1Z7N

ATP Phosphoribosyl transferase (HisZG ATP-PRTase) from Lactococcus lactis with bound PRPP substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.291 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog.

Champagne, K.S.Sissler, M.Larrabee, Y.Doublie, S.Francklyn, C.S.

(2005) J Biol Chem 280: 34096-34104

  • DOI: https://doi.org/10.1074/jbc.M505041200
  • Primary Citation of Related Structures:  
    1Z7M, 1Z7N

  • PubMed Abstract: 

    ATP phosphoribosyl transferase (ATP-PRT) joins ATP and 5-phosphoribosyl-1-pyrophosphate (PRPP) in a highly regulated reaction that initiates histidine biosynthesis. The unusual hetero-octameric version of ATP-PRT includes four HisG(S) catalytic subunits based on the periplasmic binding protein fold and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. Here, we present the first structure of a PRPP-bound ATP-PRT at 2.9 A and provide a structural model for allosteric activation based on comparisons with other inhibited and activated ATP-PRTs from both the hetero-octameric and hexameric families. The activated state of the octameric enzyme is characterized by an interstitial phosphate ion in the HisZ-HisG interface and new contacts between the HisZ motif 2 loop and the HisG(S) dimer interface. These contacts restructure the interface to recruit conserved residues to the active site, where they activate pyrophosphate to promote catalysis. Additionally, mutational analysis identifies the histidine binding sites within a region highly conserved between HisZ and the functional HisRS. Through the oligomerization and functional re-assignment of protein domains associated with aminoacylation and phosphate binding, the HisZ-HisG octameric ATP-PRT acquired the ability to initiate the synthesis of a key metabolic intermediate in an allosterically regulated fashion.


  • Organizational Affiliation

    Department of Microbiology and Molecular Genetics and Biochemistry, University of Vermont, Burlington, Vermont 05405, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP phosphoribosyltransferase regulatory subunit
A, B, C, D
344Lactococcus lactisMutation(s): 0 
Gene Names: hisZ
UniProt
Find proteins for Q02147 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q02147 
Go to UniProtKB:  Q02147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02147
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP phosphoribosyltransferase
E, F, G, H
208Lactococcus lactisMutation(s): 0 
Gene Names: hisG
EC: 2.4.2.17
UniProt
Find proteins for Q02129 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q02129 
Go to UniProtKB:  Q02129
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02129
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.291 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.684α = 90
b = 222.936β = 90
c = 86.38γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-09
    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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Structure summary