5X6C

Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii

Summary for 5X6C

• Entry DOI: 10.2210/pdb5x6c/pdb
• Related: 5x6b
• Descriptor: O-phosphoserine--tRNA(Cys) ligase, Uncharacterized protein MJ1481, ADENOSINE-5'-TRIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: o-phosphoseryl-trna synthetase, multiple domain protein, coiled-coil insertion, rna binding protein
• Biological source: Methanocaldococcus jannaschii DSM 2661; More
• Total number of polymer chains: 4
• Total formula weight: 179655.74

Authors

Chen, M.,Kato, K.,Yao, M. (deposition date: 2017-02-21, release date: 2017-12-06, Last modification date: 2023-11-22)

Primary citation

Chen, M.,Kato, K.,Kubo, Y.,Tanaka, Y.,Liu, Y.,Long, F.,Whitman, W.B.,Lill, P.,Gatsogiannis, C.,Raunser, S.,Shimizu, N.,Shinoda, A.,Nakamura, A.,Tanaka, I.,Yao, M.
Structural basis for tRNA-dependent cysteine biosynthesis
Nat Commun, 8:1521-1521, 2017

PubMed Abstract: Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNA followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNA, respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNA between SepRS and SepCysS distant active sites. This channeling mechanism could facilitate the consecutive reactions of the two-step indirect pathway of Cys-tRNA synthesis (tRNA-dependent cysteine biosynthesis) to prevent challenge of translational fidelity, and may reflect the mechanism that cysteine was originally added into genetic code.

PubMed: 29142195
DOI: 10.1038/s41467-017-01543-y

Experimental method

X-RAY DIFFRACTION (3.101 Å)