PDBsum entry 2c8m

Ligase

PDB id: 2c8m

Contents

Protein chains

241 a.a. *

Ligands

LPA ×4

Waters ×484

* Residue conservation analysis

PDB id:

2c8m

Name:

Ligase

Title:

Structure of protein ta0514, putative lipoate protein ligase from t. Acidophilum with bound lipoic acid

Structure:

Lipoate-protein ligase a. Chain: a, b, c, d. Engineered: yes

Source:

Thermoplasma acidophilum. Organism_taxid: 273075. Strain: dsm 1728. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.89Å R-factor: 0.208 R-free: 0.239

Authors:

E.Mcmanus,R.N.Perham,B.F.Luisi

Key ref:

E.McManus et al. (2006). Structure of a Putative Lipoate Protein Ligase from Thermoplasma acidophilum and the Mechanism of Target Selection for Post-translational Modification. J Mol Biol, 356, 625-637. PubMed id: 16384580 DOI: 10.1016/j.jmb.2005.11.057

Date:

06-Dec-05 Release date: 15-Dec-05

Protein chains

Q9HKT1  (LPLAN_THEAC) -  Lipoate-protein ligase A subunit 1 from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)

Seq: 262 a.a.

Struc: 241 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.1.20 - lipoate--protein ligase.
• Reaction: L-lysyl-[lipoyl-carrier protein] + (R)-lipoate + ATP = N₆-[(R)-lipoyl]- L-lysyl-[lipoyl-carrier protein] + AMP + diphosphate + H⁺
• Cofactor: Mg(2+)

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

reference

DOI no: 10.1016/j.jmb.2005.11.057

J Mol Biol 356:625-637 (2006)

PubMed id: 16384580

Structure of a Putative Lipoate Protein Ligase from Thermoplasma acidophilum and the Mechanism of Target Selection for Post-translational Modification.

E.McManus, B.F.Luisi, R.N.Perham.

ABSTRACT

Lipoyl-lysine swinging arms are crucial to the reactions catalysed by the 2-oxo acid dehydrogenase multienzyme complexes. A gene encoding a putative lipoate protein ligase (LplA) of Thermoplasma acidophilum was cloned and expressed in Escherichia coli. The recombinant protein, a monomer of molecular mass 29kDa, was catalytically inactive. Crystal structures in the absence and presence of bound lipoic acid were solved at 2.1A resolution. The protein was found to fall into the alpha/beta class and to be structurally homologous to the catalytic domains of class II aminoacyl-tRNA synthases and biotin protein ligase, BirA. Lipoic acid in LplA was bound in the same position as biotin in BirA. The structure of the T.acidophilum LplA and limited proteolysis of E.coli LplA together highlighted some key features of the post-translational modification. A loop comprising residues 71-79 in the T.acidophilum ligase is proposed as interacting with the dithiolane ring of lipoic acid and discriminating against the entry of biotin. A second loop comprising residues 179-193 was disordered in the T.acidophilum structure; tryptic cleavage of the corresponding loop in the E.coli LplA under non-denaturing conditions rendered the enzyme catalytically inactive, emphasizing its importance. The putative LplA of T.acidophilum lacks a C-terminal domain found in its counterparts in E.coli (Gram-negative) or Streptococcus pneumoniae (Gram-positive). A gene encoding a protein that appears to have structural homology to the additional domain in the E.coli and S.pneumoniae enzymes was detected alongside the structural gene encoding the putative LplA in the T.acidophilum genome. It is likely that this protein is required to confer activity on the LplA as currently purified, one protein perhaps catalysing the formation of the obligatory lipoyl-AMP intermediate, and the other transferring the lipoyl group from it to the specific lysine residue in the target protein.

Selected figure(s)

Figure 2.
Figure 2. Structure of the LplA of T. acidophilium with lipoic acid bound at the active site. The red colouring denotes the boundaries of the disordered region that comprises residues 179-193. The lipoic acid is depicted in sticks and designated with an arrowhead. The helices of interest are numbered H1 and H2; the b-strands of interest are numbered B4, B7 and B8.

Figure 3.
Figure 3. Lipoic acid binding in the LplA of T. acidophilum. (a) 2F[o] -F[c] map of electron density from a crystal of the native LplA soaked with R,S-lipoic acid. Lipoic acid can be seen forming interactions with Arg72 which itself forms a hydrogen bond with the carbonyl oxygen of Gly77. This interaction is shown by the broken red lines. The bond distances to the carbonyl oxygen are 3.06 and 2.86 Å. (b) Amino acid residues in the lipoic acid binding site that are highly conserved in LplAs. The residue numbers are shown in black using T. acidophilum LplA numbering. (c) Comparison of the proposed lipoic acid-binding sites in the T. acidophilum and E. coli lipoate protein ligases. The T. acidophilum protein and lipoic acid are coloured green whereas the E. coli protein and lipoic acid are coloured blue.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 625-637) copyright 2006.

Figures were selected by an automated process.