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The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While rel...

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Autores principales: Cuff, Alison, Redfern, Oliver C., Greene, Lesley, Sillitoe, Ian, Lewis, Tony, Dibley, Mark, Reid, Adam, Pearl, Frances, Dallman, Tim, Todd, Annabel, Garratt, Richard, Thornton, Janet, Orengo, Christine
Formato: Texto
Lenguaje:English
Publicado: Cell Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741583/
https://www.ncbi.nlm.nih.gov/pubmed/19679085
http://dx.doi.org/10.1016/j.str.2009.06.015
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author Cuff, Alison
Redfern, Oliver C.
Greene, Lesley
Sillitoe, Ian
Lewis, Tony
Dibley, Mark
Reid, Adam
Pearl, Frances
Dallman, Tim
Todd, Annabel
Garratt, Richard
Thornton, Janet
Orengo, Christine
author_facet Cuff, Alison
Redfern, Oliver C.
Greene, Lesley
Sillitoe, Ian
Lewis, Tony
Dibley, Mark
Reid, Adam
Pearl, Frances
Dallman, Tim
Todd, Annabel
Garratt, Richard
Thornton, Janet
Orengo, Christine
author_sort Cuff, Alison
collection PubMed
description This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can result in significant differences in the global structures. Applying similar protocols to examine the extent to which structural overlaps occur between different fold groups, it appears this effect is confined to just a few architectures and is largely due to small, recurring super-secondary motifs (e.g., αβ-motifs, α-hairpins). Although 24% of superfamilies overlap with superfamilies having different folds, only 14% of nonredundant structures in CATH are involved in overlaps. Nevertheless, the existence of these overlaps suggests that, in some regions of structure space, the fold universe should be seen as more continuous.
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spelling pubmed-27415832009-09-17 The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space Cuff, Alison Redfern, Oliver C. Greene, Lesley Sillitoe, Ian Lewis, Tony Dibley, Mark Reid, Adam Pearl, Frances Dallman, Tim Todd, Annabel Garratt, Richard Thornton, Janet Orengo, Christine Structure Article This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can result in significant differences in the global structures. Applying similar protocols to examine the extent to which structural overlaps occur between different fold groups, it appears this effect is confined to just a few architectures and is largely due to small, recurring super-secondary motifs (e.g., αβ-motifs, α-hairpins). Although 24% of superfamilies overlap with superfamilies having different folds, only 14% of nonredundant structures in CATH are involved in overlaps. Nevertheless, the existence of these overlaps suggests that, in some regions of structure space, the fold universe should be seen as more continuous. Cell Press 2009-08-12 /pmc/articles/PMC2741583/ /pubmed/19679085 http://dx.doi.org/10.1016/j.str.2009.06.015 Text en © 2009 ELL & Excerpta Medica. https://creativecommons.org/licenses/by/3.0/ Open Access under CC BY 3.0 (https://creativecommons.org/licenses/by/3.0/) license
spellingShingle Article
Cuff, Alison
Redfern, Oliver C.
Greene, Lesley
Sillitoe, Ian
Lewis, Tony
Dibley, Mark
Reid, Adam
Pearl, Frances
Dallman, Tim
Todd, Annabel
Garratt, Richard
Thornton, Janet
Orengo, Christine
The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
title The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
title_full The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
title_fullStr The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
title_full_unstemmed The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
title_short The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space
title_sort cath hierarchy revisited—structural divergence in domain superfamilies and the continuity of fold space
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741583/
https://www.ncbi.nlm.nih.gov/pubmed/19679085
http://dx.doi.org/10.1016/j.str.2009.06.015
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