PDBsum entry 2cv2

Ligase/RNA

PDB id: 2cv2

Contents

Protein chains

468 a.a. *

DNA/RNA

Ligands

GSU ×2

Metals

_MG ×2

_CL ×2

Waters ×325

* Residue conservation analysis

PDB id:

2cv2

Name:

Ligase/RNA

Title:

Glutamyl-tRNA synthetase from thermus thermophilus in complex with tRNA(glu) and an enzyme inhibitor, glu-ams

Structure:

tRNA. Chain: c, d. Engineered: yes. Glutamyl-tRNA synthetase. Chain: a, b. Synonym: glutamate--tRNA ligase, glurs. Engineered: yes

Source:

Synthetic: yes. Other_details: in vitro transcription. Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.69Å R-factor: 0.200 R-free: 0.260

Authors:

S.Sekine,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

S.Sekine et al. (2006). Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure, 14, 1791-1799. PubMed id: 17161369 DOI: 10.1016/j.str.2006.10.005

Date:

31-May-05 Release date: 05-Sep-06

Protein chains

P27000  (SYE_THET8) -  Glutamate--tRNA ligase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 468 a.a.

Struc: 468 a.a.

DNA/RNA chains

G-G-C-C-C-C-A-U-C-G-U-C-U-A-G-C-G-G-U-U-A-G-G-A-C-G-C-G-G-C-C-C-U-C-U-C-A-A-G- 75 bases

G-G-C-C-C-C-A-U-C-G-U-C-U-A-G-C-G-G-U-U-A-G-G-A-C-G-C-G-G-C-C-C-U-C-U-C-A-A-G- 75 bases

Enzyme reactions

• Enzyme class: E.C.6.1.1.17 - glutamate--tRNA ligase.
• Reaction: tRNA(Glu) + L-glutamate + ATP = L-glutamyl-tRNA(Glu) + AMP + diphosphate

tRNA(Glu) + L-glutamate + ATP = L-glutamyl-tRNA(Glu) (Bound ligand (Het Group name = GSU) matches with 52.78% similarity) + AMP + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2006.10.005

Structure 14:1791-1799 (2006)

PubMed id: 17161369

Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase.

S.Sekine, M.Shichiri, S.Bernier, R.Chênevert, J.Lapointe, S.Yokoyama.

ABSTRACT

Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that require the cognate tRNA for specific amino acid recognition and activation. We analyzed the role of tRNA in amino acid recognition by crystallography. In the GluRS*tRNA(Glu)*Glu structure, GluRS and tRNA(Glu) collaborate to form a highly complementary L-glutamate-binding site. This collaborative site is functional, as it is formed in the same manner in pretransition-state mimic, GluRS*tRNA(Glu)*ATP*Eol (a glutamate analog), and posttransition-state mimic, GluRS*tRNA(Glu)*ESA (a glutamyl-adenylate analog) structures. In contrast, in the GluRS*Glu structure, only GluRS forms the amino acid-binding site, which is defective and accounts for the binding of incorrect amino acids, such as D-glutamate and L-glutamine. Therefore, tRNA(Glu) is essential for formation of the completely functional binding site for L-glutamate. These structures, together with our previously described structures, reveal that tRNA plays a crucial role in accurate positioning of both L-glutamate and ATP, thus driving the amino acid activation.

Selected figure(s)

Figure 3.
Figure 3. Glutamate Interaction Manners in the Absence and Presence of tRNA^Glu
(A) A stereo view showing the manner of glutamate recognition by the GluRS•tRNA^Glu complex in the ERS/tRNA/Glu structure. The bound glutamate, the protein amino acid residues, and A76 are colored green, white, and salmon, respectively.
(B) The GluRS-glutamate interaction in the ERS/Glu structure (stereo view). The glutamate molecule is colored yellow.

Figure 6.
Figure 6. Glutamol in ERS/tRNA/ATP/Eol and Glutamyl-Sulfamoyl Adenosine in ERS/tRNA/ESA
(A) Schematic drawings of L-glutamate (upper) and L-glutamol (Eol; lower) (Desjardins et al., 1998).
(B) Schematic drawings of L-glutamyl-adenylate (upper) and 5′-O-[N-(L-glutamyl)-sulfamoyl] adenosine (ESA; lower). ESA is a nonhydrolyzable analog of glutamyl-adenylate, and it is known as a potent competitive inhibitor of E. coli GluRS with respect to glutamic acid (K[i] = 2.8 nM) (Bernier et al., 2005).
(C) The annealed |F[o] − F[c]| omit electron density contoured at 3 σ, showing the L-glutamol molecule in ERS/tRNA/ATP/Eol. Two alternative conformations of the Eol molecule (cyan and marine) are superimposed.
(D) The omit electron density map corresponding to glutamyl-sulfamoyl adenosine in ERS/tRNA/ESA. The refined ESA model (light green) is superimposed on the density contoured at 3 σ.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1791-1799) copyright 2006.

Figures were selected by an automated process.