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Catalytic Site Atlas

CSA: Help and Documentation Page

The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.
The CSA contains 2 types of entry:

  • Original hand-annotated entries, derived from the primary literature. References for these entries are given.
  • Homologous entries, found by sequence comparison methods to one of the original entries. The equivalent residues, which align in sequence to the catalytic residues found in the original entry are documented.
Access to the CSA is via PDB ID, UniProtKB ID or E.C. number. Accessing via PDB ID takes you straight to the CSA entry for that PDB, while accessing via UniProtKB ID or E.C. number gives a list of all PDB codes for structures assigned that particular UniProtKB identifier or E.C. number.

Each CSA entry lists the catalytic residues found in that entry, using PDB residue numbering. Each site is also marked with an evidence tag, which is either "Literature reference" or "Homologue". If the entry is by sequence comparison you can follow the link to the original entry. The active site can be visualised using a JMol viewer and each catalytic site in the structure can be highlighted and zoomed into by selecting from the drop down list on the left hand side of the viewer as well as further rendering options.

Each entry contains a link to a list of homologous entries found by homology, and a link to other PDB structures with identical E.C. numbers or UniProKB identifier to the entry you are viewing.

Homologous entries

Entries in the CSA can be divided into literature entries (for which the catalytic residues are derived directly from papers) and homologous entries, found by sequence comparison to one of the original entries.

Catalytic Site Atlas Entries

  1. E.C. Name - The name of the enzyme according to the E.C.
  2. Species - The species fot the relevant enzyme.
  3. E.C. Number - The E.C. number as assigned by the E.C.
  4. CSA Homologues - Number of homologues found in the CSA for the specific enzyme.
  5. CSA Entries with UniProt ID - Link to a list of enzyme structures which share the same SWISS-PROT identifier as the enzyme.
  6. CSA Entries with EC Number - Link to a list of enzyme structures which share the same EC number as the enzyme shown here. Those with entries in the CSA are shown as hyperlinks.
  7. PDBe Entry - Link to PDBe PDB site.
  8. PDBSum Entry - Link to PDBsum summary of the enzyme structure.
  9. MACiE Entry - A link to the relevant entry in MACiE.

CSA entry annotated from literature

  1. Introduction - A brief introduction of the enzyme\'s function.
  2. Mechanism - A detailed description of the mechanism of the enzyme.
  3. Reaction - The chemical representation of the reaction.
  4. Catalytic Sites - The section showing the catalytic residues found in literature.
  5. Residue - The specific residue involved in catalysis
  6. Chain - The chain in the protein on which the catalytic residue occurs.
  7. Number - The residue number in the chain as found in the structure.
  8. UniProtKB Number - The residue number as found in the UniProtKB sequence.
  9. Functional Part - The part of the residue that takes part in the catalytic reaction.
  10. Function - The role played by the specific residue in the reaction.
  11. Target - Which part of the reaction the catalytic residue lays a role in.
  12. Description - Detailed description of the role played by the residue in catalysis.


CSA entry annotated by homology

  1. Annotated by Homology - The specific site that is shown as well as a link to the structure that was used to annotate the function.
  2. Residue - The residue predicted to be involved in catalysis.
  3. Chain - The chain on which the residue is located.
  4. PDB Number - The number of the annotated residue in the current structure.
  5. UniProtKB Number - The number of the annotated residue in the UniProtKB sequence.

References

  • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Craig T. Porter, Gail J. Bartlett, and Janet M. Thornton (2004) Nucl. Acids. Res. 32: D129-D133.
  • Analysis of Catalytic Residues in Enzyme Active Sites. Gail J. Bartlett, Craig T. Porter, Neera Borkakoti, and Janet M. Thornton (2002) J Mol Biol 324:105-121.
  • Using a Library of Structural Templates to Recognise Catalytic Sites and Explore their Evolution in Homologous Families. James W. Torrance, Gail J. Bartlett, Craig T. Porter, Janet M. Thornton (2005) J Mol Biol. 347:565-81
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