8CRH | pdb_00008crh

Crystal structure of Candida auris dihydrofolate reductase complexed with NADPH and cycloguanil

PDB DOI: https://doi.org/10.2210/pdb8CRH/pdb

Classification: HYDROLASE
Organism(s): Candidozyma auris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-08 Released: 2023-08-02
Deposition Author(s): Kirkman, T.J., Dias, M.V.B.
Funding Organization(s): UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.183 (Depositor), 0.184 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of dihydrofolate reductase from the emerging pathogenic fungus Candida auris.

Kirkman, T., Sketcher, A., de Morais Barroso, V., Ishida, K., Tosin, M., Dias, M.V.B.

(2023) Acta Crystallogr D Struct Biol 79: 735-745

PubMed: 37428844 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2059798323004709
Primary Citation Related Structures:
7ZZX, 8A0N, 8CRH

PubMed Abstract:
Candida auris has emerged as a global health problem with a dramatic spread by nosocomial transmission and a high mortality rate. Antifungal therapy for C. auris infections is currently limited due to widespread resistance to fluconazole and amphotericin B and increasing resistance to the front-line drug echinocandin. Therefore, new treatments are urgently required to combat this pathogen. Dihydrofolate reductase (DHFR) has been validated as a potential drug target for Candida species, although no structure of the C. auris enzyme (CauDHFR) has been reported. Here, crystal structures of CauDHFR are reported as an apoenzyme, as a holoenzyme and in two ternary complexes with pyrimethamine and cycloguanil, which are common antifolates, at near-atomic resolution. Preliminary biochemical and biophysical assays and antifungal susceptibility testing with a variety of classical antifolates were also performed, highlighting the enzyme-inhibition rates and the inhibition of yeast growth. These structural and functional data might provide the basis for a novel drug-discovery campaign against this global threat.

Organizational Affiliation

Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom.

Macromolecule Content

Total Structure Weight: 51.08 kDa
Atom Count: 4,198
Modeled Residue Count: 409
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A [auth B], B [auth A]	208	Candidozyma auris	Mutation(s): 0 Gene Names: QG37_02791 EC: 1.5.1.3
UniProt
Find proteins for A0A0L0P1H8 (Candidozyma auris) Explore A0A0L0P1H8 Go to UniProtKB: A0A0L0P1H8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0L0P1H8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain D [auth B] MOL2 format, chain H [auth A] MOL2 format, chain D [auth B] mmCIF format, chain H [auth A] mmCIF format, chain D [auth B]	D [auth B], H [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain D [auth B] Focus chain H [auth A] Interactions & Density Focus chain D [auth B] Focus chain H [auth A]
VIL (Subject of Investigation/LOI) Query on VIL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain E [auth B] SDF format, chain C [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth B]	C [auth B], E [auth B], G [auth A], I [auth A]	5-(4-chlorophenyl)-6,6-dimethyl-1,4-dihydro-1,3,5-triazine-2,4-diamine C₁₁ H₁₆ Cl N₅ NDMGACCSLHFEAQ-SNVBAGLBSA-N		Interactions Focus chain C [auth B] Focus chain E [auth B] Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth B] Focus chain G [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain F [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth B]	F [auth B], J [auth A], K [auth A], L [auth A], M [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain F [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]