CATH -- a hierarchic classification of protein domain structures

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CATH -- a hierarchic classification of protein domain structures (1997)

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by C A Orengo , A D Michie , S Jones , D T Jones , M B Swindells , J M Thornton

Venue:	STRUCTURE
Citations:	470 - 33 self

BibTeX

@ARTICLE{Orengo97cath--,
    author = {C A Orengo and A D Michie and S Jones and D T Jones and M B Swindells and J M Thornton},
    title = {CATH -- a hierarchic classification of protein domain structures},
    journal = {STRUCTURE},
    year = {1997},
    volume = {5},
    pages = {1093--1108}
}

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Abstract

Background: Protein evolution gives rise to families of structurally related proteins, within which sequence identities can be extremely low. As a result, structure-based classifications can be effective at identifying unanticipated relationships in known structures and in optimal cases function can also be assigned. The ever increasing number of known protein structures is too large to classify all proteins manually, therefore, automatic methods are needed for fast evaluation of protein structures. Results: We present a semi-automatic procedure for deriving a novel hierarchical classification of protein domain structures (CATH). The four main levels of our classification are protein class (C), architecture (A), topology (T) and homologous superfamily (H). Class is the simplest level, and it essentially describes the secondary structure composition of each domain. In contrast, architecture summarises the shape revealed by the orientations of the secondary structure units, such as barrels and sandwiches. At the topology level, sequential connectivity is considered, such that members of the same architecture might have quite different topologies. When structures belonging to the same T-level have suitably high similarities combined with similar functions, the proteins are assumed to be evolutionarily related and put into the same homologous superfamily. Conclusions: Analysis of the structural families generated by CATH reveals the prominent features of protein structure space. We find that nearly a third of the homologous superfamilies (H-levels) belong to ten major T-levels, which we call superfolds, and furthermore that nearly two-thirds of these H-levels cluster into nine simple architectures. A database of well-characterised protein structure families, such as CATH, will facilitate the assignment of structure–function/ evolution relationships to both known and newly determined protein structures.

Keyphrases

protein domain structure hierarchic classification protein structure h-levels cluster secondary structure unit unanticipated relationship main level sequence identity automatic method structural family novel hierarchical classification structure function evolution relationship different topology homologous superfamily well-characterised protein structure family topology level secondary structure composition major t-levels prominent feature protein evolution known protein structure protein structure space protein class similar function semi-automatic procedure fast evaluation optimal case function related protein sequential connectivity simple architecture structure-based classification known structure high similarity

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