4KS9 | pdb_00004ks9

Crystal Structure of Malonyl-CoA decarboxylase (Rmet_2797) from Cupriavidus metallidurans, Northeast Structural Genomics Consortium Target CrR76


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.286 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4KS9

This is version 1.4 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: https://doi.org/10.1016/j.str.2013.05.001
  • Primary Citation Related Structures: 
    2YGW, 4KS9, 4KSA, 4KSF

  • 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 2.3 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.

Macromolecule Content 

  • Total Structure Weight: 96.11 kDa 
  • Atom Count: 6,535 
  • Modeled Residue Count: 787 
  • Deposited Residue Count: 856 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Malonyl-CoA decarboxylase
A, B
428Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: matARmet_2797Rmet_2797 (MCD)
EC: 4.1.1.9
UniProt
Find proteins for Q1LJK6 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LJK6 
Go to UniProtKB:  Q1LJK6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1LJK6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.286 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.015α = 90
b = 69.392β = 103.8
c = 74.362γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description