title: Modeling studies of potato nucleoside triphosphate diphosphohydrolase NTPDase1: an insight into the catalytic mechanism.
abstract: Nucleoside triphosphate diphosphohydrolase--NTPDase1 (apyrase, EC 3.6.1.5) was modeled based on sequence homology. The single polypeptide chain of apyrase is folded into two domains. The putative catalytic site with the apyrase conserved regions (ACR 1-5) is located between these two domains. Modeling confirmed that apyrase belongs to the actin superfamily of proteins. The amino acids interacting with the nucleoside triphosphate substrate and probably involved in the catalyzed hydrolysis were identified. The proposed two-step catalytic mechanism of hydrolysis involves Thr127 and Thr55 as potential nucleophilic factors responsible for the cleavage of the Pgamma and Pbeta anhydride bonds, respectively. Their action seems to be assisted by Glu170 and Glu78 residues, respectively. The presence of two nucleophiles in the active site of apyrase explains the differences in the hydrolytic activity between apyrases and other enzymes belonging to the NTPDase family.
authors.affiliation: Department of Crystallochemistry and Biocrystallography, Institute of Chemistry, Toruń, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Kozakiewicz
authors.forename: Piotr
authors.initials: P
authors.lastname: Neumann
authors.forename: Mariusz
authors.initials: M
authors.lastname: Banach
authors.forename: Michał
authors.initials: M
authors.lastname: Komoszyński
authors.forename: Andrzej
authors.initials: A
authors.lastname: Wojtczak
mesh_terms: D000199:Actins / Q000737:chemistry; D000595:Amino Acid Sequence; D000812:Anhydrides / Q000737:chemistry; D001081:Apyrase / Q000737:chemistry*; D001671:Biochemistry / Q000379:methods*; D002384:Catalysis; D020134:Catalytic Domain; D018698:Glutamic Acid / Q000737:chemistry; D006868:Hydrolysis; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D011198:Solanum tuberosum / Q000201:enzymology*
chemical_list: D000199:Actins; D000812:Anhydrides; D010940:Plant Proteins; D018698:Glutamic Acid; D001081:Apyrase