PDBsum entry 3e9h

Ligase

PDB id: 3e9h

Contents

Protein chains

484 a.a. *

Ligands

KAA ×4

Metals

_MG ×4

Waters ×464

* Residue conservation analysis

PDB id:

3e9h

Name:

Ligase

Title:

Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with l-lysylsulfamoyl adenosine

Structure:

Lysyl-tRNA synthetase. Chain: a, b, c, d. Synonym: lysine--tRNA ligase, lysrs. Engineered: yes

Source:

Bacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.190 R-free: 0.241

Authors:

H.Sakurama,T.Takita,B.Mikami,T.Itoh,K.Yasukawa,K.Inouye

Key ref:

H.Sakurama et al. (2009). Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate. J Biochem (tokyo), 145, 555-563. PubMed id: 19174549

Date:

22-Aug-08 Release date: 14-Jul-09

Protein chains

Q9RHV9  (SYK_GEOSE) -  Lysine--tRNA ligase from Geobacillus stearothermophilus

Seq: 494 a.a.

Struc: 484 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.6 - lysine--tRNA ligase.
• Reaction: tRNA(Lys) + L-lysine + ATP = L-lysyl-tRNA(Lys) + AMP + diphosphate

tRNA(Lys) + L-lysine + ATP = L-lysyl-tRNA(Lys) (Bound ligand (Het Group name = KAA) matches with 52.78% similarity) + AMP + diphosphate

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

reference

J Biochem (tokyo) 145:555-563 (2009)

PubMed id: 19174549

Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate.

H.Sakurama, T.Takita, B.Mikami, T.Itoh, K.Yasukawa, K.Inouye.

ABSTRACT

Aminoacyl-tRNA synthetase forms an enzyme-bound intermediate, aminoacyladenylate in the amino-acid activation reaction. This reaction is monitored by measuring the ATP-PPi exchange reason in which [(32)P]PPi is incorporated into ATP. We previously reported that L-lysine hydroxamate completely inhibited the L-lysine-dependent ATP-PPi exchange reaction catalysed by lysyl-tRNA synthetase from Bacillus stearothermophilus (BsLysRS). Several experiments suggested that BsLysRS can adenylate L-lysine hydroxamate, but the enzyme-bound lysyladenylate-like compound does not undergo the nucleophilic attack of PPi. This contrasts with the two reports for seryl-tRNA synthetase (SerRS): (i) L-serine hydroxamate was utilized by yeast SerRS as a substrate in the ATP-PPi exchange; and (ii) a seryladenylate-like compound was formed from L-serine hydroxamate in the crystal structure of Thermus thermophilus SerRS. To gain clues about the mechanistic difference, we have determined the crystal structures of two complexes of BsLysRS with the adenylate of L-lysine hydroxamate and with 5'-O-[N-(L-Lysyl)sulphamoyl] adenosine. The comparisons of the two BsLysRS structures and the above SerRS structure revealed the specific side-chain shift of Glu411 of BsLysRS in the complex with the adenylate of L-lysine hydroxamate. In support of other structural comparisons, the result suggested that Glu411 plays a key role in the arrangement of PPi for the nucleophilic attack.