2CSX

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

PDB DOI: https://doi.org/10.2210/pdb2CSX/pdb
NAKB: 2CSX

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.302
R-Value Work: 0.239
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 166.41 kDa
Atom Count: 11,058
Modelled Residue Count: 1,078
Deposited Residue Count: 1,144
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O67298
Sequence Annotations Expand
Reference Sequence