6N93

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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.


Macromolecules
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
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KGA
Query on KGA

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
K [auth C]
M [auth C]
P [auth D]
G [auth A],
J [auth B],
K [auth C],
M [auth C],
P [auth D],
R [auth E],
S [auth E],
T [auth F],
V [auth F]
[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-propan-2-ylidene]-bis(oxidanidyl)azanium
C24 H38 N8 O20 P3
JOSUZLPXQGIVES-ZSJPKINUSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
N [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
KG7
Query on KG7

Download Ideal Coordinates CCD File 
W [auth F](2E)-2-(hydroxyimino)propanoic acid
C3 H5 N O3
MVGBKLTYYAYYGY-DUXPYHPUSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth D],
X [auth F]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
NI
Query on NI

Download Ideal Coordinates CCD File 
H [auth A],
O [auth D],
U [auth F]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
L [auth C]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.179α = 90
b = 114.653β = 90
c = 194.554γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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, Derived calculations, Refinement description