6TCD

Crystal structure of Salmo salar RidA-2

Summary for 6TCD

• Entry DOI: 10.2210/pdb6tcd/pdb
• Descriptor: Ribonuclease UK114, ACETATE ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: rida, imine deaminase, yigf/yer057c/uk114, unknown function
• Biological source: Salmo salar (Atlantic salmon)
• Total number of polymer chains: 6
• Total formula weight: 89008.95

Authors

Ricagno, S.,Visentin, C.,Di Pisa, F.,Digiovanni, S.,Oberti, L.,Degani, G.,Popolo, L.,Bartorelli, A. (deposition date: 2019-11-05, release date: 2020-07-29, Last modification date: 2024-01-24)

Primary citation

Digiovanni, S.,Visentin, C.,Degani, G.,Barbiroli, A.,Chiara, M.,Regazzoni, L.,Di Pisa, F.,Borchert, A.J.,Downs, D.M.,Ricagno, S.,Vanoni, M.A.,Popolo, L.
Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage.
Sci Rep, 10:10135-10135, 2020

PubMed Abstract: Reactive Intermediate Deaminase (Rid) protein superfamily includes eight families among which the RidA is conserved in all domains of life. RidA proteins accelerate the deamination of the reactive 2-aminoacrylate (2AA), an enamine produced by some pyridoxal phosphate (PLP)-dependent enzymes. 2AA accumulation inhibits target enzymes with a detrimental impact on fitness. As a consequence of whole genome duplication, teleost fish have two ridA paralogs, while other extant vertebrates contain a single-copy gene. We investigated the biochemical properties of the products of two paralogs, identified in Salmo salar. RidA-1 and RidA-2 complemented the growth defect of a Salmonella enterica ridA mutant, an in vivo model of 2AA stress. In vitro, both proteins hydrolyzed 2-imino acids (IA) to keto-acids and ammonia. RidA-1 was active on IA derived from nonpolar amino acids and poorly active or inactive on IA derived from other amino acids tested. In contrast, RidA-2 had a generally low catalytic efficiency, but showed a relatively higher activity with IA derived from L-Glu and aromatic amino acids. The crystal structures of RidA-1 and RidA-2 provided hints of the remarkably different conformational stability and substrate specificity. Overall, RidA-1 is similar to the mammalian orthologs whereas RidA-2 displays unique properties likely generated by functional specialization of a duplicated ancestral gene.

PubMed: 32576850
DOI: 10.1038/s41598-020-66663-w

Experimental method

X-RAY DIFFRACTION (1.36 Å)