1RY2

Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP

Jogl, G.Tong, L.

(2004) Biochemistry 43: 1425-1431

  • DOI: 10.1021/bi035911a
  • Primary Citation of Related Structures:  
    1RY2

  • PubMed Abstract: 
  • Acetyl-coenzyme A synthetase (ACS) belongs to the family of AMP-forming enzymes that also includes acyl-CoA synthetases, firefly luciferase, and nonribosomal peptide synthetases. ACS catalyzes the two-step activation of acetate to acetyl-CoA: formation of an acetyl-AMP intermediate from acetate and ATP and the transfer of the acetyl group to CoA ...

    Acetyl-coenzyme A synthetase (ACS) belongs to the family of AMP-forming enzymes that also includes acyl-CoA synthetases, firefly luciferase, and nonribosomal peptide synthetases. ACS catalyzes the two-step activation of acetate to acetyl-CoA: formation of an acetyl-AMP intermediate from acetate and ATP and the transfer of the acetyl group to CoA. In mammals, the acetyl-CoA product is used for biosynthesis of long chain fatty acids as well as energy production. We have determined the crystal structure of yeast ACS in a binary complex with AMP at 2.3 A resolution. The structure contains a large, N-terminal domain and a small, C-terminal domain. AMP is bound at the interface between the two domains. This structure represents a new conformation for the ACS enzyme, which may be competent for catalyzing the first step of the reaction. A Lys residue that is critical for this step is located in the active site. A rotation of 140 degrees in the small domain is needed for the binding of CoA and the catalysis of the second step. In contrast to the monomeric bacterial enzyme, yeast ACS is a stable trimer.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
acetyl-coenzyme A synthetase 1A663Saccharomyces cerevisiaeMutation(s): 0 
EC: 6.2.1.1
UniProt
Find proteins for Q01574 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01574 
Go to UniProtKB:  Q01574
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.13α = 90
b = 107.13β = 90
c = 54.79γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
CNSrefinement
COMOphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2003-12-19 
  • Released Date: 2004-03-09 
  • Deposition Author(s): Jogl, G., Tong, L.

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation