Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

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Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies.

Stunkard, L.M.Dixon, A.D.Huth, T.J.Lohman, J.R.

(2019) J Am Chem Soc 141: 5121-5124

  • DOI: https://doi.org/10.1021/jacs.9b00650
  • Primary Citation of Related Structures:  
    6N92, 6N93, 6N94, 6N95, 6N96, 6N97

  • PubMed Abstract: 

    Malonyl-thioesters are reactive centers of malonyl-CoA and malonyl- S-acyl carrier protein, essential to fatty acid, polyketide and various specialized metabolite biosynthesis. Enzymes that create or use malonyl-thioesters spontaneously hydrolyze or decarboxylate reactants on the crystallographic time frame preventing determination of structure-function relationships. To address this problem, we have synthesized a panel of methylmalonyl-CoA analogs with the carboxylate represented by a sulfonate or nitro and the thioester retained or represented by an ester or amide. Structures of Escherichia coli methylmalonyl-CoA decarboxylase in complex with our analogs affords insight into substrate binding and the catalytic mechanism. Counterintuitively, the negatively charged sulfonate and nitronate functional groups of our analogs bind in an active site hydrophobic pocket. Upon decarboxylation the enolate intermediate is protonated by a histidine preventing CO 2 -enolate recombination, yielding propionyl-CoA. Activity assays support a histidine catalytic acid and reveal the enzyme displays significant hydrolysis activity. Our structures also provide insight into this hydrolysis activity. Our analogs inhibit decarboxylation/hydrolysis activity with low micromolar K i values. This study sets precedents for using malonyl-CoA analogs with carboxyate isosteres to study the complicated structure-function relationships of acyl-CoA carboxylases, trans-carboxytransferases, malonyltransferases and β-ketoacylsynthases.

  • Organizational Affiliation

    Department of Biochemistry , Purdue University , West Lafayette , Indiana 47907 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylmalonyl-CoA decarboxylase
A, B, C, D, E
A, B, C, D, E, F
261Escherichia coli K-12Mutation(s): 1 
Gene Names: scpBmmcDygfGb2919JW2886
EC: 4.1.1
Find proteins for P52045 (Escherichia coli (strain K12))
Explore P52045 
Go to UniProtKB:  P52045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52045
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO5

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
O [auth D]
R [auth E]
H [auth A],
J [auth B],
L [auth C],
O [auth D],
R [auth E],
T [auth F]
(2~{R})-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]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid
C24 H40 N7 O21 P3 S
Query on LCV

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth C]
N [auth D]
G [auth A],
I [auth B],
K [auth C],
M [auth C],
N [auth D],
Q [auth E],
S [auth F],
U [auth F]
(2~{S})-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]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid
C24 H40 N7 O21 P3 S
Query on IMD

Download Ideal Coordinates CCD File 
C3 H5 N2
Binding Affinity Annotations 
IDSourceBinding Affinity
SO5 Binding MOAD:  6N96 Ki: 3800 (nM) from 1 assay(s)
LCV Binding MOAD:  6N96 Ki: 3800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.148α = 90
b = 114.66β = 90
c = 192.705γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description