6F8Y

Crystal structure of P. abyssi Sua5 complexed with L-threonine

Summary for 6F8Y

• Entry DOI: 10.2210/pdb6f8y/pdb
• Related: 6F87 6F89
• Descriptor: Threonylcarbamoyl-AMP synthase, THREONINE (3 entities in total)
• Functional Keywords: nucleotidyltransferase, trna modification, threonylcarbamoylation, transferase
• Biological source: Pyrococcus abyssi (strain GE5 / Orsay)
• Total number of polymer chains: 4
• Total formula weight: 153265.10

Authors

Pichard-Kostuch, A.,Zhang, W.,Liger, D.,Daugeron, M.C.,Letoquart, J.,Li de la Sierra-Gallay, I.,Forterre, P.,Collinet, B.,van Tilbeurgh, H.,Basta, T. (deposition date: 2017-12-13, release date: 2018-04-25, Last modification date: 2024-01-17)

Primary citation

Pichard-Kostuch, A.,Zhang, W.,Liger, D.,Daugeron, M.C.,Letoquart, J.,Li de la Sierra-Gallay, I.,Forterre, P.,Collinet, B.,van Tilbeurgh, H.,Basta, T.
Structure-function analysis of Sua5 protein reveals novel functional motifs required for the biosynthesis of the universal t6A tRNA modification.
RNA, 24:926-938, 2018

PubMed Abstract: -threonyl-carbamoyl adenosine (tA) is a universal tRNA modification found at position 37, next to the anticodon, in almost all tRNAs decoding ANN codons (where N = A, U, G, or C). tA stabilizes the codon-anticodon interaction and hence promotes translation fidelity. The first step of the biosynthesis of tA, the production of threonyl-carbamoyl adenylate (TC-AMP), is catalyzed by the Sua5/TsaC family of enzymes. While TsaC is a single domain protein, Sua5 enzymes are composed of the TsaC-like domain, a linker and an extra domain called SUA5 of unknown function. In the present study, we report structure-function analysis of Sua5 (-Sua5). Crystallographic data revealed binding sites for bicarbonate substrate and pyrophosphate product. The linker of -Sua5 forms a loop structure that folds into the active site gorge and closes it. Using structure-guided mutational analysis, we established that the conserved sequence motifs in the linker and the domain-domain interface are essential for the function of -Sua5. We propose that the linker participates actively in the biosynthesis of TC-AMP by binding to ATP/PPi and by stabilizing the -carboxy-l-threonine intermediate. Hence, TsaC orthologs which lack such a linker and SUA5 domain use a different mechanism for TC-AMP synthesis.

PubMed: 29650678
DOI: 10.1261/rna.066092.118

Experimental method

X-RAY DIFFRACTION (2.86 Å)