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

Valentin A. Ilyin, Brenda Temple, Mei Hu, Genpei Li, Yuhui Yin, Patrice Vachette, Charles W. Carter

Research output: Contribution to journalArticle

61 Citations (Scopus)

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 gites 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.

Original languageEnglish (US)
Pages (from-to)218-231
Number of pages14
JournalProtein Science
Volume9
Issue number2
StatePublished - 2000
Externally publishedYes

Fingerprint

Tryptophan-tRNA Ligase
Adenine Nucleotides
Ligases
Crystal structure
Binding Sites
Ligands
Bearings (structural)
Anticodon
Biochemistry
Relocation
Entropy
Adenosine Monophosphate
Transfer RNA
X ray scattering
Tryptophan
Conformations
Catalytic Domain
Adenosine Triphosphate
Monomers
X-Rays

Keywords

  • ATP binding site
  • Induced fit
  • Maximum entropy
  • Nonpolar nuclei
  • Tryptophanyl-tRNA synthetase

ASJC Scopus subject areas

  • Biochemistry

Cite this

2.9 Å Crystal structure of ligand-free tryptophanyl-tRNA synthetase : Domain movements fragment the adenine nucleotide binding site. / Ilyin, Valentin A.; Temple, Brenda; Hu, Mei; Li, Genpei; Yin, Yuhui; Vachette, Patrice; Carter, Charles W.

In: Protein Science, Vol. 9, No. 2, 2000, p. 218-231.

Research output: Contribution to journalArticle

Ilyin, Valentin A. ; Temple, Brenda ; Hu, Mei ; Li, Genpei ; Yin, Yuhui ; Vachette, Patrice ; Carter, Charles W. / 2.9 Å Crystal structure of ligand-free tryptophanyl-tRNA synthetase : Domain movements fragment the adenine nucleotide binding site. In: Protein Science. 2000 ; Vol. 9, No. 2. pp. 218-231.
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T1 - 2.9 Å Crystal structure of ligand-free tryptophanyl-tRNA synthetase

T2 - Domain movements fragment the adenine nucleotide binding site

AU - Ilyin, Valentin A.

AU - Temple, Brenda

AU - Hu, Mei

AU - Li, Genpei

AU - Yin, Yuhui

AU - Vachette, Patrice

AU - Carter, Charles W.

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AB - 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 gites 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.

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KW - Maximum entropy

KW - Nonpolar nuclei

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