7LVP

Cryptococcus neoformans AIR synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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

Structural features of Cryptococcus neoformans bifunctional GAR/AIR synthetase may present novel antifungal drug targets.

Chua, S.M.H.Wizrah, M.S.I.Luo, Z.Lim, B.Y.J.Kappler, U.Kobe, B.Fraser, J.A.

(2021) J Biol Chem 297: 101091-101091

  • DOI: https://doi.org/10.1016/j.jbc.2021.101091
  • Primary Citation of Related Structures:  
    7LVO, 7LVP

  • PubMed Abstract: 

    Cryptococcus neoformans is a fungus that causes life-threatening systemic mycoses. During infection of the human host, this pathogen experiences a major change in the availability of purines; the fungus can scavenge the abundant purines in its environmental niche of pigeon excrement, but must employ de novo biosynthesis in the purine-poor human CNS. Eleven sequential enzymatic steps are required to form the first purine base, IMP, an intermediate in the formation of ATP and GTP. Over the course of evolution, several gene fusion events led to the formation of multifunctional purine biosynthetic enzymes in most organisms, particularly the higher eukaryotes. In C. neoformans, phosphoribosyl-glycinamide synthetase (GARs) and phosphoribosyl-aminoimidazole synthetase (AIRs) are fused into a bifunctional enzyme, while the human ortholog is a trifunctional enzyme that also includes GAR transformylase. Here we functionally, biochemically, and structurally characterized C. neoformans GARs and AIRs to identify drug targetable features. GARs/AIRs are essential for de novo purine production and virulence in a murine inhalation infection model. Characterization of GARs enzymatic functional parameters showed that C. neoformans GARs/AIRs have lower affinity for substrates glycine and PRA compared with the trifunctional metazoan enzyme. The crystal structure of C. neoformans GARs revealed differences in the glycine- and ATP-binding sites compared with the Homo sapiens enzyme, while the crystal structure of AIRs shows high structural similarity compared with its H. sapiens ortholog as a monomer but differences as a dimer. The alterations in functional and structural characteristics between fungal and human enzymes could potentially be exploited for antifungal development.


  • Organizational Affiliation

    Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia; School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AIR synthase336Cryptococcus neoformans var. grubii H99Mutation(s): 0 
Gene Names: CNAG_06314
EC: 6.3.3.1 (PDB Primary Data), 6.3.4.13 (UniProt)
UniProt
Find proteins for J9VYP5 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VYP5 
Go to UniProtKB:  J9VYP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VYP5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download Ideal Coordinates CCD File 
D [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GLY
Query on GLY

Download Ideal Coordinates CCD File 
G [auth A]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.3α = 90
b = 85.769β = 91.698
c = 37.018γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description