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Evolution of vitamin B2 biosynthesis: eubacterial RibG and fungal Rib2 deaminases.
Sheng Chia Chen1, Chieh Yi Shen, Te Ming Yen
1Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan.
Acta Crystallographica. Section D, Biological Crystallography
|February 7, 2013
Summary
Bacillus subtilis RibG crystal structure reveals substrate-induced conformational changes crucial for riboflavin biosynthesis. These findings illuminate enzyme catalysis mechanisms and substrate recognition in deaminases.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- Riboflavin biosynthesis involves pyrimidine deamination by specific enzymes like bacterial RibG and yeast Rib2.
- RibG and Rib2 exhibit distinct substrate specificities for ribose and ribitol, respectively.
Purpose of the Study:
- To elucidate the structural basis of Bacillus subtilis RibG's catalytic mechanism.
- To understand substrate recognition mechanisms in RibG and Rib2 through structural modeling and mutational analysis.
Main Methods:
- X-ray crystallography of Bacillus subtilis RibG complexed with a deaminase product.
- Homology modeling of yeast Rib2 structure.
- Site-directed mutagenesis and functional analysis.
Main Results:
- The crystal structure of B. subtilis RibG revealed substrate-induced loop movements and significant conformational changes.
- The catalytic zinc ion coordinates with a distorted carbonyl moiety of the bound product.
- A conserved amino-binding pocket, formed by carbonyl backbones preceding the PCXXC motif, was identified as essential for substrate recognition.
Conclusions:
- Substrate-induced conformational changes in RibG are vital for catalysis.
- The identified amino-binding pocket is a key feature for substrate recognition in RibG and is conserved across related deaminases.
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