO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.220 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.132	α = 90
b = 107.913	β = 90
c = 70.98	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-04 
• Released Date: 1999-01-13 
Deposition Author(s): Delboni, L.F., Mande, S.C., Hol, W.G.J.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations