PDBsum entry: 1u7x

Ligase

PDB id: 1u7x

Contents

Protein chains

306 a.a. *

Metals

__K

* Residue conservation analysis

PDB id:

1u7x

Name:

Ligase

Title:

Crystal structure of a mutant m. Jannashii tyrosyl-tRNA synthetase specific for o-methyl-tyrosine

Structure:

Tyrosyl-tRNA synthetase. Chain: a, b. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes. Mutation: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: tyrs. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.229 R-free: 0.308

Authors:

Y.Zhang,L.Wang,P.G.Schultz,I.A.Wilson

Key ref:

Y.Zhang et al. (2005). Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine. Protein Sci, 14, 1340-1349. PubMed id: 15840835 DOI: 10.1110/ps.041239305

Date:

04-Aug-04 Release date: 24-May-05

Protein chains

Q57834  (SYY_METJA) -  Tyrosyl-tRNA synthetase

Seq: 306 a.a.

Struc: 306 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.6.1.1.1 - Tyrosine--tRNA ligase.
• Reaction: ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: translation (3 terms)
• Biochemical function: nucleotide binding (5 terms)

reference

DOI no: 10.1110/ps.041239305

Protein Sci 14:1340-1349 (2005)

PubMed id: 15840835

Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine.

Y.Zhang, L.Wang, P.G.Schultz, I.A.Wilson.

ABSTRACT

The Methanococcus jannaschii tRNA(Tyr)/TyrRS pair has been engineered to incorporate unnatural amino acids into proteins in E. coli. To reveal the structural basis for the altered specificity of mutant TyrRS for O-methyl-L-tyrosine (OMeTyr), the crystal structures for the apo wild-type and mutant M. jannaschii TyrRS were determined at 2.66 and 3.0 A, respectively, for comparison with the published structure of TyrRS complexed with tRNA(Tyr) and substrate tyrosine. A large conformational change was found for the anticodon recognition loop 257-263 of wild-type TyrRS upon tRNA binding in order to facilitate recognition of G34 of the anticodon loop through pi-stacking and hydrogen bonding interactions. Loop 133-143, which is close to the tRNA acceptor stem-binding site, also appears to be stabilized by interaction with the tRNA(Tyr). Binding of the substrate tyrosine results in subtle and cooperative movements of the side chains within the tyrosine-binding pocket. In the OMeTyr-specific mutant synthetase structure, the signature motif KMSKS loop and acceptor stem-binding loop 133-143 were surprisingly ordered in the absence of bound ATP and tRNA. The active-site mutations result in altered hydrogen bonding and steric interactions which favor binding of OMeTyr over L-tyrosine. The structure of the mutant and wild-type TyrRS now provide a basis for generating new active-site libraries to evolve synthetases specific for other unnatural amino acids.

Selected figure(s)

Figure 2.
Figure 2. Comparison of wild-type apo and bound M. jannaschii TyrRS's. (A) Stereo view of the B-value distribution of the apo wild-type M. jannaschii TyrRS structure. The structure trace is colored by B-values with a gradient ranging from low (25 Å2, blue) through medium (average B-value 59 Å2, yellow) to high (100 Å2, red), which highlights the more disordered regions of the structure (red). (B) Stereo view of the superimposition of apo wild-type M. jannaschii TyrRS and the bound structure (PDB code 1j1u [PDB] ;Kobayashi et al. 2003) of M. jannaschii TyrRS with tRNA (blue). Complexed M. jannaschii TyrRS is colored by its rms deviation (C ) from the apo wild-type TyrRS structure (gray) with a gradient ranging from low (0.2 Å, green) via medium (1.8 Å, yellow) to high (>4.0 Å, red).

Figure 5.
Figure 5. Amino acid-binding site in wild-type TyrRS and OMeTyr-specific mutant. (A) Hydrophobic interactions and hydrogen bonds between substrate tyrosine and M. jannaschii TyrRS. Hydrogen bonds are represented with dashed lines and labeled with distances in Å, and hydrophobic interactions are indicated by red spiked arcs. The distances in parentheses in red are the distances between the apo enzyme superimposed on the tyrosine ligand position from the bound structure (Kobayashi et al. 2003). (B) Stereo view of the superimposition of wild-type M. jannaschii TyrRS and OMeTyr-specific mutant synthetase to illustrate conformational differences. Apo mutant M. jannaschii TyrRS is colored by its rms deviation (C ) from the apo wild-type TyrRS structure (gray) with a gradient ranging from low (0.2 Å, green) via medium (1.8 Å, yellow) to high (>4.0 Å, red). (C) Stereo view of OMeTyr-specific mutant synthetase superimposed with wild-type apo M. jannaschii TyrRS (gray) to highlight mutated residues. The mutant enzyme is colored with cyan helices and pink -strands. The four residues subjected to mutation are represented by ball-and-stick with their oxygen atoms colored red. Bonds/carbon atoms are colored green in the mutant enzyme but blue in wild-type.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 1340-1349) copyright 2005.

Figures were selected by an automated process.