An alternative conformation of human TrpRS suggests a role of zinc in activating non-enzymatic function

Abstract

Tryptophanyl-tRNA synthetase (TrpRS) in vertebrates contains a N-terminal extension in front of the catalytic core. Proteolytic removal of the N-terminal 93 amino acids gives rise to T2-TrpRS, which has potent anti-angiogenic activity mediated through its extracellular interaction with VE-cadherin. Zinc has been shown to have anti-angiogenic effects and can bind to human TrpRS. However, the connection between zinc and the anti-angiogenic function of TrpRS has not been explored. Here we report that zinc binding can induce structural relaxation in human TrpRS to facilitate the proteolytic generation of a T2-TrpRS-like fragment. The zinc-binding site is likely to be contained within T2-TrpRS, and the zinc-bound conformation of T2-TrpRS is mimicked by mutation H130R. We determined the crystal structure of H130R T2-TrpRS at 2.8 Å resolution, which reveals drastically different conformation from that of wild-type (WT) T2-TrpRS. The conformational change creates larger binding surfaces for VE-cadherin as suggested by molecular dynamic simulations. Surface plasmon resonance analysis indicates more than 50-fold increase in binding affinity of H130R T2-TrpRS for VE-cadherin, compared to WT T2-TrpRS. The enhanced interaction is also confirmed by a cell-based binding analysis. These results suggest that zinc plays an important role in activating TrpRS for angiogenesis regulation.

The zinc-binding domain of mammalian prolyl-tRNA synthetase is indispensable for catalytic activity and organism viability

“…In AARSs that ligate Ile, Leu, Val, Glu, Gln, Trp, and Met, Zn 2+ contributes to efficient catalysis. TrpRS contains a consensus ZBD, and is activated by Zn 2+ ; however, Zn 2+ has not been observed in multiple crystal structures suggesting weak interaction with the ZBD ( Doublie et al., 1995 ; Xu et al., 2018 ; Yang et al., 2007 ). Zn 2+ can contribute to AARS discrimination between cognate and non-cognate amino acids.…”

WARS1 and SARS1 : Two tRNA synthetases implicated in autosomal recessive microcephaly

“…For each of the 20 canonical amino acids, there is one specific ARS, except for glutamic acid and proline, which, in humans, interact with the same multifunctional ARS (EPRS1). Apart from their recognized enzymatic function, ARSs also act beyond aminoacylation (Fukui et al, 2009; Guo et al, 2010; Xu et al, 2018).…”

Peculiarities of aminoacyl-tRNA synthetases from trypanosomatids

“…For group 3 aaRSs, template 4q2t ( 67) was used to model the ArgRS, 5bnz for the GluRS, 4yrf (68) for the HisRS, 6ldk (69) for the IleRS and 1nyq (70) for the ThrRS. Finally, for group 4 aaRSs, template 6od8 was used to model both the cytosolic and mitochondrial isoforms of the AspRS, templates 6bni and 6ilh were used to model the cytosolic and mitochondrial isoforms of the LysRS, respectively, and templates 5ujj (71) and 1r6t (72) to model the cytosolic and mitochondrial isoforms of the TrpRS, respectively. All homology models' figures were rendered in UCSF ChimeraX (73).…”