6WFI

Methylmalonyl-CoA epimerase in complex with 2-nitronate-propionyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
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
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KFV (Subject of Investigation/LOI)
Query on KFV

Download Ideal Coordinates CCD File 
G [auth A][1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium
C24 H38 N8 O19 P3 S
BLWVPDVKNPMTPY-ZSJPKINUSA-N
PEG
Query on PEG

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F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CO
Query on CO

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B [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.837α = 90
b = 68.837β = 90
c = 103.37γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling
ARP/wARPmodel building
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

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