PDBsum entry 3h9c

Ligase

PDB id: 3h9c

Contents

Protein chain

544 a.a. *

Ligands

CIT

Metals

_ZN

Waters ×1048

* Residue conservation analysis

PDB id:

3h9c

Name:

Ligase

Title:

Structure of methionyl-tRNA synthetase: crystal form 2

Structure:

Methionyl-tRNA synthetase. Chain: a. Fragment: m547 domain: unp residues 2-548. Synonym: methionine-tRNA ligase, metrs. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: b2114, jw2101, metg. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.167 R-free: 0.191

Authors:

E.Schmitt,I.C.Tanrikulu,T.H.Yoo,M.Panvert,D.A.Tirrell,Y.Mechulam

Key ref:

E.Schmitt et al. (2009). Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity. J Mol Biol, 394, 843-851. PubMed id: 19837083 DOI: 10.1016/j.jmb.2009.10.016

Date:

30-Apr-09 Release date: 08-Dec-09

Protein chain

P00959  (SYM_ECOLI) -  Methionine--tRNA ligase from Escherichia coli (strain K12)

Seq: 677 a.a.

Struc: 544 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.10 - methionine--tRNA ligase.
• Reaction: tRNA(Met) + L-methionine + ATP = L-methionyl-tRNA(Met) + AMP + diphosphate

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

reference

DOI no: 10.1016/j.jmb.2009.10.016

J Mol Biol 394:843-851 (2009)

PubMed id: 19837083

Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity.

E.Schmitt, I.C.Tanrikulu, T.H.Yoo, M.Panvert, D.A.Tirrell, Y.Mechulam.

ABSTRACT

Methionyl-tRNA synthetase (MetRS) specifically binds its methionine substrate in an induced-fit mechanism, with methionine binding causing large rearrangements. Mutated MetRS able to efficiently aminoacylate the methionine (Met) analog azidonorleucine (Anl) have been identified by saturation mutagenesis combined with in vivo screening procedures. Here, the crystal structure of such a mutated MetRS was determined in the apo form as well as complexed with Met or Anl (1.4 to 1.7 A resolution) to reveal the structural basis for the altered specificity. The mutations result in both the loss of important contacts with Met and the creation of new contacts with Anl, thereby explaining the specificity shift. Surprisingly, the conformation induced by Met binding in wild-type MetRS already occurs in the apo form of the mutant enzyme. Therefore, the mutations cause the enzyme to switch from an induced-fit mechanism to a lock-and-key one, thereby enhancing its catalytic efficiency.

Selected figure(s)

Figure 2.
Fig. 2. Unliganded MetRS-SLL is in the met-on conformation. Top panel: the active-site region of unliganded MetRS-SLL (yellow) was superimposed to that of unliganded MetRS (PDB ID: 1QQT; blue). Motions of aromatic residues are indicated by arrows. Bottom panel: same as top panel but unliganded MetRS was replaced by MetRS:Met (PDB ID: 1F4L; blue). The bound methionine is shown in green.

Figure 4.
Fig. 4. Schematic representation of hydrophobic (red broken lines) and electrostatic (green broken lines) interactions made between MetRS-SLL and Anl. Anl is represented with blue bonds. Carbons are in black, nitrogens are in dark blue, oxygens are in red, and sulfurs are in yellow. Water molecules are symbolized as light blue spheres. Relevant hydrogen-bonding distances are indicated in angstroms. The electrostatic interaction between Wat2 and the N2 atom of Anl is indicated by a blue broken line.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 394, 843-851) copyright 2009.

Figures were selected by the author.