1PFY

METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH METHIONYL SULPHAMOYL ADENOSINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase.

Crepin, T.Schmitt, E.Mechulam, Y.Sampson, P.B.Vaughan, M.D.Honek, J.F.Blanquet, S.

(2003) J.Mol.Biol. 332: 59-72

  • Primary Citation of Related Structures:  1P7P, 1PFU, 1PFV, 1PFW, 1PG0, 1PG2

  • PubMed Abstract: 
  • Binding of methionine to methionyl-tRNA synthetase (MetRS) is known to promote conformational changes within the active site. However, the contribution of these rearrangements to enzyme catalysis is not fully understood. In this study, several methio ...

    Binding of methionine to methionyl-tRNA synthetase (MetRS) is known to promote conformational changes within the active site. However, the contribution of these rearrangements to enzyme catalysis is not fully understood. In this study, several methionine and methionyl adenylate analogues were diffused into crystals of the monomeric form of Escherichia coli methionyl-tRNA synthetase. The structures of the corresponding complexes were solved at resolutions below 1.9A and compared to those of the enzyme free or complexed with methionine. Residues Y15 and W253 play key roles in the strength of the binding of the amino acid and of its analogues. Indeed, full motions of these residues are required to recover the maximum in free energy of binding. Residue Y15 also controls the size of the hydrophobic pocket where the amino acid side-chain interacts. H301 appears to participate to the specific recognition of the sulphur atom of methionine. Complexes with methionyl adenylate analogues illustrate the shielding by MetRS of the region joining the methionine and adenosine moieties. Finally, the structure of MetRS complexed to a methionine analogue mimicking the tetrahedral carbon of the transition state in the aminoacylation reaction was solved. On the basis of this model, we propose that, in response to the binding of the 3'-end of tRNA, Y15 moves again in order to deshield the anhydride bond in the natural adenylate.


    Organizational Affiliation

    Laboratoire de Biochimie, Unité Mixte de Recherche no 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionyl-tRNA synthetase
A
551Escherichia coli (strain K12)Gene Names: metG
EC: 6.1.1.10
Find proteins for P00959 (Escherichia coli (strain K12))
Go to UniProtKB:  P00959
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MSP
Query on MSP

Download SDF File 
Download CCD File 
A
5'-O-[(L-METHIONYL)-SULPHAMOYL]ADENOSINE
C15 H25 N7 O7 S2
SQDXXTAOGLOMRP-VOLIQSIHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MSPIC50: ~7 nM BINDINGMOAD
MSPIC50: 7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.803α = 90.00
b = 45.193β = 107.31
c = 86.412γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
CNSrefinement
MOSFLMdata reduction
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance