Article
Functional evolution of PLP-dependent enzymes based on active-site structural similarities
Jonathan Catazaro,
Adam Caprez,
Ashu Guru,
David Swanson,
Robert Powers,
Jonathan Catazaro
Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
Search for more papers by this authorAdam Caprez
Holland Computing Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0150
Search for more papers by this authorAshu Guru
Holland Computing Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0150
Search for more papers by this authorDavid Swanson
Holland Computing Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0150
Search for more papers by this authorCorresponding Author
Robert Powers
Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
Correspondence to: Robert Powers, Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304. E-mail: [email protected]Search for more papers by this authorJonathan Catazaro,
Adam Caprez,
Ashu Guru,
David Swanson,
Robert Powers,
Jonathan Catazaro
Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
Search for more papers by this authorAdam Caprez
Holland Computing Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0150
Search for more papers by this authorAshu Guru
Holland Computing Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0150
Search for more papers by this authorDavid Swanson
Holland Computing Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0150
Search for more papers by this authorCorresponding Author
Robert Powers
Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588-0304
Correspondence to: Robert Powers, Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304. E-mail: [email protected]Search for more papers by this authorABSTRACT
Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5′-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. Proteins 2014; 82:2597–2608. © 2014 Wiley Periodicals, Inc.
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