2YGW

Crystal structure of human MCD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

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

  • DOI: 10.1016/j.str.2013.05.001
  • Primary Citation of Related Structures:  
    4KS9, 4KSF, 4KSA, 2YGW

  • 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, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL AB460Homo sapiensMutation(s): 5 
Gene Names: MLYCD
EC: 4.1.1.9
Find proteins for O95822 (Homo sapiens)
Explore O95822 
Go to UniProtKB:  O95822
NIH Common Fund Data Resources
PHAROS:  O95822
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
A, B
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.627α = 90
b = 175.342β = 90
c = 151.756γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2013-07-17
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Database references, Structure summary