PDBsum entry 1vbn

Ligase

PDB id: 1vbn

Contents

Protein chains

318 a.a. *

Ligands

YSA ×2

Waters ×115

* Residue conservation analysis

PDB id:

1vbn

Name:

Ligase

Title:

Escherichia coli tyrosyl-tRNA synthetase mutant complexed with tyr-ams

Structure:

Tyrosyl-tRNA synthetase. Chain: a, b. Fragment: residues 5-322. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.217 R-free: 0.283

Authors:

T.Kobayashi,K.Sakamoto,T.Takimura,K.Kamata,R.Sekine,S.Nishimura, S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Kobayashi et al. (2005). Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion. Proc Natl Acad Sci U S A, 102, 1366-1371. PubMed id: 15671170 DOI: 10.1073/pnas.0407039102

Date:

27-Feb-04 Release date: 25-Jan-05

Protein chains

P0AGJ9  (SYY_ECOLI) -  Tyrosine--tRNA ligase from Escherichia coli (strain K12)

Seq: 424 a.a.

Struc: 318 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

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

tRNA(Tyr) + L-tyrosine + ATP = L-tyrosyl-tRNA(Tyr) (Bound ligand (Het Group name = YSA) matches with 48.72% similarity) + AMP + diphosphate + H(+)

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

reference

DOI no: 10.1073/pnas.0407039102

Proc Natl Acad Sci U S A 102:1366-1371 (2005)

PubMed id: 15671170

Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion.

T.Kobayashi, K.Sakamoto, T.Takimura, R.Sekine, V.P.Kelly, K.Vincent, K.Kamata, S.Nishimura, S.Yokoyama.

ABSTRACT

The genetic code in a eukaryotic system has been expanded by the engineering of Escherichia coli tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically recognize 3-iodo-L-tyrosine rather than L-tyrosine. In the present study, we determined the 3-iodo-L-tyrosine- and L-tyrosine-bound structures of the 37V195C mutant of the E. coli TyrRS catalytic domain at 2.0-A resolution. The gamma-methyl group of Val-37 and the sulfur atom of Cys-195 make van der Waals contacts with the iodine atom of 3-iodo-L-tyrosine. The Val-37 and Cys-195 side chains are rigidly fixed by the neighboring residues forming the hydrophobic core of the TyrRS. The major roles of the two mutations are different for the 3-iodo-L-tyrosine-selective recognition in the first step of the aminoacylation reaction (the amino acid activation step): the Y37V mutation eliminates the fatal steric repulsion with the iodine atom, and the Q195C mutation reduces the L-tyrosine misrecognition. The structure of the 37V195C mutant TyrRS complexed with an L-tyrosyladenylate analogue was also solved, indicating that the 3-iodo-L-tyrosine and L-tyrosine side chains are similarly discriminated in the second step (the aminoacyl transfer step). These results demonstrate that the amino acid-binding pocket on the 37V195C mutant is optimized for specific 3-iodo-L-tyrosine recognition.

Selected figure(s)

Figure 2.
Fig. 2. Comparison of the substrate-binding site structures of E. coli TyrRSs. (A-C) The amino acid-binding site of the wild-type TyrRS·L-tyrosine (A) (19), 37V195C TyrRS·3-iodo-L-tyrosine (B), and 37V195C TyrRS·L-tyrosine (C) complexes. The colors of the atoms are the same as in Fig. 1 C and D. The hydrogen bonds are indicated by pink broken lines. (D) Superposed 37V195C (light blue) and wild-type (green) TyrRS·L-tyrosine structures. The water molecules are shown by balls. The water molecule that hydrogen-bonds to the L-tyrosine is labeled "Wat." (E) Superposed 37V195C mutant TyrRS structures complexed with 3-iodo-L-tyrosine (pink) and L-tyrosine (light blue).

Figure 4.
Fig. 4. Superposed 37V195C (pink) and wild-type (light blue) (19) TyrRS·Tyr-AMS structures. The nitrogen, oxygen, and sulfur atoms are colored blue, red, and yellow, respectively.

Figures were selected by an automated process.