3EQ6

Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in a ternary complex with products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A

Kochan, G.Pilka, E.S.von Delft, F.Oppermann, U.Yue, W.W.

(2009) J.Mol.Biol. 388: 997-1008

  • DOI: 10.1016/j.jmb.2009.03.064
  • Primary Citation of Related Structures:  2WD9, 3GPC, 2VZE, 3B7W, 3C5E, 3DAY

  • PubMed Abstract: 
  • Acyl-CoA synthetases belong to the superfamily of adenylate-forming enzymes, and catalyze the two-step activation of fatty acids or carboxylate-containing xenobiotics. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermed ...

    Acyl-CoA synthetases belong to the superfamily of adenylate-forming enzymes, and catalyze the two-step activation of fatty acids or carboxylate-containing xenobiotics. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. Here, we report the first crystal structure of a medium-chain acyl-CoA synthetase ACSM2A, in a series of substrate/product/cofactor complexes central to the catalytic mechanism. We observed a substantial rearrangement between the N- and C-terminal domains, driven purely by the identity of the bound ligand in the active site. Our structures allowed us to identify the presence or absence of the ATP pyrophosphates as the conformational switch, and elucidated new mechanistic details, including the role of invariant Lys557 and a divalent magnesium ion in coordinating the ATP pyrophosphates, as well as the involvement of a Gly-rich P-loop and the conserved Arg472-Glu365 salt bridge in the domain rearrangement.


    Organizational Affiliation

    Structural Genomics Consortium, Old Road Research Campus Building, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acyl-coenzyme A synthetase ACSM2A
A, B
570Homo sapiensGene Names: ACSM2A (ACSM2, MACS2)
EC: 6.2.1.2
Find proteins for Q08AH3 (Homo sapiens)
Go to Gene View: ACSM2A
Go to UniProtKB:  Q08AH3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
BCO
Query on BCO

Download SDF File 
Download CCD File 
A, B
Butyryl Coenzyme A
S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)
C25 H42 N7 O17 P3 S
CRFNGMNYKDXRTN-CITAKDKDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.028α = 90.00
b = 98.041β = 94.12
c = 116.660γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CrystalCleardata collection
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2015-02-11
    Type: Non-polymer description
  • Version 1.3: 2016-02-03
    Type: Non-polymer description