6SCY

U34-tRNA thiolase NcsA from Methanococcus maripaludis with its [4Fe-4S] cluster

Summary for 6SCY

• Entry DOI: 10.2210/pdb6scy/pdb
• Descriptor: [4Fe-4S]-dependent U34-ARNt thiolase, ZINC ION, IRON/SULFUR CLUSTER, ... (6 entities in total)
• Functional Keywords: trna thiolase, iron-sulfur cluster, rna binding protein
• Biological source: Methanococcus maripaludis (strain S2 / LL); More
• Total number of polymer chains: 2
• Total formula weight: 75791.40

Authors

Bimai, O.,Legrand, P.,Golinelli-Pimpaneau, B. (deposition date: 2019-07-25, release date: 2020-08-26, Last modification date: 2024-01-24)

Primary citation

Bimai, O.,Legrand, P.,Ravanat, J.L.,Touati, N.,Zhou, J.,He, N.,Lenon, M.,Barras, F.,Fontecave, M.,Golinelli-Pimpaneau, B.
The thiolation of uridine 34 in tRNA, which controls protein translation, depends on a [4Fe-4S] cluster in the archaeum Methanococcus maripaludis.
Sci Rep, 13:5351-5351, 2023

PubMed Abstract: Thiolation of uridine 34 in the anticodon loop of several tRNAs is conserved in the three domains of life and guarantees fidelity of protein translation. U34-tRNA thiolation is catalyzed by a complex of two proteins in the eukaryotic cytosol (named Ctu1/Ctu2 in humans), but by a single NcsA enzyme in archaea. We report here spectroscopic and biochemical experiments showing that NcsA from Methanococcus maripaludis (MmNcsA) is a dimer that binds a [4Fe-4S] cluster, which is required for catalysis. Moreover, the crystal structure of MmNcsA at 2.8 Å resolution shows that the [4Fe-4S] cluster is coordinated by three conserved cysteines only, in each monomer. Extra electron density on the fourth nonprotein-bonded iron most likely locates the binding site for a hydrogenosulfide ligand, in agreement with the [4Fe-4S] cluster being used to bind and activate the sulfur atom of the sulfur donor. Comparison of the crystal structure of MmNcsA with the AlphaFold model of the human Ctu1/Ctu2 complex shows a very close superposition of the catalytic site residues, including the cysteines that coordinate the [4Fe-4S] cluster in MmNcsA. We thus propose that the same mechanism for U34-tRNA thiolation, mediated by a [4Fe-4S]-dependent enzyme, operates in archaea and eukaryotes.

PubMed: 37005440
DOI: 10.1038/s41598-023-32423-9

Experimental method

X-RAY DIFFRACTION (2.81 Å)