1PG4 | pdb_00001pg4

Acetyl CoA Synthetase, Salmonella enterica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.183 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1PG4

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The 1.75 A Crystal Structure of Acetyl-CoA Synthetase Bound to Adenosine-5'-propylphosphate and Coenzyme A

Gulick, A.M.Starai, V.J.Horswill, A.R.Homick, K.M.Escalante-Semerena, J.C.

(2003) Biochemistry 42: 2866-2873

  • DOI: https://doi.org/10.1021/bi0271603
  • Primary Citation Related Structures: 
    1PG3, 1PG4

  • PubMed Abstract: 

    Acetyl-coenzyme A synthetase catalyzes the two-step synthesis of acetyl-CoA from acetate, ATP, and CoA and belongs to a family of adenylate-forming enzymes that generate an acyl-AMP intermediate. This family includes other acyl- and aryl-CoA synthetases, firefly luciferase, and the adenylation domains of the modular nonribosomal peptide synthetases. We have determined the X-ray crystal structure of acetyl-CoA synthetase complexed with adenosine-5'-propylphosphate and CoA. The structure identifies the CoA binding pocket as well as a new conformation for members of this enzyme family in which the approximately 110-residue C-terminal domain exhibits a large rotation compared to structures of peptide synthetase adenylation domains. This domain movement presents a new set of residues to the active site and removes a conserved lysine residue that was previously shown to be important for catalysis of the adenylation half-reaction. Comparison of our structure with kinetic and structural data of closely related enzymes suggests that the members of the adenylate-forming family of enzymes may adopt two different orientations to catalyze the two half-reactions. Additionally, we provide a structural explanation for the recently shown control of enzyme activity by acetylation of an active site lysine.


  • Organizational Affiliation
    • Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203-1149, USA. gulick@hwi.buffalo.edu

Macromolecule Content 

  • Total Structure Weight: 147.11 kDa 
  • Atom Count: 10,837 
  • Modeled Residue Count: 1,272 
  • Deposited Residue Count: 1,304 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
acetyl-CoA synthetase
A, B
652Salmonella entericaMutation(s): 1 
Gene Names: ACS
EC: 6.2.1.1
UniProt
Find proteins for Q8ZKF6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZKF6 
Go to UniProtKB:  Q8ZKF6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZKF6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA

Query on COA



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
PRX

Query on PRX



Download:Ideal Coordinates CCD File
F [auth A],
M [auth B]
ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER
C13 H20 N5 O7 P
XAMXMSZRQHPMRX-QYVSTXNMSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.183 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.994α = 90
b = 143.016β = 91.32
c = 71.731γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    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: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection