title: In silico identification and characterization of 1-aminocyclopropane-1-carboxylate deaminase from Phytophthora sojae.
abstract: As part of an effort to obtain a fungal 1-aminocyclopropane-1-carboxylate deaminase encoding gene from Phytophthora sojae expressed sequence Tag database, we identify and characterize the ACCD from P. sojae using bioinformatics data mining tools and techniques. Computed structural model of P. sojae ACCD was found to consist of mixed α/β motifs and probable loops. The predicted model resembles the structure of Pseudomonas ACCD (RMSD-0.44 Å). The main differences observed between them are the presence of partial length of domain one, and longer helix α4. Ramachandran plot analysis revealed that portion of all residues falling into the most favorable regions was 95.0%. The substrate - and geometrical- docking of developed structure postulated functional capability of ACCD to carry out ACC cleavage reaction. The catalytic site in homo-tetrameric structure open to opposite directions separated by ∼37.97 Å distance arranged around central axis. This study provides a comprehensive identification and characterization of the ACCD in P. sojae and it may be helpful in the transcriptional and expression based study of P. sojae pathogenesis.
authors.affiliation: National Bureau of Agriculturally Important Microorganisms (ICAR), Kusmaur, Kaithauli, Mau Nath Bhanjan, 275101, Uttar Pradesh, India.
authors.forename: Nidhi
authors.initials: N
authors.lastname: Singh
authors.forename: Sudhanshu
authors.initials: S
authors.lastname: Kashyap
mesh_terms: D000595:Amino Acid Sequence; D001232:Aspergillus fumigatus / Q000201:enzymology; D001483:Base Sequence; D019755:Carbon-Carbon Lyases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D020407:Internet; D008024:Ligands; D062105:Molecular Docking Simulation; D010802:Phylogeny; D010838:Phytophthora / Q000201:enzymology*; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D013379:Substrate Specificity
chemical_list: D008024:Ligands; C033634:1-aminocyclopropane-1-carboxylate deaminase; D019755:Carbon-Carbon Lyases