3vqy | pdb_00003vqy

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

spinqualitylabelsall models 3vqy, resolution 2.40Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3vqy is a 1 chain structure with sequence from Dsm 2053. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ANP, LBY, MG Related: 2e3c, 2zcd, 2zce, 2zin, 2zio, 3vqv, 3vqw, 3vqx Gene: pylS (DSM 2053) Activity: Pyrrolysine--tRNA(Pyl) ligase, with EC number 6.1.1.26 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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()-(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(alpha) position of BocLys-AMP protrudes from the active site. The beta7-beta8 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 beta7-beta8 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 degrees around the C(beta) atom. 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.,Yanagisawa T, Sumida T, Ishii R, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2013 Jan;69(Pt 1):5-15. doi:, 10.1107/S0907444912039881. Epub 2012 Dec 20. PMID:23275158 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Aminoacyl tRNA Synthetase Pyrrolysyl-tRNA synthetase

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