PDBsum entry 2e89

Ligase

PDB id: 2e89

Contents

Protein chains

317 a.a. *

Ligands

ATP ×4

LYS

Metals

_MG

Waters ×65

* Residue conservation analysis

PDB id:

2e89

Name:

Ligase

Title:

Crystal structure of aquifex aeolicus tils in a complex with atp, magnesium ion, and l-lysine

Structure:

tRNA(ile)-lysidine synthase. Chain: a, b, c, d. Synonym: tRNA(ile)-lysidine synthetase, tRNA(ile)-2-lysyl-cytidine synthase. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.50Å R-factor: 0.229 R-free: 0.274

Authors:

M.Kuratani,Y.Yoshikawa,S.Takahashi,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

M.Kuratani et al. (2007). Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine. Structure, 15, 1642-1653. PubMed id: 18073113 DOI: 10.1016/j.str.2007.09.020

Date:

19-Jan-07 Release date: 13-Nov-07

Protein chains

O67728  (TILS_AQUAE) -  tRNA(Ile)-lysidine synthase from Aquifex aeolicus (strain VF5)

Seq: 317 a.a.

Struc: 317 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.4.19 - tRNA(Ile)-lysidine synthetase.
• Reaction: cytidine₃₄ in tRNA(Ile2) + L-lysine + ATP = lysidine₃₄ in tRNA(Ile2) + AMP + diphosphate + H⁺

cytidine(34) in tRNA(Ile2) (Bound ligand (Het Group name = ATP) corresponds exactly) + L-lysine + ATP (Bound ligand (Het Group name = LYS) corresponds exactly) = lysidine(34) in tRNA(Ile2) + AMP + diphosphate + H(+)

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

reference

DOI no: 10.1016/j.str.2007.09.020

Structure 15:1642-1653 (2007)

PubMed id: 18073113

Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine.

M.Kuratani, Y.Yoshikawa, Y.Bessho, K.Higashijima, T.Ishii, R.Shibata, S.Takahashi, K.Yutani, S.Yokoyama.

ABSTRACT

In the bacterial genetic-code system, the codon AUA is decoded as isoleucine by tRNA(Ile)(2) with the lysidine residue at the wobble position. Lysidine is derived from cytidine, with ATP and L-lysine, by tRNA(Ile) lysidine synthetase (TilS), which is an N-type ATP pyrophosphatase. In this study, we determined the crystal structure of Aquifex aeolicus TilS, complexed with ATP, Mg2+, and L-lysine, at 2.5 A resolution. The presence of the TilS-specific subdomain causes the active site to have two separate gateways, a large hole and a narrow tunnel on the opposite side. ATP is bound inside the hole, and L-lysine is bound at the entrance of the tunnel. The conserved Asp36 in the PP-motif coordinates Mg2+. In these initial binding modes, the ATP, Mg2+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex.

Selected figure(s)

Figure 2.
Figure 2. Overall Structure
(A–C) |Fo| − |Fc| simulated annealing omit maps. (A) The electron density of the AMPPNP (blue, contoured at 4σ). (B) The electron densities of the ATP (blue, 5.5σ) and the Mg^2+ (brown, 4σ). The continuity of the electron densities of the Mg^2+, Asp36, and Asp137 is shown by omitting these three molecules (yellow, 3σ). (C) The electron densities of the L-lysine (blue, 3.5σ).
(D) Ribbon model of the TilS dimer. Two subunits (molecules A and B of TilS/ATP/Mg/Lys) are colored pink and cyan, respectively. The ATP and L-lysine molecules are shown by stick models.
(E) A stereoview of the TilS monomer (molecule B of TilS/ATP/Mg/Lys). The N-terminal domain (NTD), the TilS-specific subdomain (TSD), the linker, and the C-terminal domain (CTD1) are colored pink, yellow, green, and cyan, respectively. The graphic figures in this paper were prepared with CueMol (http://cuemol.sourceforge.jp/en/) and were rendered with POVRAY (http://www.povray.org/).

Figure 7.
Figure 7. ATP Recognition
(A) The amino acid residues that recognize the ATP and Mg^2+ (stereoview). The ATP is shown by a stick model. The Mg^2+ and water molecules are shown as gray and red spheres, respectively. Hydrogen bonds are shown as dotted lines.
(B) Recognition of the AMPPNP, shown as in (A). The nitrogen atom between the P[β] and P[γ] atoms is colored blue.
(C) AMP and pyrophosphate binding by E. coli GMP synthetase, depicted as in (A).
(D and E) Extended (D) and U-shaped (E) ATP conformations in the structures of the E. coli argininosuccinate synthetase complexed with ATP (D) and with both ATP and citrulline (E), respectively. The side chain of Asp22 in (D) is missing in the coordinates (1KP2).
(F) Comparison of the ATP conformation. The U-shaped ATP, with three manganese ions (Mn1, Mn2, and Mn3) in the structure of LysU (PDB code: 1E24) was superposed based on the adenine ring. The phosphate atoms are colored orange, and the manganese ions are colored magenta.
(G) Docking model of TilS and the cytidine residue of tRNA^Ile[2] (stereoview). The phosphate atoms of the ATP and the side chain of Asp36 were moved manually. The L-lysine was moved manually, and the model structure is colored light gray and is indicated as (L-lysine).

The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 1642-1653) copyright 2007.

Figures were selected by an automated process.