2AF3

Phosphotransacetylase from Methanosarcina thermophila soaked with Coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1128/JB.188.3.1143-1154.2006
  • Primary Citation of Related Structures:  
    2AF3, 2AF4

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphate acetyltransferaseA [auth C],
B [auth D]
333Methanosarcina thermophilaMutation(s): 0 
Gene Names: pta
EC: 2.3.1.8
UniProt
Find proteins for P38503 (Methanosarcina thermophila)
Explore P38503 
Go to UniProtKB:  P38503
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38503
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.469α = 90
b = 114.469β = 90
c = 127.832γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description