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2.9 Å crystal structure of ligand‐free tryptophanyl‐tRNA synthetase: Domain movements fragment the adenine nucleotide binding site
Author(s) -
Ilyin Valentin A.,
Temple Brenda,
Hu Mei,
Carter Charles W.,
Li Genpei,
Yin Yuhui,
Vachette Patrice
Publication year - 2000
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.9.2.218
Subject(s) - transfer rna , binding site , nucleotide , chemistry , aminoacyl trna synthetase , fragment (logic) , stereochemistry , biology , biochemistry , gene , rna , computer science , programming language
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, R free = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl‐5′AMP complex (TAM; Doublie 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.