1E1C

METHYLMALONYL-COA MUTASE H244A Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.219 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Protection of Radical Intermediates at the Active Site of Adenosylcobalamin-Dependent Methylmalonyl-Coa Mutase

Thoma, N.H.Evans, P.R.Leadlay, P.F.

(2000) Biochemistry 39: 9213

  • DOI: https://doi.org/10.1021/bi0004302
  • Primary Citation of Related Structures:  
    1E1C

  • PubMed Abstract: 

    Adenosylcobalamin-dependent methylmalonyl-CoA mutase catalyzes the interconversion of methylmalonyl-CoA and succinyl-CoA via radical intermediates generated by substrate-induced homolysis of the coenzyme carbon-cobalt bond. From the structure of methylmalonyl-CoA mutase it is evident that the deeply buried active site is completely shielded from solvent with only a few polar contacts made between the protein and the substrate. Site-directed mutants of amino acid His244, a residue close to the inferred site of radical chemistry, were engineered to investigate its role in catalysis. Two mutants, His244Ala and His244Gln, were characterized using kinetic and spectroscopic techniques. These results confirmed that His244 is not an essential residue. However, compared with that of the wild type, k(cat) was lowered by 10(2)- and 10(3)-fold for the His244Gln and His244Ala mutants, respectively, while the K(m) for succinyl-CoA was essentially unchanged in both cases. The primary kinetic tritium isotope effect (k(H)/k(T)) for the His244Gln mutant was 1.5 +/- 0.3, and tritium partitioning was now found to be dependent on the substrate used to initiate the reaction, indicating that the rearrangement of the substrate radical to the product radical was extremely slow. The His244Ala mutant underwent inactivation under aerobic conditions at a rate between 1 and 10% of the initial rate of turnover. The crystal structure of the His244Ala mutant, determined at 2.6 A resolution, indicated that the mutant enzyme is unaltered except for a cavity in the active site which is occupied by an ordered water molecule. Molecular oxygen reaching this cavity may lead directly to inactivation. These results indicate that His244 assists directly in the unusual carbon skeleton rearrangement and that alterations in this residue substantially lower the protection of reactive radical intermediates during catalysis.


  • Organizational Affiliation

    Cambridge Centre for Molecular Recognition and Department of Biochemistry, University of Cambridge, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHYLMALONYL-COA MUTASE ALPHA CHAIN
A, C
727Propionibacterium freudenreichii subsp. shermaniiMutation(s): 1 
EC: 5.4.99.2
UniProt
Find proteins for P11653 (Propionibacterium freudenreichii subsp. shermanii)
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Go to UniProtKB:  P11653
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11653
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
METHYLMALONYL-COA MUTASE BETA CHAIN
B, D
637Propionibacterium freudenreichii subsp. shermaniiMutation(s): 0 
EC: 5.4.99.2
UniProt
Find proteins for P11652 (Propionibacterium freudenreichii subsp. shermanii)
Explore P11652 
Go to UniProtKB:  P11652
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11652
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.398α = 90
b = 161.829β = 90
c = 166.949γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-07
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Data collection, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2017-06-28
    Changes: Data collection
  • Version 1.3: 2023-12-06
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description