title: What's My Substrate? Computational Function Assignment of Candida parapsilosis ADH5 by Genome Database Search, Virtual Screening, and QM/MM Calculations.
abstract: Zinc-dependent medium chain reductase from Candida parapsilosis can be used in the reduction of carbonyl compounds to pharmacologically important chiral secondary alcohols. To date, the nomenclature of cpADH5 is differing (CPCR2/RCR/SADH) in the literature, and its natural substrate is not known. In this study, we utilized a substrate docking based virtual screening method combined with KEGG, MetaCyc pathway, and Candida genome databases search for the discovery of natural substrates of cpADH5. The virtual screening of 7834 carbonyl compounds from the ZINC database provided 94 aldehydes or methyl/ethyl ketones as putative carbonyl substrates. Out of which, 52 carbonyl substrates of cpADH5 with catalytically active docking pose were identified by employing mechanism based substrate docking protocol. Comparison of the virtual screening results with KEGG, MetaCyc database search, and Candida genome pathway analysis suggest that cpADH5 might be involved in the Ehrlich pathway (reduction of fusel aldehydes in leucine, isoleucine, and valine degradation). Our QM/MM calculations and experimental activity measurements affirmed that butyraldehyde substrates are the potential natural substrates of cpADH5, suggesting a carbonyl reductase role for this enzyme in butyraldehyde reduction in aliphatic amino acid degradation pathways. Phylogenetic tree analysis of known ADHs from Candida albicans shows that cpADH5 is close to caADH5. We therefore propose, according to the experimental substrate identification and sequence similarity, the common name butyraldehyde dehydrogenase cpADH5 for Candida parapsilosis CPCR2/RCR/SADH.
authors.affiliation: Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany.
authors.forename: Gaurao V
authors.initials: GV
authors.lastname: Dhoke
authors.affiliation: Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany.
authors.forename: Yunus
authors.initials: Y
authors.lastname: Ensari
authors.affiliation: Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany.
authors.forename: Mehdi D
authors.initials: MD
authors.lastname: Davari
authors.affiliation: Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany.
authors.forename: Anna Joëlle
authors.initials: AJ
authors.lastname: Ruff
authors.affiliation: Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany.|DWI-Leibniz Institut für Interaktive Materialien , Forckenbeckstraße 50, 52056 Aachen, Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Schwaneberg
authors.affiliation: Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Bocola
mesh_terms: D000426:Alcohol Dehydrogenase / Q000737:chemistry / Q000378:metabolism*; D000438:Alcohols / Q000378:metabolism; D000595:Amino Acid Sequence; D002175:Candida / Q000201:enzymology* / Q000235:genetics*; D030541:Databases, Genetic; D004353:Drug Evaluation, Preclinical / Q000379:methods; D023281:Genomics / Q000379:methods*; D007700:Kinetics; D009243:NAD / Q000378:metabolism; D011487:Protein Conformation; D011789:Quantum Theory; D013379:Substrate Specificity; D014584:User-Computer Interface
chemical_list: D000438:Alcohols; D009243:NAD; D000426:Alcohol Dehydrogenase