2X1L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


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:  
    2X1L, 2X1M

  • 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 demonstrated the flexibility of the multidomain enzyme ...

    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 Struct Biol Cryst Commun 65: 618

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHIONYL-TRNA SYNTHETASEA, B, C524Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: metGMSMEG_5441
EC: 6.1.1.10
UniProt
Find proteins for A0R3E2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R3E2 
Go to UniProtKB:  A0R3E2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R3E2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADN
Query on ADN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C]
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
CXS
Query on CXS

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C]
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
L [auth C]
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
2HP
Query on 2HP

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C]
DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.95α = 90
b = 138.91β = 124.84
c = 123.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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