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Classification of doubly wound nucleotide binding topologies using automated loop searches
1Protein Engineering Research Institute, Osaka, Japan.
Protein Science : a Publication of the Protein Society
|December 1, 1993
Summary
This study classifies nucleotide binding protein structures using loop conformations. It reveals unexpected functional similarities between flavodoxin and tryptophan synthetase binding sites despite different sequences and topologies.
Area of Science:
- Structural biology
- Protein science
- Bioinformatics
Background:
- Doubly wound alpha/beta nucleotide binding proteins share common structural features.
- Binding sites are often located in clefts formed by topological switch points.
Purpose of the Study:
- To classify nucleotide binding protein topologies based on structural features.
- To identify functional relationships between proteins using structural motifs.
Main Methods:
- Classification of doubly wound alpha/beta nucleotide binding topologies.
- Identification of seven distinct loop conformations near the N-terminus switch point.
- Scanning the Protein Data Bank (PDB) using these loop conformations as motifs.
Main Results:
- Seven distinct loop conformations were identified, defining specific structural classes.
- The Protein Data Bank scan effectively identified functional relationships.
- A previously unrecognized similarity was found between coenzyme binding sites of flavodoxin and tryptophan synthetase.
Conclusions:
- Loop conformations serve as effective structural motifs for protein classification and functional relationship discovery.
- Structural similarities can exist between proteins with no sequence or topological homology.
- This classification provides new insights into protein evolution and function.