lecture3 - Bioinformatics 2 lecture 3 Structure...

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Bioinformatics 2 -- lecture 3 Structure classifcation TOPS Domains
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CATH • Class • Architecture • Topology • Homology http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html
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Structure classification: SCOP • Contains information about classification of protein structures and within that classification, their sequences • http://scop.berkeley.edu
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Structure classification: SCOP (1) class (2) fold (3) superfamily (4) family (5) protein (6) species global characteristics (no evolutionary relation) Similar “topology” . Distant evolutionary cousins? Clear structural homology Clear sequence homology functionally identical unique sequences http://scop.berkeley.edu
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protein classes 1. all α (126) 2. all β (81) 3. α / β (87) 4. α + β (151) 5. multidomain (21) 6. membrane (21) 7. small (10) 8. coiled coil (4) 9. low-resolution (4) 10. peptides (61) 11. designed proteins (17) number of sub-categories (126) possibly not complete, or erroneous Not true classes
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class: α / β proteins Folds : TIM-barrel (22) swivelling beta/beta/alpha domain (5) spoIIaa-like (2) favodoxin-like (10) restriction endonuclease-like (2) ribokinase-like (2) chelatase-like (2) Mainly parallel beta sheets (beta-alpha-beta units) Many Folds have historical names. “TIM” barrel was ±rst seen in TIM. These classi±cations are done by eye, mostly.
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fold: flavodoxin-like Superfamilies: 1.Catalase, C-terminal domain (1) 2.CheY-like (1) 3.Succinyl-CoA synthetase domains (1) 4.Flavoproteins (3) 5.Cobalamin (vitamin B12)-binding domain (1) 6.Ornithine decarboxylase N-terminal "wing" domain (1)
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lecture3 - Bioinformatics 2 lecture 3 Structure...

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