6U69

Crystal structure of Yck2 from Candida albicans, apoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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

Overcoming Fungal Echinocandin Resistance through Inhibition of the Non-essential Stress Kinase Yck2.

Caplan, T.Lorente-Macias, A.Stogios, P.J.Evdokimova, E.Hyde, S.Wellington, M.A.Liston, S.Iyer, K.R.Puumala, E.Shekhar-Guturja, T.Robbins, N.Savchenko, A.Krysan, D.J.Whitesell, L.Zuercher, W.J.Cowen, L.E.

(2020) Cell Chem Biol 27: 269-282.e5

  • DOI: https://doi.org/10.1016/j.chembiol.2019.12.008
  • Primary Citation of Related Structures:  
    6U69, 6U6A

  • PubMed Abstract: 

    New strategies are urgently needed to counter the threat to human health posed by drug-resistant fungi. To explore an as-yet unexploited target space for antifungals, we screened a library of protein kinase inhibitors for the ability to reverse resistance of the most common human fungal pathogen, Candida albicans, to caspofungin, a widely used antifungal. This screen identified multiple 2,3-aryl-pyrazolopyridine scaffold compounds capable of restoring caspofungin sensitivity. Using chemical genomic, biochemical, and structural approaches, we established the target for our most potent compound as Yck2, a casein kinase 1 family member. Combination of this compound with caspofungin eradicated drug-resistant C. albicans infection while sparing co-cultured human cells. In mice, genetic depletion of YCK2 caused an ∼3-log 10 decline in fungal burden in a model of systemic caspofungin-resistant C. albicans infection. Structural insights and our tool compound's profile in culture support targeting the Yck2 kinase function as a broadly active antifungal strategy.


  • Organizational Affiliation

    Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine protein kinase309Candida albicans SC5314Mutation(s): 0 
Gene Names: YCK2orf19.7001CAALFM_C305650WA
EC: 2.7.11.1
UniProt
Find proteins for A0A1D8PKB4 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore A0A1D8PKB4 
Go to UniProtKB:  A0A1D8PKB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D8PKB4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.771α = 90
b = 91.771β = 90
c = 119.83γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2020-05-13
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description