2AF4

Phosphotransacetylase from Methanosarcina thermophila co-crystallized with coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.147 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and functional studies suggest a catalytic mechanism for the phosphotransacetylase from Methanosarcina thermophila.

Lawrence, S.H.Luther, K.B.Schindelin, H.Ferry, J.G.

(2006) J.Bacteriol. 188: 1143-1154

  • DOI: 10.1128/JB.188.3.1143-1154.2006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphotransacetylase (EC 2.3.1.8) catalyzes reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. Two crystal structures of phosphotransacetylase from the methanogenic archaeon ...

    Phosphotransacetylase (EC 2.3.1.8) catalyzes reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. Two crystal structures of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila in complex with the substrate CoA revealed one CoA (CoA1) bound in the proposed active site cleft and an additional CoA (CoA2) bound at the periphery of the cleft. The results of isothermal titration calorimetry experiments are described, and they support the hypothesis that there are distinct high-affinity (equilibrium dissociation constant [KD], 20 microM) and low-affinity (KD, 2 mM) CoA binding sites. The crystal structures indicated that binding of CoA1 is mediated by a series of hydrogen bonds and extensive van der Waals interactions with the enzyme and that there are fewer of these interactions between CoA2 and the enzyme. Different conformations of the protein observed in the crystal structures suggest that domain movements which alter the geometry of the active site cleft may contribute to catalysis. Kinetic and calorimetric analyses of site-specific replacement variants indicated that there are catalytic roles for Ser309 and Arg310, which are proximal to the reactive sulfhydryl of CoA1. The reaction is hypothesized to proceed through base-catalyzed abstraction of the thiol proton of CoA by the adjacent and invariant residue Asp316, followed by nucleophilic attack of the thiolate anion of CoA on the carbonyl carbon of acetyl phosphate. We propose that Arg310 binds acetyl phosphate and orients it for optimal nucleophilic attack. The hypothesized mechanism proceeds through a negatively charged transition state stabilized by hydrogen bond donation from Ser309.


    Related Citations: 
    • Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila
      Iyer, P.P.,Lawrence, S.H.,Luther, K.B.,Rajashankar, K.R.,Yennawar, H.P.,Ferry, J.G.,Schindelin, H.
      (2004) Structure 12: 559


    Organizational Affiliation

    Department of Biochemistry, Center for Structural Biology, SUNY Stony Brook, Stony Brook, NY 11794-5115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphate acetyltransferase
C, D
333Methanosarcina thermophilaMutation(s): 0 
Gene Names: pta
EC: 2.3.1.8
Find proteins for P38503 (Methanosarcina thermophila)
Go to UniProtKB:  P38503
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
C, D
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.147 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.203 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 116.488α = 90.00
b = 116.488β = 90.00
c = 127.460γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance