2REQ

METHYLMALONYL-COA MUTASE, NON-PRODUCTIVE COA COMPLEX, IN OPEN CONFORMATION REPRESENTING SUBSTRATE-FREE STATE

• PDB DOI: https://doi.org/10.2210/pdb2REQ/pdb

• Classification: ISOMERASE
• Organism(s): Propionibacterium freudenreichii subsp. shermanii
• Mutation(s): No 


• Deposited: 1997-09-22 Released: 1998-01-28 
• Deposition Author(s): Evans, P.R., Mancia, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.325 
• R-Value Work: 0.259 

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

• PubMed: 9655823 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 303.33 kDa 
• Atom Count: 21,240 
• Modelled Residue Count: 2,688 
• Deposited Residue Count: 2,728 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYLMALONYL-COA MUTASE	A, C	727	Propionibacterium freudenreichii subsp. shermanii	Mutation(s): 0  Gene Names: MUTA, MUTB EC: 5.4.99.2
UniProt
Find proteins for P11653 (Propionibacterium freudenreichii subsp. shermanii) Explore P11653  Go to UniProtKB:  P11653

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYLMALONYL-COA MUTASE	B, D	637	Propionibacterium freudenreichii subsp. shermanii	Mutation(s): 0  Gene Names: MUTA, MUTB EC: 5.4.99.2
UniProt
Find proteins for P11652 (Propionibacterium freudenreichii subsp. shermanii) Explore P11652  Go to UniProtKB:  P11652

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12	F [auth A], H [auth C]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
COA	E [auth A], G [auth C]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.325 
• R-Value Work: 0.259 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.95	α = 90
b = 162.06	β = 108.75
c = 104.2	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Evans, P.R., Mancia, F.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: 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