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2.9 Å Crystal structure of ligand-free tryptophanyl-tRNA synthetase: Domain movements fragment the adenine nucleotide binding site

Published online by Cambridge University Press:  01 February 2000

VALENTIN A. ILYIN
Affiliation:
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27514
BRENDA TEMPLE
Affiliation:
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27514
MEI HU
Affiliation:
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27514
GENPEI LI
Affiliation:
Department of Physical Chemistry, Peking University, Beijing, Peoples Republic of China
YUHUI YIN
Affiliation:
Department Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
PATRICE VACHETTE
Affiliation:
LURE, Orsay, France
CHARLES W. CARTER
Affiliation:
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27514
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Abstract

The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) was solved at 2.9 Å using a combination of molecular replacement and maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, Rfree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl–5′AMP complex (TAM; Doublié S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17–31). In agreement with small-angle solution X-ray scattering experiments, unliganded TrpRS has a conformation in which both monomers open, leaving only the tryptophan-binding regions of their active sites intact. The amino terminal αA-helix, TIGN, and KMSKS signature sequences, and the distal helical domain rotate as a single rigid body away from the dinucleotide-binding fold domain, opening the AMP binding site, seen in the TAM complex, into two halves. Comparison of side-chain packing in ligand-free TrpRS and the TAM complex, using identification of nonpolar nuclei (Ilyin VA, 1994, Protein Eng 7:1189–1195), shows that significant repacking occurs between three relatively stable core regions, one of which acts as a bearing between the other two. These domain rearrangements provide a new structural paradigm that is consistent in detail with the “induced-fit” mechanism proposed for TyrRS by Fersht et al. (Fersht AR, Knill-Jones JW, Beduelle H, Winter G, 1988, Biochemistry 27:1581–1587). Coupling of ATP binding determinants associated with the two catalytic signature sequences to the helical domain containing the presumptive anticodon-binding site provides a mechanism to coordinate active-site chemistry with relocation of the major tRNA binding determinants.

Type
Research Article
Copyright
© 2000 The Protein Society

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