PDBsum entry 1kog

Ligase/RNA

PDB id: 1kog

Contents

Protein chains

(+ 2 more) 401 a.a. *

DNA/RNA

Ligands

TSB ×8

Metals

_ZN ×8

Waters ×170

* Residue conservation analysis

PDB id:

1kog

Name:

Ligase/RNA

Title:

Crystal structure of e. Coli threonyl-tRNA synthetase interacting with the essential domain of its mRNA operator

Structure:

Threonyl-tRNA synthetase mRNA. Chain: i, j, k, l, m, n, o, p. Engineered: yes. Mutation: yes. Other_details: domain d2 of the trs mRNA operator from e.Coli (nucleotides -49 to -13). Threonyl-tRNA synthetase. Chain: a, b, c, d, e, f, g, h. Fragment: catalytic and anticodon binding domains (residues 242 to

Source:

Synthetic: yes. Other_details: this is the natural sequence of domain d2 of the trs mRNA operator from e. Coli, covering residues -49 to -13 (69 to 105 in the present coordinate file) of e.Coli trs mRNA, except for the first 3 base pairs. It was synthesized in vitro by t7 transcription.. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli.

Biol. unit:

Tetramer (from PDB file)

Resolution:

3.50Å R-factor: 0.251 R-free: 0.287

Authors:

A.Torres-Larrios,A.C.Dock-Bregeon,P.Romby,B.Rees,R.Sankaranarayanan, J.Caillet,M.Springer,C.Ehresmann,B.Ehresmann,D.Moras

Key ref:

A.Torres-Larios et al. (2002). Structural basis of translational control by Escherichia coli threonyl tRNA synthetase. Nat Struct Biol, 9, 343-347. PubMed id: 11953757

Date:

20-Dec-01 Release date: 26-Apr-02

Protein chains

P0A8M3  (SYT_ECOLI) -  Threonine--tRNA ligase from Escherichia coli (strain K12)

Seq: 642 a.a.

Struc: 401 a.a.

DNA/RNA chains

G-G-C-G-U-A-U-G-U-G-A-U-C-U-U-U-C-G-U-G-U-G-G-G-U-C-A-C-C-A-C-U-G-C-G-C-C 37 bases

G-G-C-G-U-A-U-G-U-G-A-U-C-U-U-U-C-G-U-G-U-G-G-G-U-C-A-C-C-A-C-U-G-C-G-C-C 37 bases

G-G-C-G-U-A-U-G-U-G-A-U-C-U-U-U-C-G-U-G-U-G-G-G-U-C-A-C-C-A-C-U-G-C-G-C-C 37 bases

G-G-C-G-U-A-U-G-U-G-A-U-C-U-U-U-C-G-U-G-U-G-G-G-U-C-A-C-C-A-C-U-G-C-G-C-C 37 bases

G-G-C-G-U-A-U-G-U-G-A-U-C-U-U-U-C-G-U-G-U-G-G-G-U-C-A-C-C-A-C-U-G-C-G-C-C 37 bases

G-G-C-G-U-A-U-G-U-G-A-U-C-U-U-U-C-G-U-G-U-G-G-G-U-C-A-C-C-A-C-U-G-C-G-C-C 37 bases

G-G-C-G-U-A-U-G-U-G-A-U-C-U-U-U-C-G-U-G-U-G-G-G-U-C-A-C-C-A-C-U-G-C-G-C-C 37 bases

G-G-C-G-U-A-U-G-U-G-A-U-C-U-U-U-C-G-U-G-U-G-G-G-U-C-A-C-C-A-C-U-G-C-G-C-C 37 bases

Enzyme reactions

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

tRNA(Thr) + L-threonine + ATP = L-threonyl-tRNA(Thr) (Bound ligand (Het Group name = TSB) matches with 55.88% similarity) + AMP + diphosphate + H(+)

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

reference

Nat Struct Biol 9:343-347 (2002)

PubMed id: 11953757

Structural basis of translational control by Escherichia coli threonyl tRNA synthetase.

A.Torres-Larios, A.C.Dock-Bregeon, P.Romby, B.Rees, R.Sankaranarayanan, J.Caillet, M.Springer, C.Ehresmann, B.Ehresmann, D.Moras.

ABSTRACT

Escherichia coli threonyl-tRNA synthetase (ThrRS) represses the translation of its own messenger RNA by binding to an operator located upstream of the initiation codon. The crystal structure of the complex between the core of ThrRS and the essential domain of the operator shows that the mRNA uses the recognition mode of the tRNA anticodon loop to initiate binding. The final positioning of the operator, upon which the control mechanism is based, relies on a characteristic RNA motif adapted to the enzyme surface. The finding of other thrS operators that have this conserved motif leads to a generalization of this regulatory mechanism to a subset of Gram-negative bacteria.