title: Human cytidine deaminase: a three-dimensional homology model of a tetrameric metallo-enzyme inferred from the crystal structure of a distantly related dimeric homologue.
abstract: Cytidine deaminase (CDA) is a cytosolic metalloprotein whose functional unit can be either a homotetramer (T-CDA) or a homodimer (D-CDA), depending on the species. In 1994, the first crystal structure of the dimeric Escherichia coli CDA has been published. However, a crystal structure of a tetrameric CDA was not determined until 2002. Prior to the disclosure of the experimentally elucidated structure of a tetrameric CDA, we derived a homology model of the human T-CDA employing the crystal structure of the dimeric E. coli CDA as a template. The comparison of our theoretical model with the crystal structure of the human T-CDA, subsequently published in 2004, validates our prediction: not only of the structural features of the monomer and the details of the binding site, but also the multimeric arrangement of the subunits were determined with high accuracy in our model. By means of a phylogenetic analysis conducted on CDAs from various organisms, we demonstrate that the E. coli CDA is one of the furthest known homologues of the human enzyme. Nonetheless, despite the evolutionary distance and, more importantly, the different multimeric arrangement of their functional units, the E. coli CDA proved to have all the necessary information to accurately infer the structure of its human homologue.
authors.affiliation: Computational Chemistry Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 12A Center Drive Rm 4051 MSC 5646, Bethesda, MD 20892-0810, USA. stefanoc@mail.nih.gov
authors.forename: Stefano
authors.initials: S
authors.lastname: Costanzi
authors.forename: Silvia
authors.initials: S
authors.lastname: Vincenzetti
authors.forename: Gloria
authors.initials: G
authors.lastname: Cristalli
authors.forename: Alberto
authors.initials: A
authors.lastname: Vita
mesh_terms: D000595:Amino Acid Sequence; D003461:Crystallography; D003564:Cytidine Deaminase / Q000737:chemistry* / Q000145:classification*; D019281:Dimerization; D004926:Escherichia coli / Q000201:enzymology; D006801:Humans; D008667:Metalloproteins / Q000737:chemistry* / Q000145:classification*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011487:Protein Conformation; D040681:Structural Homology, Protein
chemical_list: D008667:Metalloproteins; D003564:Cytidine Deaminase