3vqx Citations

A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site.

Acta Crystallogr. D Biol. Crystallogr. 69 5-15 (2013)
Related entries: 3vqy, 3vqv, 3vqw

Cited: 5 times
EuropePMC logo PMID: 23275158

Abstract

Structures of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) have been determined in a novel crystal form. The triclinic form crystals contained two PylRS dimers (four monomer molecules) in the asymmetric unit, in which the two subunits in one dimer each bind N(ℇ)-(tert-butyloxycarbonyl)-L-lysyladenylate (BocLys-AMP) and the two subunits in the other dimer each bind AMP. The BocLys-AMP molecules adopt a curved conformation and the C(α) position of BocLys-AMP protrudes from the active site. The β7-β8 hairpin structures in the four PylRS molecules represent distinct conformations of different states of the aminoacyl-tRNA synthesis reaction. Tyr384, at the tip of the β7-β8 hairpin, moves from the edge to the inside of the active-site pocket and adopts multiple conformations in each state. Furthermore, a new crystal structure of the BocLys-AMPPNP-bound form is also reported. The bound BocLys adopts an unusually bent conformation, which differs from the previously reported structure. It is suggested that the present BocLys-AMPPNP-bound, BocLys-AMP-bound and AMP-bound complexes represent the initial binding of an amino acid (or pre-aminoacyl-AMP synthesis), pre-aminoacyl-tRNA synthesis and post-aminoacyl-tRNA synthesis states, respectively. The conformational changes of Asn346 that accompany the aminoacyl-tRNA synthesis reaction have been captured by X-ray crystallographic analyses. The orientation of the Asn346 side chain, which hydrogen-bonds to the carbonyl group of the amino-acid substrate, shifts by a maximum of 85-90° around the C(β) atom.

Reviews citing this publication (1)

  1. Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool. Wan W, Tharp JM, Liu WR. Biochim. Biophys. Acta 1844 1059-1070 (2014)

Articles citing this publication (4)

  1. Polyspecific pyrrolysyl-tRNA synthetases from directed evolution. Guo LT, Wang YS, Nakamura A, Eiler D, Kavran JM, Wong M, Kiessling LL, Steitz TA, O'Donoghue P, Söll D. Proc. Natl. Acad. Sci. U.S.A. 111 16724-16729 (2014)
  2. Structural insights into incorporation of norbornene amino acids for click modification of proteins. Schneider S, Gattner MJ, Vrabel M, Flügel V, López-Carrillo V, Prill S, Carell T. Chembiochem 14 2114-2118 (2013)
  3. Multiple site-specific installations of Nε-monomethyl-L-lysine into histone proteins by cell-based and cell-free protein synthesis. Yanagisawa T, Takahashi M, Mukai T, Sato S, Wakamori M, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S. Chembiochem 15 1830-1838 (2014)
  4. Structural basis for the site-specific incorporation of lysine derivatives into proteins. Flügel V, Vrabel M, Schneider S. PLoS ONE 9 e96198 (2014)