1QQT

METHIONYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI

• PDB DOI: https://doi.org/10.2210/pdb1QQT/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-06-08 Released: 2000-01-01 
• Deposition Author(s): Mechulam, Y., Schmitt, E., Maveyraud, L., Zelwer, C., Nureki, O., Yokoyama, S., Konno, M., Blanquet, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.174 

Literature

Crystal structure of Escherichia coli methionyl-tRNA synthetase highlights species-specific features.

Mechulam, Y., Schmitt, E., Maveyraud, L., Zelwer, C., Nureki, O., Yokoyama, S., Konno, M., Blanquet, S.

(1999) J Mol Biol 294: 1287-1297

• PubMed: 10600385 
• DOI: https://doi.org/10.1006/jmbi.1999.3339
• Primary Citation of Related Structures:  
  1QQT


• PubMed Abstract: 
  

  The 3D structure of monomeric C-truncated Escherichia coli methionyl-tRNA synthetase, a class 1 aminoacyl-tRNA synthetase, has been solved at 2.0 A resolution. Remarkably, the polypeptide connecting the two halves of the Rossmann fold exposes two identical knuckles related by a 2-fold axis but with zinc in the distal knuckle only. Examination of available MetRS orthologs reveals four classes according to the number and zinc content of the putative knuckles. Extreme cases are exemplified by the MetRS of eucaryotic or archaeal origin, where two knuckles and two metal ions are expected, and by the mitochondrial enzymes, which are predicted to have one knuckle without metal ion.

---

Organizational Affiliation: 

Laboratoire de Biochimie, Ecole Polytechnique, CNRS UMR 7654, Palaiseau Cedex, F-91128, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.91 kDa 
• Atom Count: 4,561 
• Modelled Residue Count: 546 
• Deposited Residue Count: 551 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHIONYL-TRNA SYNTHETASE	A	551	Escherichia coli	Mutation(s): 0  EC: 6.1.1.10
UniProt
Find proteins for P00959 (Escherichia coli (strain K12)) Explore P00959  Go to UniProtKB:  P00959

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.214 
• R-Value Work: 0.170 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.15	α = 90
b = 46.3	β = 109.06
c = 87.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-01 
Deposition Author(s): Mechulam, Y., Schmitt, E., Maveyraud, L., Zelwer, C., Nureki, O., Yokoyama, S., Konno, M., Blanquet, S.

Revision History  

• Version 1.0: 2000-01-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations