2CT8

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

• PDB DOI: https://doi.org/10.2210/pdb2CT8/pdb
• NAKB: 2CT8

• Classification: Ligase/RNA
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-05-23 Released: 2005-09-20 
• Deposition Author(s): Nakanishi, K., Ogiso, Y., Nakama, T., Fukai, S., Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.272 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

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

• PubMed: 16155581 
• 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).

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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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 166.75 kDa 
• Atom Count: 11,134 
• Modelled Residue Count: 1,078 
• Deposited Residue Count: 1,142 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase	C [auth A], D [auth B]	497	Aquifex aeolicus	Mutation(s): 0  EC: 6.1.1.10
UniProt
Find proteins for O67298 (Aquifex aeolicus (strain VF5)) Explore O67298  Go to UniProtKB:  O67298

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (74-MER)	A [auth C], B [auth D]	74	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MSP	E [auth A], F [auth B]	5'-O-[(L-METHIONYL)-SULPHAMOYL]ADENOSINE C15 H25 N7 O7 S2 SQDXXTAOGLOMRP-VOLIQSIHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.272 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.488	α = 90
b = 110.614	β = 90
c = 161.009	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-20 
Deposition Author(s): Nakanishi, K., Ogiso, Y., Nakama, T., Fukai, S., Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• 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