4KSA

Crystal Structure of Malonyl-CoA decarboxylase from Rhodopseudomonas palustris, Northeast Structural Genomics Consortium Target RpR127


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of malonyl-coenzyme a decarboxylase provide insights into its catalytic mechanism and disease-causing mutations.

Froese, D.S.Forouhar, F.Tran, T.H.Vollmar, M.Kim, Y.S.Lew, S.Neely, H.Seetharaman, J.Shen, Y.Xiao, R.Acton, T.B.Everett, J.K.Cannone, G.Puranik, S.Savitsky, P.Krojer, T.Pilka, E.S.Kiyani, W.Lee, W.H.Marsden, B.D.von Delft, F.Allerston, C.K.Spagnolo, L.Gileadi, O.Montelione, G.T.Oppermann, U.Yue, W.W.Tong, L.

(2013) Structure 21: 1182-1192

  • DOI: 10.1016/j.str.2013.05.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human ...

    Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malonyl-CoA decarboxylase
A, B, C, D
453Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)Mutation(s): 0 
Gene Names: MCD (MLYCD)
EC: 4.1.1.9
Find proteins for Q6NCB2 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Go to UniProtKB:  Q6NCB2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 141.505α = 90.00
b = 159.765β = 90.00
c = 108.622γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
SnBphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2013-07-24
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description