2X1L

Crystal structure of Mycobacterium smegmatis methionyl-tRNA synthetase in complex with methionine and adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Flexibility and Communication within the Structure of the Mycobacterium Smegmatis Methionyl-tRNA Synthetase.

Ingvarsson, H.Unge, T.

(2010) FEBS J. 277: 3947

  • DOI: 10.1111/j.1742-4658.2010.07784.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two structures of monomeric methionyl-tRNA synthetase, from Mycobacterium smegmatis, in complex with the ligands methionine/adenosine and methionine, were analyzed by X-ray crystallography at 2.3 Å and at 2.8 Å, respectively. The structures demonstra ...

    Two structures of monomeric methionyl-tRNA synthetase, from Mycobacterium smegmatis, in complex with the ligands methionine/adenosine and methionine, were analyzed by X-ray crystallography at 2.3 Å and at 2.8 Å, respectively. The structures demonstrated the flexibility of the multidomain enzyme. A new conformation of the structure was identified in which the connective peptide domain bound more closely to the catalytic domain than described previously. The KMSKS(301-305) loop in our structures was in an open and inactive conformation that differed from previous structures by a rotation of the loop of about 90° around hinges located at Asn297 and Val310. The binding of adenosine to the methionyl-tRNA synthetase methionine complex caused a shift in the KMSKS domain that brought it closer to the catalytic domain. The potential use of the adenosine-binding site for inhibitor binding was evaluated and a potential binding site for a specific allosteric inhibitor was identified.


    Related Citations: 
    • Crystallization of Mycobacterium Smegmatis Methionyl-tRNA Synthetase in the Presence of Methionine and Adenosine.
      Ingvarsson, H.,Jones, T.A.,Unge, T.
      (2009) Acta Crystallogr.,Sect.F 65: 618


    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala Biomedical Center, Uppsala University, Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHIONYL-TRNA SYNTHETASE
A, B, C
524Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: metG
EC: 6.1.1.10
Find proteins for A0R3E2 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R3E2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CXS
Query on CXS

Download SDF File 
Download CCD File 
A, B, C
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
ADN
Query on ADN

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
2HP
Query on 2HP

Download SDF File 
Download CCD File 
A, B, C
DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M
 Ligand Interaction
MET
Query on MET

Download SDF File 
Download CCD File 
A, B, C
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 155.950α = 90.00
b = 138.910β = 124.84
c = 123.310γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection
  • Version 1.4: 2019-01-30
    Type: Data collection, Experimental preparation