Evolution of vitamin B2 biosynthesis: eubacterial RibG and fungal Rib2 deaminases. (6th February 2013)

• Record Type: Journal Article
• Authors: Chen, Sheng‐Chia; Shen, Chieh‐Yi; Yen, Te‐Ming; Yu, Hui‐Chia; Chang, Ting‐Hao; Lai, Wen‐Lin; Liaw, Shwu‐Huey
• Is Part Of: Acta crystallographica. Volume 69:Part 2(2013:Feb.)
• Page Start: 227
• Page End: 236
• Publication Date: 2013-02-06
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S0907444912044903
• Languages: English
• ISSNs: 0907-4449

Abstract

<abstract abstract-type="main" xml:lang="en"> <title> <x xml:space="preserve">Abstract</x> </title> <p>Eubacterial RibG and yeast Rib2 possess a deaminase domain for pyrimidine deamination in the second and third steps, respectively, of riboflavin biosynthesis. These enzymes are specific for ribose and ribitol, respectively. Here, the crystal structure of <italic>Bacillus subtilis</italic> RibG in complex with a deaminase product is reported at 2.56 Å resolution. Two loops move towards the product on substrate binding, resulting in interactions with the ribosyl and phosphate groups and significant conformational changes. The product carbonyl moiety is bent out of the pyrimidine ring to coordinate to the catalytic zinc ion. Such distortions in the bound substrate and product may play an essential role in enzyme catalysis. The yeast Rib2 structure was modelled and a mutational analysis was carried out in order to understand the mechanism of substrate recognition in these two enzymes. Detailed structural comparisons revealed that the two consecutive carbonyl backbones that occur prior to the PC<italic>XX</italic>C signature constitute a binding hole for the target amino group of the substrate. This amino‐binding hole is essential in <italic>B. subtilis</italic> RibG and is also conserved in the RNA/DNA‐editing deaminases.</p> </abstract>