Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition

Abstract

Methanogenic archaea possess unusual seryl-tRNA synthetase (SerRS), evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. The two types of SerRSs show only minimal sequence similarity, primarily within class II conserved motifs 1, 2 and 3. Here, we report a 2.5 Å resolution crystal structure of the atypical methanogenic Methanosarcina barkeri SerRS and its complexes with ATP, serine and the nonhydrolysable seryl-adenylate analogue 5 0 -O-(N-serylsulfamoyl)adenosine. The structures reveal two idiosyncratic features of methanogenic SerRSs: a novel N-terminal tRNA-binding domain and an active site zinc ion. The tetra-coordinated Zn 2 þ ion is bound to three conserved protein ligands (Cys306, Glu355 and Cys461) and binds the amino group of the serine substrate. The absolute requirement of the metal ion for enzymatic activity was confirmed by mutational analysis of the direct zinc ion ligands. This zinc-dependent serine recognition mechanism differs fundamentally from the one employed by the bacterial-type SerRSs. Consequently, SerRS represents the only known aminoacyl-tRNA synthetase system that evolved two distinct mechanisms for the recognition of the same amino-acid substrate.

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

“…Although both reveal some similarities in their mode of tRNA Ser recognition, there are remarkable differences in their identity requirements, such as the G1:C72 base pair and the number of unpaired nucleotides at the base of the variable stem that are both required by the rare SerRS (Korencic et al 2004). Serine recognition of the rare form is also dependent on a zinc ion present in the active site, which is not found in the common SerRS (Bilokapic et al 2006). Despite their differences, the rare and common forms perform identical functions, aminoacylating serine and ligating it to its cognate tRNA molecule.…”

Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis

“…Although the sequence similarity between bacterial homologs and the catalytic core of methanogenic-type SerRS is rather low (15-21% sequence identity or less), the signature motifs of class II aminoacyl-tRNA synthetases are preserved in the sequence of truncated SerRS homologs. Residues that bind the zinc ion in the active site of aSerRS, required for serine binding (10), are strictly conserved in all inspected aSerRS-like sequences. There is a notable lack of sequence conservation in the region corresponding to the helix-turn-helix (HTH) motif of methanogenic-type SerRS from Methanosarcina barkeri (mMbSerRS) (Fig.…”

“…These truncated SerRS homologs are structurally related to the catalytic core of highly diverged, atypical seryltRNA synthetases (aSerRS) found only in methanogenic archaea. We have recently shown that methanogenic-type SerRSs display several idiosyncratic structural features and exhibit a different mode of substrate recognition in comparison with bacterial-type SerRSs (10)(11)(12). Truncated SerRS homologs are deprived of the tRNA-binding domain and lack canonical tRNA aminoacylating activity.…”

Toward understanding phosphoseryl-tRNA Cys formation: The crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase

“…Furthermore, PheRS does not have a sequence insertion corresponding to the inserted domain of SepRS. Indeed, the only other synthetase of known structure that has a domain, albeit a smaller one, inserted in the same region of the catalytic domain as SepRS is Methanosarcina barkeri SerRS (27). Finally, database searches for similar structures by using the DALI server (28) have failed to find significant similarities between the structure of the C-terminal domain of SepRS and structures deposited in the protein data bank.…”