PDBsum entry: 1tkg

Ligase

PDB id: 1tkg

Contents

Protein chain

224 a.a. *

Ligands

SSA

Waters ×306

* Residue conservation analysis

PDB id:

1tkg

Name:

Ligase

Title:

Crystal structure of the editing domain of threonyl-tRNA synthetase complexed with an analog of seryladenylate

Structure:

Threonyl-tRNA synthetase. Chain: a. Fragment: domains n1 and n2 (residues 1-224). Synonym: threonine--tRNA ligase, thrrs. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: thrs, b1719, c2116, sf1512, s1630. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.50Å R-factor: 0.201 R-free: 0.219

Authors:

A.C.Dock-Bregeon,B.Rees,A.Torres-Larios,G.Bey,J.Caillet, D.Moras

Key ref:

A.C.Dock-Bregeon et al. (2004). Achieving error-free translation; the mechanism of proofreading of threonyl-tRNA synthetase at atomic resolution. Mol Cell, 16, 375-386. PubMed id: 15525511 DOI: 10.1016/j.molcel.2004.10.002

Date:

08-Jun-04 Release date: 30-Nov-04

Protein chain

P0A8M3  (SYT_ECOLI) -  Threonyl-tRNA synthetase

Seq: 642 a.a.

Struc: 224 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.3 - Threonine--tRNA ligase.
• Reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)

ATP + L-threonine + tRNA(Thr) = AMP (Bound ligand (Het Group name = SSA) matches with 57.00% similarity) + diphosphate + L-threonyl-tRNA(Thr)

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 (2 terms)
• Biochemical function: nucleotide binding (3 terms)

reference

DOI no: 10.1016/j.molcel.2004.10.002

Mol Cell 16:375-386 (2004)

PubMed id: 15525511

Achieving error-free translation; the mechanism of proofreading of threonyl-tRNA synthetase at atomic resolution.

A.C.Dock-Bregeon, B.Rees, A.Torres-Larios, G.Bey, J.Caillet, D.Moras.

ABSTRACT

The fidelity of aminoacylation of tRNA(Thr) by the threonyl-tRNA synthetase (ThrRS) requires the discrimination of the cognate substrate threonine from the noncognate serine. Misacylation by serine is corrected in a proofreading or editing step. An editing site has been located 39 A away from the aminoacylation site. We report the crystal structures of this editing domain in its apo form and in complex with the serine product, and with two nonhydrolyzable analogs of potential substrates: the terminal tRNA adenosine charged with serine, and seryl adenylate. The structures show how serine is recognized, and threonine rejected, and provide the structural basis for the editing mechanism, a water-mediated hydrolysis of the mischarged tRNA. When the adenylate analog binds in the editing site, a phosphate oxygen takes the place of one of the catalytic water molecules, thereby blocking the reaction. This rules out a correction mechanism that would occur before the binding of the amino acid on the tRNA.

Selected figure(s)

Figure 3.
Figure 3. The Ligands in the Editing Pocket(A, C, and E) The structure of the pocket and the ligands with annealed omit maps (the ligands and the surrounding water molecules were omitted from the structure factor calculation). Secondary structure elements are colored as in Figure 2.(B, D, and F) Schematic representation of the interactions between the ligands, protein residues, and solvent molecules, with putative H bonds in dotted lines and distances in Ångströms.(A and B) SerA76, the analog of the terminal adenosine of a tRNA bound to serine.(C and D) Serine.(E and F) SerAMS, the analog of seryl-adenylate.

Figure 6.
Figure 6. Model for the Translocation(A) Surface representation of E. coli ThrRS obtained with the program MSMS (http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html) with the catalytic domain in blue, the editing domain in pink, and the anticodon binding domain in yellow. The tRNA scaffold is shown in green in a “ladder” representation. The three zones where ThrRS is in direct contact with the tRNA are highlighted by a deeper hue of the surface of the residues involved. The two positions of the amino acid bound A76 are indicated by ovals. The arrow indicates the movement of the CCA between the synthetic site and the editing site.(B) A close-up of the two positions of the tRNA acceptor arm in stereoscopic representation: the synthetic conformation with the tRNA (backbone in yellow) entering the catalytic site (blue) as observed in the synthetic complex (Sankaranarayanan et al., 1999) and the editing conformation in the editing site (pink). The base of A73, the nucleotides C74 and C75, and the phosphate 76 have been modeled (purple). The ribose and base of A76 with the bound serine are those of SerA76, in orange, as determined in the present work.

The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 16, 375-386) copyright 2004.

Figures were selected by the author.