CATH - Protein Structure Classification

Introduction

The CATH database is a hierarchical domain classification of protein structures in the Brookhaven protein databank. All non-protein, model, and "C-alpha only" structures are not classified in CATH. Only crystal structures solved to resolution better than 3.0 angstroms are considered, together with NMR structures. This filtering of the Brookhaven databank is performed using the program SIFT (Michie et al, (1996)). There are four major levels in this hierarchy; Class, Architecture, Topology (fold family) and Homologous superfamily. Each level is described below, together with the methods used for assigning structures to a specific family.
 
 

Domains

Multidomain proteins are subdivided into their constituent domains using a consensus procedure (Jones et al, submitted), based on three independent algorithms for domain recognition (DETECTIVE (Swindells, 1995), PUU (Holm & Sander, 1994) and DOMAK (Siddiqui and Barton, 1995). This currently allows approximately 53% of the proteins (i.e. those for which these algorithms agree) to be defined as single or multidomain proteins automatically. The remaining structures are assigned domain definitions manually, by choosing what was determined to be the best assignment made by one of the algorithms, a new assignment, or an alternative assignment obtained from the literature. The multidomain proteins are then split into their separate domains. All the classification is performed on individual protein domains. 
 
 

The CATH hierarchy

Class is determined according to the secondary structure composition and packing within the structure. It can be assigned automatically for over 90% of the known structures using the method of Michie et al. (1996). For the remainder, manual inspection is used and where necessary information from the literature taken into account. Three major classes are recognised; mainly-alpha, mainly-beta and alpha-beta. This last class (alpha-beta) includes both alternating alpha/beta structures and alpha+beta structures, as originally defined by Levitt and Chothia (1976). A fourth class is also identified which contains protein domains which have low secondary structure content. 
 
 

This describes the overall shape of the domain structure as determined by the orientations of the secondary structures but ignores the connectivity between the secondary structures. It is currently assigned manually using a simple description of the secondary structure arrangement e.g. barrel or 3-layer sandwich. Reference is made to the literature for well-known architectures (e.g the beta-propellor or alpha four helix bundle). Procedures are being developed for automating this step. 
 
 

Structures are grouped into fold families at this level depending on both the overall shape and connectivity of the secondary structures. This is done using the structure comparison algorithm SSAP (Taylor & Orengo (1989)). Parameters for clustering domains into the same fold family have been determined by empirical trials throughout the databank (Orengo et al. (1992), Orengo et al. (1993)). Structures which have a SSAP score of 70 and where at least 60% of the larger protein matches the smaller protein are assigned to the same T level or fold family. 

Some fold families are very highly populated (Orengo et al. (1994)) particularly within the mainly-beta 2-layer sandwich architectures and the alpha-beta 3-layer sandwich architectures. In order to appreciate the structural relationships within these families more easily, they are currently subdivided using a higher cutoff on the SSAP score (75 for some mainly-beta and alpha-beta families, 80 for some mainly-alpha families, together with a higher overlap requirement (70%)).
 
 

This level groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous. Similarities are identified first by sequence comparisons and subsequently by structure comparison using SSAP. Structures are clustered into the same homologous superfamily if they satisfy one of the following criteria: 

• Sequence identity >= 35%, 60% of larger structure equivalent to smaller 
• SSAP score >= 80.0 and sequence identity >= 20%

60% of larger structure equivalent to smaller 
• SSAP score >= 80.0, 60% of larger structure equivalent to smaller, and 

domains which have related functions

Structures within each H-level are further clustered on sequence identity. Domains clustered in the same sequence families have sequence identities >35% (with at least 60% of the larger domain equivalent to the smaller), indicating highly similar structures and functions. 

DIAGRAM DEPICTING THE HIERARCHICAL NATURE OF CATH