The Structure of Thymidylate Kinase from Candida albicans Reveals a Unique Structural Element

Abstract

The structure of thymidylate kinase from Candida albicans, determined by X-ray crystallography, is reported to a resolution of 2.45 Å with a final R of 0.223. Thymidylate kinase from C. albicans possesses a unique 15-residue loop that is not seen in thymidylate kinases from other genera. The structure reported here reveals that the conformation of this loop is constrained by both intra- and intersubunit hydrogen bonding, and a number of key residues in this loop are conserved among different Candida species that are medically important. The substrate specificity of the enzyme was determined using a novel nuclear magnetic resonance-based assay as well as a traditional coupled assay. The enzyme is active against 3'-azido-3'-deoxythymidine monophosphate and moderately active with dGMP. The distinct functional and structural differences between the C. albicans enzyme and the human enzyme suggest that thymidylate kinase is an appropriate target for the development of new antifungal agents.

Docking Prediction, Antifungal Activity, Anti-Biofilm Effects on Candida spp., and Toxicity against Human Cells of Cinnamaldehyde

“…The investigated receptors (PDB IDs) were: 14-α-demethylase (PDB ID: 5TZ1) [62] whose binder is (R)-2-(2,4-Difluorophenyl)-1,1-difluoro-3-(1Htetrazol-1-yl)-1-(5-(4-2,2,2trifluoroethoxy)phenyl)pyridin-2-yl)propan-2-ol (VT1); ∆-14-sterol reductase (PDB ID: 4QUV) [63], which binds to NADPH Dihydro-Nicotinamide-Adenine-Dinucleotide Phosphate (NDP); 1,3-β-glucan synthase (PDB ID: 1EQP) [64]; and thymidylate synthase (PDB ID 5UIV) [65], whose binders are Thymidine-5 -Phosphate (TMP) and squalene epoxidase (PDB ID 4MAI) [66]. Receptor selection was defined according to current medication targets recommended for the treatment of candidiasis.…”

Protein-Protein Interactions in Candida albicans

“…The absence of many interactions from the literature in the BioGRID (and other databases) also shows that PPI data are not generally sent to databases such as the BioGRID. A remarkable example is that the BioGRID database, release 3.4.156, mentioned only one interaction that was found with crystallography (van den Berg et al, 2016) while several structures of C. albicans proteins or enzymes showing PPIs have already been studied with crystallography (Whitlow et al, 1997; Senay et al, 2003; Echt et al, 2004; Morgunova et al, 2007; Raczynska et al, 2007; Hast and Beese, 2008; Santini et al, 2008; Arachea et al, 2010; Rocha et al, 2011; Nakamura et al, 2013; Sheng et al, 2013; Yan et al, 2015; Nasser et al, 2016; Tonthat et al, 2016; Hong et al, 2017; Sinha and Rule, 2017; Dostal et al, 2018; Garcia et al, 2018; Kiliszek et al, 2019) and mentioned in the protein data bank 1 . A second observation during our literature search for PPIs in C. albicans is that certain “keywords” commonly used in papers studying PPIs are not often used by C. albicans researchers in their manuscripts.…”

The Ca-loop in thymidylate kinase is critical for growth and contributes to pyrimidine drug sensitivity of Candida albicans

“…1A). The structure-based alignment (PDB codes 5UIV and 1E2D) (13,14) shows that the Candida-specific Ca-loop starts from Phe-107 to Lys-118. We have previously developed a series of hTMPK inhibitors (15,16).…”

“…It has been shown that CaTMPK in complex with ADP and dTMP (PDB code 5UIV) at a resolution of 2.45 Å has a unique surface-exposed loop (termed Ca-loop) (13). However, the functional significance of the Ca-loop in CaTMPK and the molecular mechanism by which the Ca-loop affects catalysis remain unexplored.…”