7WG2

EVAA-KlAte1

Summary for 7WG2

• Entry DOI: 10.2210/pdb7wg2/pdb
• Descriptor: Arginyltransferase, ZINC ION (3 entities in total)
• Functional Keywords: arginyl-trna protein transferase 1, transferase
• Biological source: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
• Total number of polymer chains: 1
• Total formula weight: 58007.69

Authors

Kim, M.K.,Kim, B.H.,Oh, S.-J.,Song, H.K. (deposition date: 2021-12-28, release date: 2022-09-14, Last modification date: 2024-05-29)

Primary citation

Kim, B.H.,Kim, M.K.,Oh, S.J.,Nguyen, K.T.,Kim, J.H.,Varshavsky, A.,Hwang, C.S.,Song, H.K.
Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates.
Proc.Natl.Acad.Sci.USA, 119:e2209597119-e2209597119, 2022

PubMed Abstract: N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNA as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast . The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNA, and a 3'-proximal segment of the tRNA moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.

PubMed: 35878037
DOI: 10.1073/pnas.2209597119

Experimental method

X-RAY DIFFRACTION (1.76 Å)