3VQY

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and AMPPNP (form 2)

Summary for 3VQY

• Entry DOI: 10.2210/pdb3vqy/pdb
• Related: 2e3c 2zcd 2zce 2zin 2zio 3vqv 3vqw 3vqx
• Descriptor: Pyrrolysine--tRNA ligase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, N~6~-(tert-butoxycarbonyl)-L-lysine, ... (5 entities in total)
• Functional Keywords: structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, aminoacyl-trna synthetase, pyrrolysyl-trna synthetase, amppnp, boclys, ligase
• Biological source: Methanosarcina mazei
• Total number of polymer chains: 1
• Total formula weight: 34145.27

Authors

Yanagisawa, T.,Sumida, T.,Ishii, R.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2012-04-02, release date: 2013-01-02, Last modification date: 2023-11-08)

Primary citation

Yanagisawa, T.,Sumida, T.,Ishii, R.,Yokoyama, S.
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.,Sect.D, 69:5-15, 2013

PubMed 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.

PubMed: 23275158
DOI: 10.1107/S0907444912039881

Experimental method

X-RAY DIFFRACTION (2.4 Å)