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Classification of doubly wound nucleotide binding topologies using automated loop searches
Author(s) -
Swindells Mark B.
Publication year - 1993
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560021214
Subject(s) - binding site , loop (graph theory) , similarity (geometry) , flavodoxin , computational biology , network topology , nucleotide , topology (electrical circuits) , protein data bank , structural similarity , biology , protein structure , chemistry , biochemistry , computer science , artificial intelligence , mathematics , gene , combinatorics , ferredoxin , enzyme , image (mathematics) , operating system
A classification is presented of doubly wound α/β nucleotide binding topologies, whose binding sites are located in the cleft formed by a topological switch point. In particular, the switch point loop nearest the N‐terminus is used to identify specific structural classes of binding protein. This yields seven structurally distinct loop conformations, which are subsequently used as motifs for scanning the Protein Data Bank. The searches, which are effective at identifying functional relationships within a large database of structures, reveal a remarkable and previously unnoticed similarity between the coenzyme binding sites of flavodoxin and tryptophan synthetase, even though there is no sequence or topological similarity between them.