The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

Abstract

The Catalytic Site Atlas (CSA) provides catalytic residue annotation for enzymes in the Protein Data Bank. It is available online at http://www.ebi.ac.uk/thornton-srv/databases/CSA. The database consists of two types of annotated site: an original hand-annotated set containing information extracted from the primary literature, using defined criteria to assign catalytic residues, and an additional homologous set, containing annotations inferred by PSI-BLAST and sequence alignment to one of the original set. The CSA can be queried via Swiss-Prot identifier and EC number, as well as by PDB code. CSA Version 1.0 contains 177 original hand- annotated entries and 2608 homologous entries, and covers approximately 30% of all EC numbers found in PDB. The CSA will be updated on a monthly basis to include homologous sites found in new PDBs, and new hand-annotated enzymes as and when their annotation is completed.

Figure 1

Schematic description of CSA database. The blue block demonstrates the ‘original’ enzyme data for enolase, PDB code 5enl. The central block shows ‘homologous’ enzymes identified by PSI-BLAST analysis, and one of these, PDB code 1pdz, is highlighted in green as an example homologue. The green block at the bottom demonstrates the ‘homologous’ enzyme datzyme data set, in Venn diagram form. The number of residues annotated by each database is given, along with the number of identical residues found in both databases.

Figure 2

A comparison of residue annotation between the CSA and SwissProt (left) and PDB (right) for the ‘original’ enzyme dataset, in Venn diagram form. The number of residues annotated by each database is given, along with the number of identical residues found in both databases.

Figure 3

EC wheel functional description of the ‘original’ enzyme set (above) and the ‘homologous’ enzyme set (below) in the CSA database. The EC classification (7) assigns a four-digit number to the reaction catalysed by an enzyme, where the first digit denotes the class of reaction (1.-.-.- oxidoreductases, 2.-.-.- transferases, 3.-.-.- hydrolases, 4.-.-.- lyases, 5.-.-.- isomerases and 6.-.-.- ligases) and subsequent levels define the reaction in more detail by substrate, bond broken, etc. The outer wheel segments are proportional to the number of enzyme structures in the database with a particular EC number.

Figure 3

EC wheel functional description of the ‘original’ enzyme set (above) and the ‘homologous’ enzyme set (below) in the CSA database. The EC classification (7) assigns a four-digit number to the reaction catalysed by an enzyme, where the first digit denotes the class of reaction (1.-.-.- oxidoreductases, 2.-.-.- transferases, 3.-.-.- hydrolases, 4.-.-.- lyases, 5.-.-.- isomerases and 6.-.-.- ligases) and subsequent levels define the reaction in more detail by substrate, bond broken, etc. The outer wheel segments are proportional to the number of enzyme structures in the database with a particular EC number.