Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 84556.34 
• Atom Count: 4975 
• Residue Count: 722 
• Unique protein chains: 1

1RQG

Methionyl-tRNA synthetase from Pyrococcus abyssi

• DOI: 10.2210/pdb1RQG/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus abyssi (strain GE5 / Orsay)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-12-05 Released: 2004-05-25 
• Deposition Author(s): Crepin, T., Schmitt, E., Blanquet, S., Mechulam, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.297 
• R-Value Work: 0.244 

Literature

Three-dimensional structure of methionyl-tRNA synthetase from Pyrococcus abyssi.

Crepin, T., Schmitt, E., Blanquet, S., Mechulam, Y.

(2004) Biochemistry 43: 2635-2644

• PubMed: 14992601 
• DOI: 10.1021/bi0356247


• PubMed Abstract: 
  

In class 1 aminoacyl-tRNA synthetases, methionyl-tRNA synthetases (MetRS) are homodimers or monomers depending on the presence or absence of a domain appended at the C-side of the polypeptide chain. Beyond this C-domain, all MetRS display a highly conserved catalytic core with a Rossmann fold, the two halves of which are linked by a connective peptide (CP). Three-dimensional folding of CP and its putative zinc content have served as a basis to propose a division of the MetRS family into four subgroups. All subgroups but one, which is predicted to display two zincs per MetRS polypeptide, have been characterized. In the present study, the 3D structure of MetRS from Pyrococcus abyssi could be solved at 2.9 A resolution. The data obtained and atomic absorption spectroscopic measurements establish the presence of two metal ions per polypeptide chain. This finding brings strong support to the above classification. In the crystal, the C-terminal dimerization domain is disordered. This observation is thought to reflect marked flexibility of the two core moieties with respect to the C-domains in the dimer. Gel shift experiments were performed with the isolated C-terminal dimerization domain and a core monomeric MetRS, both derived from the P. abyssi enzyme. Complex formation between the C-domain and the core enzyme could not be evidenced. Moreover, association of tRNA(Met) to the core enzyme is enhanced in the presence of the C-domain. Together, these experiments suggest positive control in trans by the C-domain on recognition of tRNA by the core moiety of MetRS.

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Organizational Affiliation: 

Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau Cedex, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Methionyl-tRNA synthetase	A	722	Pyrococcus abyssi (strain GE5 / Orsay)	Mutation(s): 0  Gene Names: metG (metS) EC: 6.1.1.10
Find proteins for Q9V011 (Pyrococcus abyssi (strain GE5 / Orsay)) Go to UniProtKB:  Q9V011

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.297 
• R-Value Work: 0.244 
• Space Group: I 4₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 113.150	α = 90.00
b = 113.150	β = 90.00
c = 287.016	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
AMoRE	phasing
SCALA	data scaling
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-05 
• Released Date: 2004-05-25 
• Deposition Author(s): Crepin, T., Schmitt, E., Blanquet, S., Mechulam, Y.

Revision History 

• Version 1.0: 2004-05-25
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance