7Z8U

Catalytic subunit HisG R56A mutant from Psychrobacter arcticus ATPPRT (HisGZ) in complex with ATP and PRPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation.

Fisher, G.Corbella, M.Alphey, M.S.Nicholson, J.Read, B.J.Kamerlin, S.C.L.da Silva, R.G.

(2022) Nat Commun 13: 7607-7607

  • DOI: https://doi.org/10.1038/s41467-022-34960-9
  • Primary Citation of Related Structures:  
    7Z6R, 7Z8U

  • PubMed Abstract: 

    ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisG S while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisG S Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisG S with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisG S interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisG S to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisG S . In the Arg56Ala-HisG S mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.


  • Organizational Affiliation

    School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP phosphoribosyltransferase232Psychrobacter arcticusMutation(s): 1 
Gene Names: hisGPsyc_1903
EC: 2.4.2.17
UniProt
Find proteins for Q4FQF7 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4))
Explore Q4FQF7 
Go to UniProtKB:  Q4FQF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4FQF7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.09α = 90
b = 33.9β = 103.52
c = 89.265γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M010996/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description