Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Export

@article{WLT96, abstract = {It is well established that sequence templates (e.g., PROSITE) and databases are powerful tools for identifying biological function and tertiary structure for an unknown protein sequence. Here we describe a method for automatically deriving 3D templates from the protein structures deposited in the Brookhaven Protein Data Bank. As an example, we describe a template derived for the Ser-His-Asp catalytic triad found in the serine proteases and triacylglycerol lipases. We find that the resultant template provides a highly selective tool for automatically differentiating between catalytic and noncatalytic Ser-His-Asp associations. When applied to nonproteolytic proteins, the template picks out two "non-esterase" catalytic triads that may be of biological relevance. This suggests that the development of databases of 3D templates, such as those that currently exist for protein sequence templates, will help identify the functions of new protein structures as they are determined and pinpoint their functionally important regions.}, author = {Wallace, A. C. and Laskowski, R. A. and Thornton, J. M.}, citeulike-article-id = {388918}, journal = {Protein Sci}, keywords = {algorithm, catalytic\_triad, template}, number = {6}, pages = {1001--13}, posted-at = {2005-11-11 16:23:16}, priority = {2}, title = {Derivation of 3{D} coordinate templates for searching structural databases: application to {S}er-{H}is-{A}sp catalytic triads in the serine proteinases and lipases.}, volume = {5}, year = {1996} }

TY - JOUR ID - WLT96 L3 - citeulike-article-id:388918 N2 - It is well established that sequence templates (e.g., PROSITE) and databases are powerful tools for identifying biological function and tertiary structure for an unknown protein sequence. Here we describe a method for automatically deriving 3D templates from the protein structures deposited in the Brookhaven Protein Data Bank. As an example, we describe a template derived for the Ser-His-Asp catalytic triad found in the serine proteases and triacylglycerol lipases. We find that the resultant template provides a highly selective tool for automatically differentiating between catalytic and noncatalytic Ser-His-Asp associations. When applied to nonproteolytic proteins, the template picks out two "non-esterase" catalytic triads that may be of biological relevance. This suggests that the development of databases of 3D templates, such as those that currently exist for protein sequence templates, will help identify the functions of new protein structures as they are determined and pinpoint their functionally important regions. IS - 6 JF - Protein Sci EP - 13 TI - Derivation of 3{D} coordinate templates for searching structural databases: application to {S}er-{H}is-{A}sp catalytic triads in the serine proteinases and lipases. VL - 5 SP - 1001 KW - algorithm KW - catalytic_triad KW - template AU - Wallace, AC AU - Laskowski, RA AU - Thornton, JM PY - 1996/// ER -