2C2N

Structure of human mitochondrial malonyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural Basis for Different Specificities of Acyltransferases Associated with the Human Cytosolic and Mitochondrial Fatty Acid Synthases.

Bunkoczi, G.Misquitta, S.Wu, X.Lee, W.H.Rojkova, A.Kochan, G.Kavanagh, K.L.Oppermann, U.Smith, S.

(2009) Chem Biol 16: 667

  • DOI: https://doi.org/10.1016/j.chembiol.2009.04.011
  • Primary Citation of Related Structures:  
    2C2N, 2JFD

  • PubMed Abstract: 

    Animals employ two systems for the de novo biosynthesis of fatty acids: a megasynthase complex in the cytosol (type I) that produces mainly palmitate, and an ensemble of freestanding enzymes in the mitochondria (type II) that produces mainly octanoyl moieties. The acyltransferases responsible for initiation of fatty acid biosynthesis in the two compartments are distinguished by their different substrate specificities: the type I enzyme transfers both the acetyl primer and the malonyl chain extender, whereas the type II enzyme is responsible for translocation of only the malonyl substrate. Crystal structures for the type I and II enzymes, supported by in silico substrate docking studies and mutagenesis experiments that alter their respective specificities, reveal that, although the two enzymes adopt a similar overall fold, subtle differences at their catalytic centers account for their different specificities.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE
A, B
339Homo sapiensMutation(s): 0 
EC: 2.3.1.39
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVS2 (Homo sapiens)
Explore Q8IVS2 
Go to UniProtKB:  Q8IVS2
PHAROS:  Q8IVS2
GTEx:  ENSG00000100294 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IVS2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AE4
Query on AE4

Download Ideal Coordinates CCD File 
I [auth A]3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL
C12 H26 O6
NJRFAMBTWHGSDE-UHFFFAOYSA-N
AE3
Query on AE3

Download Ideal Coordinates CCD File 
N [auth B]2-(2-ETHOXYETHOXY)ETHANOL
C6 H14 O3
XXJWXESWEXIICW-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DXE
Query on DXE

Download Ideal Coordinates CCD File 
J [auth A]1,2-DIMETHOXYETHANE
C4 H10 O2
XTHFKEDIFFGKHM-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.573α = 90
b = 84.828β = 93.43
c = 74.565γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Refinement description, Version format compliance
  • Version 1.2: 2014-01-29
    Changes: Database references, Derived calculations
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description