2CT8

Crystal structure of Aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(Met) and methionyl-adenylate anologue

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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Literature

Structural basis for anticodon recognition by methionyl-tRNA synthetase.

Nakanishi, K., Ogiso, Y., Nakama, T., Fukai, S., Nureki, O.

(2005) Nat Struct Mol Biol 12: 931-932

  • DOI: https://doi.org/10.1038/nsmb988
  • Primary Citation of Related Structures:  
    2CSX, 2CT8

  • PubMed Abstract: 

    In the 2.7-A resolution crystal structure of methionyl-tRNA synthetase (MetRS) in complex with tRNA(Met) and a methionyl-adenylate analog, the tRNA anticodon loop is distorted to form a triple-base stack comprising C34, A35 and A38. A tryptophan residue stacks on C34 to extend the triple-base stack. In addition, C34 forms Watson-Crick-type hydrogen bonds with Arg357. This structure resolves the longstanding question of how MetRS specifically recognizes tRNA(Met).

    • Organizational Affiliation: 

    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methionyl-tRNA synthetaseC [auth A],
D [auth B]		497Aquifex aeolicusMutation(s): 0 
EC: 6.1.1.10
UniProt
Find proteins for O67298 (Aquifex aeolicus (strain VF5))
Explore O67298 
Go to UniProtKB:  O67298
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67298
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (74-MER)A [auth C],
B [auth D]		74N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.488α = 90
b = 110.614β = 90
c = 161.009γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations