Transition state analysis of adenosine triphosphate phosphoribosyltransferase

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

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Transition State Analysis of Adenosine Triphosphate Phosphoribosyltransferase.

Moggre, G.J.Poulin, M.B.Tyler, P.C.Schramm, V.L.Parker, E.J.

(2017) ACS Chem Biol 12: 2662-2670

  • DOI: https://doi.org/10.1021/acschembio.7b00484
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first step in histidine biosynthesis, a pathway essential to microorganisms and a validated target for antimicrobial drug design. The ATP-PRT enzyme catalyzes the reversible substitution reaction between phosphoribosyl pyrophosphate and ATP. The enzyme exists in two structurally distinct forms, a short- and a long-form enzyme. These forms share a catalytic core dimer but bear completely different allosteric domains and thus distinct quaternary assemblies. Understanding enzymatic transition states can provide essential information on the reaction mechanisms and insight into how differences in domain structure influence the reaction chemistry, as well as providing a template for inhibitor design. In this study, the transition state structures for ATP-PRT enzymes from Campylobacter jejuni and Mycobacterium tuberculosis (long-form enzymes) and from Lactococcus lactis (short-form) were determined and compared. Intrinsic kinetic isotope effects (KIEs) were obtained at reaction sensitive positions for the reverse reaction using phosphonoacetic acid, an alternative substrate to the natural substrate pyrophosphate. The experimental KIEs demonstrated mechanistic similarities between the three enzymes and provided experimental boundaries for quantum chemical calculations to characterize the transition states. Predicted transition state structures support a dissociative reaction mechanism with a D N *A N transition state. Weak interactions from the incoming nucleophile and a fully dissociated ATP adenine are predicted regardless of the difference in overall structure and quaternary assembly. These studies establish that despite significant differences in the quaternary assembly and regulatory machinery between ATP-PRT enzymes from different sources, the reaction chemistry and catalytic mechanism are conserved.

  • Organizational Affiliation

    Ferrier Research Institute, Victoria University of Wellington , P.O. Box 33436, Petone 5046, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP phosphoribosyltransferase286Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: hisGRv2121cMTCY261.17c
Find proteins for P9WMN1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WMN1 
Go to UniProtKB:  P9WMN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WMN1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.758α = 90
b = 134.758β = 90
c = 111.005γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Maurice Wilkins centre FundNew Zealand--
UoC Doctoral ScholarshipNew Zealand--
IRL Sir Roy McKenzie TrustNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description