Biological Assembly 1  

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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: 54519.77 
• Atom Count: 3781 
• Residue Count: 504 
• Unique protein chains: 1

1BTM

TRIOSEPHOSPHATE ISOMERASE (TIM) COMPLEXED WITH 2-PHOSPHOGLYCOLIC ACID

• DOI: 10.2210/pdb1BTM/pdb

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


• Deposited: 1995-11-11 Released: 1996-04-03 
• 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: 2.8 Å
• R-Value Work: 0.176 

Literature

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.

Delboni, L.F., Mande, S.C., Rentier-Delrue, F., Mainfroid, V., Turley, S., Vellieux, F.M., Martial, J.A., Hol, W.G.

(1995) Protein Sci. 4: 2594-2604

• PubMed: 8580851 
• DOI: 10.1002/pro.5560041217


• PubMed Abstract: 
  

The structure of the thermostable triosephosphate isomerase (TIM) from Bacillus stearothermophilus complexed with the competitive inhibitor 2-phosphoglycolate was determined by X-ray crystallography to a resolution of 2.8 A. The structure was solved by molecular replacement using XPLOR. Twofold averaging and solvent flattening was applied to improve the quality of the map. Active sites in both the subunits are occupied by the inhibitor and the flexible loop adopts the "closed" conformation in either subunit. The crystallographic R-factor is 17.6% with good geometry. The two subunits have an RMS deviation of 0.29 A for 248 C alpha atoms and have average temperature factors of 18.9 and 15.9 A2, respectively. In both subunits, the active site Lys 10 adopts an unusual phi, psi combination. A comparison between the six known thermophilic and mesophilic TIM structures was conducted in order to understand the higher stability of B. stearothermophilus TIM. Although the ratio Arg/(Arg+Lys) is higher in B. stearothermophilus TIM, the structure comparisons do not directly correlate this higher ratio to the better stability of the B. stearothermophilus enzyme. A higher number of prolines contributes to the higher stability of B. stearothermophilus TIM. Analysis of the known TIM sequences points out that the replacement of a structurally crucial asparagine by a histidine at the interface of monomers, thus avoiding the risk of deamidation and thereby introducing a negative charge at the interface, may be one of the factors for adaptability at higher temperatures in the TIM family. Analysis of buried cavities and the areas lining these cavities also contributes to the greater thermal stability of the B. stearothermophilus enzyme. However, the most outstanding result of the structure comparisons appears to point to the hydrophobic stabilization of dimer formation by burying the largest amount of hydrophobic surface area in B. stearothermophilus TIM compared to all five other known TIM structures.

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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.J.,Martial, J.A.
  (1995) J.Mol.Biol. 229: 85




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Organizational Affiliation: 

Department of Biological Structure, School of Medicine, University of Washington, Seattle 98195, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRIOSEPHOSPHATE ISOMERASE	A, B	252	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: tpiA (tpi) EC: 5.3.1.1
Find proteins for P00943 (Geobacillus stearothermophilus) Go to UniProtKB:  P00943

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Work: 0.176 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 78.610	α = 90.00
b = 108.420	β = 90.00
c = 71.210	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement
X-PLOR	phasing
X-PLOR	model building
XENGEN	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-11-11 
• Released Date: 1996-04-03 
• Deposition Author(s): Delboni, L.F., Mande, S.C., Hol, W.G.J.

Revision History 

• Version 1.0: 1996-04-03
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-04-04
  Type: Data collection, Other