4REQ

Methylmalonyl-COA Mutase substrate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.232 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism.

Mancia, F.Evans, P.R.

(1998) Structure 6: 711-720

  • DOI: https://doi.org/10.1016/s0969-2126(98)00073-2
  • Primary Citation of Related Structures:  
    2REQ, 3REQ, 4REQ

  • PubMed Abstract: 

    Methylmalonyl CoA mutase catalyses the interconversion of succinyl CoA and methylmalonyl CoA via a free radical mechanism. The enzyme belongs to a family of enzymes that catalyse intramolecular rearrangement reactions in which a group and a hydrogen atom on adjacent carbons are exchanged. These enzymes use the cofactor adenosylcobalamin (coenzyme B12) which breaks to form an adenosyl radical, thus initiating the reaction. Determination of the structure of substrate-free methylmalonyl CoA mutase was initiated to provide further insight into the mechanism of radical formation. We report here two structures of methylmalonyl CoA mutase from Propionibacterium shermanii. The first structure is of the enzyme in a nonproductive complex with CoA at 2.5 A resolution. This structure serves as a model for the substrate-free conformation of the enzyme, as it is very similar to the second much poorer 2.7 A resolution structure derived from a truly substrate-free crystal. The true substrate-free structure also shows the adenosyl group bound to the cobalt atom. Comparison of this structure with that of the previously reported complex of the enzyme with a substrate analogue shows that major conformational changes occur upon substrate binding. The substrate-binding site of the enzyme is located within a (beta alpha)8 TIM-barrel domain. In the absence of substrate, this TIM-barrel domain is split apart and the active site is accessible to solvent. When substrate binds, the barrel closes up with the substrate along its axis and the active site becomes completely buried. The closure of the active-site cavity upon substrate binding displaces the adenosyl group of the cofactor from the central cobalt atom into the active-site cavity. This triggers the formation of the free radical that initiates the rearrangement reaction. The TIM-barrel domain is substantially different from all others yet reported: in its unliganded form it is broken open, exposing the small hydrophilic sidechains which fill the centre. The typical barrel structure is only formed when substrate is bound.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology Hills Road, Cambridge, CB2 2QH, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METHYLMALONYL-COA MUTASE
A, C
727Propionibacterium freudenreichii subsp. shermaniiMutation(s): 0 
EC: 5.4.99.2
UniProt
Find proteins for P11653 (Propionibacterium freudenreichii subsp. shermanii)
Explore P11653 
Go to UniProtKB:  P11653
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11653
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
METHYLMALONYL-COA MUTASE
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12

Download Ideal Coordinates CCD File 
E [auth A],
K [auth C]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
SCA
Query on SCA

Download Ideal Coordinates CCD File 
F [auth A],
L [auth C]
SUCCINYL-COENZYME A
C25 H40 N7 O19 P3 S
VNOYUJKHFWYWIR-ITIYDSSPSA-N
MCA
Query on MCA

Download Ideal Coordinates CCD File 
G [auth A],
N [auth C]
METHYLMALONYL-COENZYME A
C25 H40 N7 O19 P3 S
MZFOKIKEPGUZEN-AGCMQPJKSA-N
5AD
Query on 5AD

Download Ideal Coordinates CCD File 
H [auth A],
M [auth C]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
O [auth C],
P [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.13α = 90
b = 160.9β = 104.64
c = 88.5γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2012-10-24
    Changes: Non-polymer description
  • Version 1.4: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-05-22
    Changes: Data collection