PDBsum entry 6tcc

Unknown function

PDB id: 6tcc

Contents

Protein chain

134 a.a.

Ligands

ACT

EDO

PEG

Waters ×94

PDB id:

6tcc

Name:

Unknown function

Title:

Crystal structure of salmo salar rida-1

Structure:

Ribonuclease uk114. Chain: a. Engineered: yes

Source:

Salmo salar. Atlantic salmon. Organism_taxid: 8030. Gene: hrsp12. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.05Å R-factor: 0.146 R-free: 0.163

Authors:

S.Ricagno,C.Visentin,F.Di Pisa,S.Digiovanni,L.Oberti,G.Degani, L.Popolo,A.Bartorelli

Key ref:

S.Digiovanni et al. (2020). 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. PubMed id: 32576850 DOI: 10.1038/s41598-020-66663-w

Date:

05-Nov-19 Release date: 29-Jul-20

Protein chain

A0A1S3KNQ3  (A0A1S3KNQ3_SALSA) -  Ribonuclease UK114 from Salmo salar

Seq: 136 a.a.

Struc: 134 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.99.10 - 2-iminobutanoate/2-iminopropanoate deaminase.
• Reaction:
  1. 2-iminobutanoate + H2O = 2-oxobutanoate + NH4⁺
  2. 2-iminopropanoate + H2O = pyruvate + NH4⁺

2-iminobutanoate + H2O = 2-oxobutanoate (Bound ligand (Het Group name = ACT) matches with 57.14% similarity) + NH4(+)

2-iminopropanoate + H2O = pyruvate + NH4(+) (Bound ligand (Het Group name = ACT) matches with 66.67% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/s41598-020-66663-w

Sci Rep 10:10135 (2020)

PubMed id: 32576850

Two novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage.

S.Digiovanni, C.Visentin, G.Degani, A.Barbiroli, M.Chiara, L.Regazzoni, F.Di Pisa, A.J.Borchert, D.M.Downs, S.Ricagno, M.A.Vanoni, L.Popolo.

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. _SsRidA-1 and _SsRidA-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. _SsRidA-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, _SsRidA-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 _SsRidA-1 and _SsRidA-2 provided hints of the remarkably different conformational stability and substrate specificity. Overall, _SsRidA-1 is similar to the mammalian orthologs whereas _SsRidA-2 displays unique properties likely generated by functional specialization of a duplicated ancestral gene.