2D6F image
Deposition Date 2005-11-13
Release Date 2006-07-11
Last Version Date 2024-03-13
Entry Detail
PDB ID:
2D6F
Keywords:
ligase/RNA
Title:
Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)
Biological Source:
Source Organism:
Methanothermobacter thermautotrophicus (Taxon ID: 145262)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.15 Å
R-Value Free:
0.29
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 21
2D6F validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Glutamyl-tRNA(Gln) amidotransferase subunit D
Gene (Uniprot):gatD
Chain IDs:C (auth: A), D (auth: B)
Chain Length:435
Number of Molecules:2
Biological Source:Methanothermobacter thermautotrophicus
UniProt ID:O26802 Pfam ID:PF18195, PF00710, PF17763
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Glutamyl-tRNA(Gln) amidotransferase subunit E
Gene (Uniprot):gatE
Chain IDs:E (auth: C), F (auth: D)
Chain Length:619
Number of Molecules:2
Biological Source:Methanothermobacter thermautotrophicus
UniProt ID:O26803 Pfam ID:PF02934, PF02938, PF02637
Ligand Molecules
ZN
Primary Citation
Structural basis of RNA-dependent recruitment of glutamine to the genetic code
Science 312 1950 1954 (2006)
PMID: 16809540 DOI: 10.1126/science.1128470

Abstact

Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA(Gln) by the heterodimeric Glu-tRNA(Gln) amidotransferase GatDE. Here we report the crystal structure of the Methanothermobacter thermautotrophicus GatDE complexed to tRNA(Gln) at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA(Gln) mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom-long channel for ammonia transport connects the active sites in GatD and GatE. tRNA(Gln) recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code.

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Primary Citation of related structures
2D6F