Methylmalonyl-CoA epimerase in complex with methylmalonyl-CoA and NH4+

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

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This is version 1.3 of the entry. See complete history


Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase.

Stunkard, L.M.Benjamin, A.B.Bower, J.B.Huth, T.J.Lohman, J.R.

(2022) Chembiochem 23: e202100487-e202100487

  • DOI: https://doi.org/10.1002/cbic.202100487
  • Primary Citation of Related Structures:  
    6WF6, 6WF7, 6WFH, 6WFI

  • PubMed Abstract: 

    Methylmalonyl-CoA epimerase (MMCE) is proposed to use general acid-base catalysis, but the proposed catalytic glutamic acids are highly asymmetrical in the active site unlike many other racemases. To gain insight into the puzzling relationships between catalytic mechanism, structure, and substrate preference, we solved Streptomyces coelicolor MMCE structures with substrate or 2-nitropropionyl-CoA, an intermediate/transition state analogue. Both ligand bound structures have a planar methylmalonate/2-nitropropionyl moiety indicating a deprotonated C2 with ≥4 Å distances to either catalytic acid. Both glutamates interact with the carboxylate/nitro group, either directly or through other residues. This suggests the proposed catalytic acids sequentially catalyze proton shifts between C2 and carboxylate of the substrate with an enolate intermediate. In addition, our structures provide a platform to design mutations for expanding substrate scope to support combinatorial biosynthesis.

  • Organizational Affiliation

    Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylmalonyl-CoA epimerase146Streptomyces coelicolor A3(2)Mutation(s): 1 
Gene Names: SCO5398
Find proteins for Q9L2C2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9L2C2 
Go to UniProtKB:  Q9L2C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L2C2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.537α = 90
b = 68.537β = 90
c = 103.15γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
ARP/wARPmodel building
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2022-01-26
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description