title: Recognition of active and inactive catalytic triads: A template based approach.
abstract: It is well established that a sequence template along with the database is a powerful tool for identifying the biological function of proteins. Here, we describe a method for predicting the catalytic nature of certain proteins among the several protein structures deposited in the Protein Data Bank (PDB). For the present study, we considered a catalytic triad template (Ser-His-Asp) found in serine proteases. We found that a geometrically optimized active site template can be used as a highly selective tool for differentiating an active protein among several inactive proteins, based on their Ser-His-Asp interactions. For any protein to be proteolytic in nature, the bond angle between Ser O(gamma)-Ser H(gamma)...His N(epsilon2) in the catalytic triad needs to be between 115 degrees and 140 degrees. The hydrogen bond distance between Ser H(gamma)...His N(epsilon2) is more flexible in nature and it varies from 2.0 A to 2.7 A while in the case of His H(delta1)...Asp O(delta1), it is from 1.6A to 2.0 A. In terms of solvent accessibility, most of the active proteins lie in the range of 10-16 A(2), which enables easy accessibility to the substrate. These observations hold good for most catalytic triads and they can be employed to predict proteolytic nature of these catalytic triads.
authors.affiliation: Bioinformatics Centre, (Centre of Excellence in Structural Biology and Bio-computing), Indian Institute of Science, Bangalore 560 012, India.
authors.forename: Vikas
authors.initials: V
authors.lastname: Gupta
authors.forename: N A Udaya
authors.initials: NA
authors.lastname: Prakash
authors.forename: V
authors.initials: V
authors.lastname: Lakshmi
authors.forename: R
authors.initials: R
authors.lastname: Boopathy
authors.forename: J
authors.initials: J
authors.lastname: Jeyakanthan
authors.forename: D
authors.initials: D
authors.lastname: Velmurugan
authors.forename: K
authors.initials: K
authors.lastname: Sekar
mesh_terms: D000595:Amino Acid Sequence; D055162:Biocatalysis; D030562:Databases, Protein; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010960:Plasminogen Activators / Q000737:chemistry; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012997:Solvents / Q000737:chemistry; D014357:Trypsin / Q000737:chemistry
chemical_list: D011506:Proteins; D012997:Solvents; D010960:Plasminogen Activators; D014357:Trypsin