4GRD

Crystal structure of Phosphoribosylaminoimidazole carboxylase catalytic subunit from Burkholderia cenocepacia J2315


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-Guided Discovery of N 5 -CAIR Mutase Inhibitors.

Belfon, K.K.J.Sharma, N.Zigweid, R.Bolejack, M.Davies, D.Edwards, T.E.Myler, P.J.French, J.B.

(2023) Biochemistry 62: 2587-2596

  • DOI: https://doi.org/10.1021/acs.biochem.2c00705
  • Primary Citation of Related Structures:  
    4GRD, 6O55

  • PubMed Abstract: 

    Because purine nucleotides are essential for all life, differences between how microbes and humans metabolize purines can be exploited for the development of antimicrobial therapies. While humans biosynthesize purine nucleotides in a 10-step pathway, most microbes utilize an additional 11th enzymatic activity. The human enzyme, aminoimidazole ribonucleotide (AIR) carboxylase generates the product 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) directly. Most microbes, however, require two separate enzymes, a synthetase (PurK) and a mutase (PurE), and proceed through the intermediate, N 5 -CAIR. Toward the development of therapeutics that target these differences, we have solved crystal structures of the N 5 -CAIR mutase of the human pathogens Legionella pneumophila (LpPurE) and Burkholderia cenocepacia (BcPurE) and used a structure-guided approach to identify inhibitors. Analysis of the structures reveals a highly conserved fold and active site architecture. Using this data, and three additional structures of PurE enzymes, we screened a library of FDA-approved compounds in silico and identified a set of 25 candidates for further analysis. Among these, we identified several new PurE inhibitors with micromolar IC 50 values. Several of these compounds, including the α 1 -blocker Alfuzosin, inhibit the microbial PurE enzymes much more effectively than the human homologue. These structures and the newly described PurE inhibitors are valuable tools to aid in further studies of this enzyme and provide a foundation for the development of compounds that target differences between human and microbial purine metabolism.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribosylaminoimidazole carboxylase catalytic subunit
A, B, C, D
173Burkholderia cenocepacia J2315Mutation(s): 0 
Gene Names: purEBceJ2315_27750BCAL2837
EC: 4.1.1.21 (PDB Primary Data), 5.4.99.18 (PDB Primary Data)
UniProt
Find proteins for B4EA21 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Explore B4EA21 
Go to UniProtKB:  B4EA21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4EA21
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.51α = 90
b = 117.18β = 90
c = 122.31γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-05-29
    Changes: Database references