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Published on: May 13, 2020
Functional evolution of PLP-dependent enzymes based on active-site structural similarities
Jonathan Catazaro1, Adam Caprez, Ashu Guru
1Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304.
Active site structures reveal evolutionary relationships in enzyme families. This method aids in functional annotation for distantly related proteins, overcoming low sequence identity challenges.
Area of Science:
- Biochemistry
- Structural Biology
- Evolutionary Biology
Background:
- Distantly related proteins exhibit low sequence identity, complicating evolutionary analysis and functional annotation.
- Active sites are slowly evolving protein features valuable for annotating distantly related proteins.
- A comprehensive evolutionary analysis of enzyme families using active-site structural similarity has been lacking.
Purpose of the Study:
- To investigate the utility of active site structures for inferring evolutionary relationships within enzyme families.
- To demonstrate that active site structures can reveal functional similarities among distantly related proteins.
- To evaluate the effectiveness of the Comparison of Protein Active Site Structures (CPASS) software and database.
Main Methods:
- Utilized the CPASS software and database for structural comparison of protein active sites.
- Focused on Pyridoxal-5'-phosphate (PLP)-dependent enzymes, known for their ancient origins.
- Analyzed active site structural similarities to infer functional and evolutionary relationships.
Main Results:
- Active site structures of PLP-dependent enzymes successfully clustered based on substrate specificity, function, and 3D fold.
- Demonstrated that active site structural similarity is a reliable indicator of functional and evolutionary relatedness.
- Validated the effectiveness of CPASS in analyzing enzyme family evolution.
Conclusions:
- Active site structures are valuable for functional evolutionary analysis, especially for distantly related proteins.
- CPASS is an effective tool for inferring evolutionary relationships based on active site structural similarities.
- This approach enhances the annotation of protein function and understanding of enzyme evolution.
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