Biological Assembly 1  

 3D View: Structure

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: 79.12 kDa 
• Atom Count: 5753 
• Residue Count: 726 
• Unique protein chains: 1

1CM7

3-ISOPROPYLMALATE DEHYDROGENASE FROM ESCHERICHIA COLI

• DOI: 10.2210/pdb1CM7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1999-05-17 Released: 1999-07-01 
• Deposition Author(s): Wallon, G., Kryger, G., Lovett, S.T., Oshima, T., Ringe, D., Petsko, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.245 
• R-Value Work: 0.173 

Literature

Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus.

Wallon, G., Kryger, G., Lovett, S.T., Oshima, T., Ringe, D., Petsko, G.A.

(1997) J Mol Biol 266: 1016-1031

• PubMed: 9086278 
• DOI: 10.1006/jmbi.1996.0797
• Primary Citation of Related Structures:  
  1WAL, 1CM7, 1CNZ


• PubMed Abstract: 
  

The basis of protein stability has been investigated by the structural comparison of themophilic enzymes with their mesophilic counterparts. A number of characteristics have been found that can contribute to the stabilization of thermophilic proteins, but no one is uniquely capable of imparting thermostability. The crystal structure of 3-isopropylmalate dehydrogenase (IPMDH) from the mesophiles Escherichia coli and Salmonella typhimurium have been determined by the method of molecular replacement using the known structure of the homologous Thermus thermophilus enzyme. The structure of the E. coli enzyme was refined at a resolution of 2.1 A to an R-factor of 17.3%, that of the S. typhimurium enzyme at 1.7 A resolution to an R-factor of 19.8%. The three structures were compared to elucidate the basis of the higher thermostability of the T. thermophilus enzyme. A mutant that created a cavity in the hydrophobic core of the thermophilic enzyme was designed to investigate the importance of packing density for thermostability. The structure of this mutant was analyzed. The main stabilizing features in the thermophilic enzyme are an increased number of salt bridges, additional hydrogen bonds, a proportionately larger and more hydrophobic subunit interface, shortened N and C termini and a larger number of proline residues. The mutation in the hydrophobic core of T. thermophilus IPMDH resulted in a cavity of 32 A3, but no significant effect on the activity and thermostability of the mutant was observed.

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Organizational Affiliation: 

Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02254-9910, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (3-ISOPROPYLMALATE DEHYDROGENASE)	A, B	363	Escherichia coli	Mutation(s): 0  Gene Names: leuB EC: 1.1.1.85
Find proteins for P30125 (Escherichia coli (strain K12)) Explore P30125  Go to UniProtKB:  P30125

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.245 
• R-Value Work: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.8	α = 90
b = 86.9	β = 93.3
c = 83.7	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-17 
• Released Date: 1999-07-01 
Deposition Author(s): Wallon, G., Kryger, G., Lovett, S.T., Oshima, T., Ringe, D., Petsko, G.A.

Revision History 

• Version 1.0: 1999-07-01
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description