PDBsum entry 2art

Ligase

PDB id: 2art

Contents

Protein chain

247 a.a. *

Ligands

LPA-AMP

Metals

_MG

Waters ×108

* Residue conservation analysis

PDB id:

2art

Name:

Ligase

Title:

Crystal structure of lipoate-protein ligase a bound with lipoyl-amp

Structure:

Lipoate-protein ligase a. Chain: a. Engineered: yes

Source:

Thermoplasma acidophilum. Organism_taxid: 2303. Gene: ta0514. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.197 R-free: 0.253

Authors:

D.J.Kim,K.H.Kim,H.H.Lee,S.J.Lee,J.Y.Ha,H.J.Yoon,S.W.Suh

Key ref:

d.o. .J.Kim et al. (2005). Crystal structure of lipoate-protein ligase A bound with the activated intermediate: insights into interaction with lipoyl domains. J Biol Chem, 280, 38081-38089. PubMed id: 16141198 DOI: 10.1074/jbc.M507284200

Date:

22-Aug-05 Release date: 04-Oct-05

Protein chain

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: 247 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⁺

L-lysyl-[lipoyl-carrier protein] + (R)-lipoate + ATP = N(6)-[(R)-lipoyl]- L-lysyl-[lipoyl-carrier protein] (Bound ligand (Het Group name = AMP) matches with 95.65% similarity) + AMP + diphosphate + H(+)

• Cofactor: Mg(2+)

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

reference

DOI no: 10.1074/jbc.M507284200

J Biol Chem 280:38081-38089 (2005)

PubMed id: 16141198

Crystal structure of lipoate-protein ligase A bound with the activated intermediate: insights into interaction with lipoyl domains.

d.o. .J.Kim, K.H.Kim, H.H.Lee, S.J.Lee, J.Y.Ha, H.J.Yoon, S.W.Suh.

ABSTRACT

Lipoic acid is the covalently attached cofactor of several multi-component enzyme complexes that catalyze key metabolic reactions. Attachment of lipoic acid to the lipoyl-dependent enzymes is catalyzed by lipoate-protein ligases (LPLs). In Escherichia coli, two distinct enzymes lipoate-protein ligase A (LplA) and lipB-encoded lipoyltransferase (LipB) catalyze independent pathways for lipoylation of the target proteins. The reaction catalyzed by LplA occurs in two steps. First, LplA activates exogenously supplied lipoic acid at the expense of ATP to lipoyl-AMP. Next, it transfers the enzyme-bound lipoyl-AMP to the epsilon-amino group of a specific lysine residue of the lipoyl domain to give an amide linkage. To gain insight into the mechanism of action by LplA, we have determined the crystal structure of Thermoplasma acidophilum LplA in three forms: (i) the apo form; (ii) the ATP complex; and (iii) the lipoyl-AMP complex. The overall fold of LplA bears some resemblance to that of the biotinyl protein ligase module of the E. coli biotin holoenzyme synthetase/bio repressor (BirA). Lipoyl-AMP is bound deeply in the bifurcated pocket of LplA and adopts a U-shaped conformation. Only the phosphate group and part of the ribose sugar of lipoyl-AMP are accessible from the bulk solvent through a tunnel-like passage, whereas the rest of the activated intermediate is completely buried inside the active site pocket. This first view of the activated intermediate bound to LplA allowed us to propose a model of the complexes between Ta LplA and lipoyl domains, thus shedding light on the target protein/lysine residue specificity of LplA.

Selected figure(s)

Figure 1.
FIGURE 1. Electron density of the bound ligands and overall fold of Ta LplA. A, 2F[o] - F[c] electron density maps of the bound ligands. Atoms of the ligands are also labeled. B, ribbon diagram of Ta LplA. Secondary structure elements were assigned by PROMOTIF (26). -Helices, -strands, and loops are colored in red, blue, and yellow, respectively. Lipoyl-AMP bound near the center of LplA is shown in sticks. All the figures except Fig. 3 are drawn with PyMOL (DeLano, 2002, The PyMOL Molecular Graphics System, www.pymol.org). C, topology diagram of Ta LplA. -Strands are shown as triangles and -helices as circles. D, stereo C trace of Ta LplA. Every tenth residue is marked by a black dot, and every twentieth residue is labeled. Three signature sequence motifs are highlighted in colored lines: motif I (RRXXGGGXV(F/Y)HD at positions 71-82) in red, motif II (KhXGXA at positions 145-150) in green, and motif III (HXX(L/M)LXXX(D/N)LXXLXXhL at positions 161-177) in blue, respectively.

Figure 2.
FIGURE 2. Lipoyl-AMP binding to the active site. A, sectional view of the modeled complex showing the target lysine of the lipoyl domain in the entrance to the lipoyl-AMP binding pocket of Ta LplA. Note that oxygen atoms of the bound lipoyl-AMP are surrounded by the positively charged surface (colored in blue). B, stereo view of the active site around the bound lipoyl-AMP. Black dotted lines denote hydrogen bonds. Red balls represent water molecules. C, stereo view of the adenine ring of the bound lipoyl-AMP and surrounding residues. Main-chain atoms between Ala^78 and His81 are shown as sticks.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 38081-38089) copyright 2005.

Figures were selected by an automated process.