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PDBsum entry 2art
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References listed in PDB file
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Key reference
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Title
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Crystal structure of lipoate-Protein ligase a bound with the activated intermediate: insights into interaction with lipoyl domains.
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Authors
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D.O. .J.Kim,
K.H.Kim,
H.H.Lee,
S.J.Lee,
J.Y.Ha,
H.J.Yoon,
S.W.Suh.
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Ref.
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J Biol Chem, 2005,
280,
38081-38089.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
38081-38089)
copyright 2005.
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