Pyridoxal-5′-phosphate-dependent catalytic antibodies

Cofactors—i.e., metal ions and coenzymes—extend the catalytic scope of enzymes and might have been among the first biological catalysts. They may be expected to efficiently extend the catalytic potential of antibodies. Monoclonal antibodies (MAbs) against Nα-phosphopyridoxyl-l-lysine were screened for 1) binding of 5′-phosphopyridoxyl amino acids, 2) binding of the planar Schiff base of pyridoxal-5′-phosphate (PLP) and amino acids, the first intermediate of all PLP-dependent reactions, and 3), catalysis of the PLP-dependent α, β-elimination reaction with β-chloro-D/L-alanine. Antibody 15A9 fulfilled all criteria and was also found to catalyze the cofactor-dependent transamination reaction of hydrophobic D-amino acids and oxo acids (k′ cat=0.42 min−1 with D-alanine at 25°C). No other reactions with either D- or L-amino acids were detected. PLP markedly contributes to catalytic effecacy—it is a 104 times more efficient acceptor of the amino group than pyruvate. The antibody ensures reaction specificity, stereospecificity, and substrate specificity, and further accelerates the transamination reaction (k′ cat(Ab)/k′ cat(PLP)=5×103). The successive screening steps simulate the selection criteria that might have been operative in the evolution of protein-assisted psyridoxal catalysi

CutDB: a proteolytic event database

Beyond the well-known role of proteolytic machinery in protein degradation and turnover, many specialized proteases play a key role in various regulatory processes. Thousands of highly specific proteolytic events are associated with normal and pathological conditions, including bacterial and viral infections. However, the information about individual proteolytic events is dispersed over multiple publications and is not easily available for large-scale analysis. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content. CutDB is publicly available at

PMAP: databases for analyzing proteolytic events and pathways

The Proteolysis MAP (PMAP, http://www.proteolysis.org) is a user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The foundation databases, ProteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic ‘Molecule Pages’, rich in molecular information. PMAP also contains two community annotated databases focused on function; CutDB has information on more than 5000 proteolytic events, and ProfileDB is dedicated to information of the substrate recognition specificity of proteases. Together, the content within these four databases will ultimately feed PathwayDB, which will be comprised of known pathways whose function can be dynamically modeled in a rule-based manner, and hypothetical pathways suggested by semi-automated culling of the literature. A Protease Toolkit is also available for the analysis of proteases and proteolysis. Here, we describe how the databases of PMAP can be used to foster understanding of proteolytic pathways, and equally as significant, to reason about proteolysis

Pyridoxal-5'-phosphate-dependent catalytic antibodies

Cofactors—i.e., metal ions and coenzymes—extend the catalytic scope of enzymes and might have been among the first biological catalysts. They may be expected to efficiently extend the catalytic potential of antibodies. Monoclonal antibodies (MAbs) against Nα-phosphopyridoxyl-l-lysine were screened for 1) binding of 5′-phosphopyridoxyl amino acids, 2) binding of the planar Schiff base of pyridoxal-5′-phosphate (PLP) and amino acids, the first intermediate of all PLP-dependent reactions, and 3), catalysis of the PLP-dependent α, β-elimination reaction with β-chloro-D/L-alanine. Antibody 15A9 fulfilled all criteria and was also found to catalyze the cofactor-dependent transamination reaction of hydrophobic D-amino acids and oxo acids (k′ cat=0.42 min−1 with D-alanine at 25°C). No other reactions with either D- or L-amino acids were detected. PLP markedly contributes to catalytic effecacy—it is a 104 times more efficient acceptor of the amino group than pyruvate. The antibody ensures reaction specificity, stereospecificity, and substrate specificity, and further accelerates the transamination reaction (k′ cat(Ab)/k′ cat(PLP)=5×103). The successive screening steps simulate the selection criteria that might have been operative in the evolution of protein-assisted psyridoxal catalysi

PMAP: databases for analyzing proteolytic events and pathways.

The Proteolysis MAP (PMAP, http://www.proteolysis.org) is a user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The foundation databases, ProteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic 'Molecule Pages', rich in molecular information. PMAP also contains two community annotated databases focused on function; CutDB has information on more than 5000 proteolytic events, and ProfileDB is dedicated to information of the substrate recognition specificity of proteases. Together, the content within these four databases will ultimately feed PathwayDB, which will be comprised of known pathways whose function can be dynamically modeled in a rule-based manner, and hypothetical pathways suggested by semi-automated culling of the literature. A Protease Toolkit is also available for the analysis of proteases and proteolysis. Here, we describe how the databases of PMAP can be used to foster understanding of proteolytic pathways, and equally as significant, to reason about proteolysis