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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Structural and functional diversity of Nudix fold
Jun Lin1, Bing Tian, Yuejin Hua
1Institute of Nuclear-Agricultural Sciences, Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, 310029, China.
Nudix hydrolases are enzymes with diverse mechanisms. This study analyzes their sequences and structures, proposing a new, objective classification for the MutT/Nudix superfamily.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Nudix hydrolases are a superfamily of enzymes catalyzing the hydrolysis of nucleoside diphosphates linked to various moieties.
- These enzymes are characterized by a conserved Nudix box sequence motif (GX5EX7REUXEEXGU).
- The catalytic mechanisms and substrate specificities within the Nudix hydrolase superfamily are highly diverse.
Purpose of the Study:
- To examine the sequences and structures of the MutT/Nudix superfamily.
- To develop a more objective classification system for Nudix hydrolase members.
- To understand the evolutionary relationships and functional diversity within the superfamily.
Main Methods:
- Utilized the QH method for evaluating structural similarities and performing structural phylogeny.
- Employed CLANS program for clustering analysis of thousands of full-sequence datasets.
- Conducted detailed sequence and structure analyses of the MutT/Nudix superfamily.
Main Results:
- Identified conserved sequence and structural features across the MutT/Nudix superfamily.
- Demonstrated the effectiveness of QH and CLANS methods for large-scale sequence and structure analysis.
- Revealed distinct clusters and potential subfamilies within the superfamily based on sequence and structural data.
Conclusions:
- A refined and objective classification of the MutT/Nudix superfamily is proposed.
- The study provides insights into the evolutionary history and functional diversification of Nudix hydrolases.
- This classification can aid in predicting the function of uncharacterized Nudix hydrolase family members.
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