5HP8

Crystal structures of RidA in complex with pyruvate

Summary for 5HP8

• Entry DOI: 10.2210/pdb5hp8/pdb
• Related: 5HP7
• Descriptor: Reactive Intermediate Deaminase A, chloroplastic, PYRUVIC ACID (3 entities in total)
• Functional Keywords: rida, enamine/imine, deamination, hydrolase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Cellular location: Plastid, chloroplast : Q94JQ4
• Total number of polymer chains: 3
• Total formula weight: 39957.60

Authors

Xie, W.,Liu, X. (deposition date: 2016-01-20, release date: 2016-10-12, Last modification date: 2023-11-15)

Primary citation

Liu, X.,Zeng, J.,Chen, X.,Xie, W.
Crystal structures of RidA, an important enzyme for the prevention of toxic side products
Sci Rep, 6:30494-30494, 2016

PubMed Abstract: The YjgF/YER057c/UK114 family proteins are highly conserved across all three domains of life, and most of them currently have no clearly defined biological roles. In vitro, these proteins were found to hydrolyze the enamine/imine intermediates generated from serine or threonine, and were renamed Reactive Intermediate Deaminase A (RidA). RidA was recently discovered in Arabidopsis thaliana, and by deaminating the toxic enamine/imine intermediates, it prevents the inactivation of many functionally important pyridoxal 5'-phosphate (PLP)-containing enzymes in plants such as branched-chain aminotransferase BCAT (IlvE). In this study, we determined the crystal structure of Arabidopsis thaliana RidA in the apo form, as well as RidA complexed with the ligand pyruvate. RidA forms the trimeric, barrel-like quaternary structure and inter-subunit cavities, and resembles most RidA family members. Each pyruvate molecule binds to the interface between two subunits, and the recognition of pyruvate is achieved by the interactions with R165 and T167. From sequence alignment and structural superposition, we identified a series of key residues responsible for the trimer assembly, whose importance was confirmed by enzymatic assays. This study provides structural insight into RidA functions in plants.

PubMed: 27458092
DOI: 10.1038/srep30494

Experimental method

X-RAY DIFFRACTION (2.3 Å)