The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution

Abstract

We report the latest release (version 3.0) of the CATH protein domain database (). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in diverse structural homologues being determined by the structural genomics initiatives, more sensitive methods have been developed for identifying boundaries in multi-domain proteins and for recognising homologues. The CATH classification update is now being driven by an integrated pipeline that links these automated procedures with validation steps, that have been made easier by the provision of information rich web pages summarising comparison scores and relevant links to external sites for each domain being classified. An analysis of the population of domains in the CATH hierarchy and several domain characteristics are presented for version 3.0. We also report an update of the CATH Dictionary of homologous structures (CATH-DHS) which now contains multiple structural alignments, consensus information and functional annotations for 1459 well populated superfamilies in CATH. CATH is directly linked to the Gene3D database which is a projection of CATH structural data onto ∼2 million sequences in completed genomes and UniProt.

Structural and Functional Assays of AtTLP18.3 Identify Its Novel Acid Phosphatase Activity in Thylakoid Lumen

“…To investigate the molecular function of AtTLP18.3 from the resolved structure, we submitted the coordinates of AtTLP18.3 to the CATH server (Kawabata, 2003;Greene et al, 2007) to reveal its structure classification. The results indicated that the folding of AtTLP18.3 belongs to a Rossmann fold (CATH code 3.40.50) with an architecture of a three-layer (aba) sandwich.…”

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

“…Protein classification could be an illustrative example to show the needs. A major goal of SCOP (structural classification of proteins) 8 and CATH (class, architecture, topology, homologous superfamily) 9 is to understand the structural, functional, and evolutionary relationships among proteins by classifying domains according to their structure. This structure-based approach may be effective in detecting distant relationships across proteins.…”

Assessing functional novelty of PSI structures via structure-function analysis of large and diverse superfamilies

“…The CATH database [4] was filtered to select superfamilies with (a) more than 20 sequence diverse relatives (sequence identity lower than 35%), (b) at least 3 different EC numbers (down to the 3rd level), and (c) structures solved as part of the Protein Structure Initiative and in particular the Midwest Center for Structural Genomics (MCSG) with which we collaborate directly. We then manually checked the set of superfamilies thus selected, to further restrict our analysis to 3 superfamilies with a wide range of molecular functions: the HUP domain superfamily (CATH 3.40.50.620) that was chosen because it is very ancient and presents a particularly striking diversity of entirely unrelated functions; the HAD superfamily (CATH 3.40.50.1000) that was chosen as one of the superfamilies considered in the above mentioned SFLD; and the PBP like superfamily (CATH 3.40.190.10) that we selected to study function diversity in a superfamily that includes many non enzymatic functions.…”