2D6F | pdb_00002d6f

Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)

• PDB DOI: https://doi.org/10.2210/pdb2D6F/pdb
• NAKB: 2D6F

• Classification: ligase/RNA
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-11-13 Released: 2006-07-11 
• Deposition Author(s): Nureki, O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structural basis of RNA-dependent recruitment of glutamine to the genetic code

Oshikane, H., Sheppard, K., Fukai, S., Nakamura, Y., Ishitani, R., Numata, T., Sherrer, R.L., Feng, L., Schmitt, E., Panvert, M., Blanquet, S., Mechulam, Y., Soll, D., Nureki, O.

(2006) Science 312: 1950-1954

• PubMed: 16809540 
• DOI: https://doi.org/10.1126/science.1128470
• Primary Citation Related Structures: 
  2D6F


• PubMed Abstract: 
  

  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.

---

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 283.16 kDa 
• Atom Count: 17,816 
• Modeled Residue Count: 2,001 
• Deposited Residue Count: 2,256 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl-tRNA(Gln) amidotransferase subunit D	C [auth A], D [auth B]	435	Methanothermobacter thermautotrophicus	Mutation(s): 0  EC: 6.3.5
UniProt
Find proteins for O26802 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26802  Go to UniProtKB:  O26802

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl-tRNA(Gln) amidotransferase subunit E	E [auth C], F [auth D]	619	Methanothermobacter thermautotrophicus	Mutation(s): 0  EC: 6.3.5
UniProt
Find proteins for O26803 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26803  Go to UniProtKB:  O26803

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tRNA	A [auth E], B [auth F]	74	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.812	α = 90
b = 140.706	β = 90
c = 186.044	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-11 
Deposition Author(s): Nureki, O.

Revision History  

• Version 1.0: 2006-07-11
  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