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PDBsum entry 1v25
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural basis of the substrate-Specific two-Step catalysis of long chain fatty acyl-Coa synthetase dimer.
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Authors
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Y.Hisanaga,
H.Ago,
N.Nakagawa,
K.Hamada,
K.Ida,
M.Yamamoto,
T.Hori,
Y.Arii,
M.Sugahara,
S.Kuramitsu,
S.Yokoyama,
M.Miyano.
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Ref.
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J Biol Chem, 2004,
279,
31717-31726.
[DOI no: ]
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PubMed id
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Abstract
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Long chain fatty acyl-CoA synthetases are responsible for fatty acid degradation
as well as physiological regulation of cellular functions via the production of
long chain fatty acyl-CoA esters. We report the first crystal structures of long
chain fatty acyl-CoA synthetase homodimer (LC-FACS) from Thermus thermophilus
HB8 (ttLC-FACS), including complexes with the ATP analogue adenosine
5'-(beta,gamma-imido) triphosphate (AMP-PNP) and myristoyl-AMP. ttLC-FACS is a
member of the adenylate forming enzyme superfamily that catalyzes the
ATP-dependent acylation of fatty acid in a two-step reaction. The first reaction
step was shown to propagate in AMP-PNP complex crystals soaked with myristate
solution. Myristoyl-AMP was identified as the intermediate. The AMP-PNP and the
myristoyl-AMP complex structures show an identical closed conformation of the
small C-terminal domains, whereas the uncomplexed form shows a variety of open
conformations. Upon ATP binding, the fatty acid-binding tunnel gated by an
aromatic residue opens to the ATP-binding site. The gated fatty acid-binding
tunnel appears only to allow one-way movement of the fatty acid during overall
catalysis. The protein incorporates a hydrophobic branch from the fatty
acid-binding tunnel that is responsible for substrate specificity. Based on
these high resolution crystal structures, we propose a unidirectional Bi Uni Uni
Bi Ping-Pong mechanism for the two-step acylation by ttLC-FACS.
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Figure 3.
FIG. 3. ttLC-FACS crystal structure. Ribbon representations
of the ttLC-FACS dimer are shown (A). In the panel, the
secondary structure of the C-terminal domain is colored in
green. In the N-terminal domain,  -helix and  -sheet
are colored in cyan and red, respectively, with the N-terminal
domain-swapping peptide colored in yellow. The electrostatic
potential surface map of ttLC-FACS dimer in the same orientation
as the representation in A. Red represents negatively charged
regions, and blue represents positively charged regions (B).
Close-up view of the N-terminal peptide involved in domain
swapping in the reverse orientation view to A (C). Residues with
carbons colored in pink against a cyan surface of one monomer
interacts with the concave surface of the other monomer colored
in yellow. There are salt bridges at the domain swapping region.
The monomer of ttLC-FACS with each secondary structure feature
is labeled according to the scheme given in Fig. 2A (D).
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Figure 6.
FIG. 6. Superimposed structures of the vicinity of linker
peptides and bound adenylates in adenylate forming enzyme
complexes in stereo. The adenylate complexed enzymes of the
known structures, DhbE (Protein Data Bank code 1mdb [PDB]
) (30), PheA (Protein Data Bank code 1amu [PDB]
) (29), SC-FACS (Protein Data Bank code 1pg3 [PDB]
) (31), and ttLC-FACS (this work) are superimposed around each
bound adenosine moiety. The backbone of the linker region
(Lys431-Asp-Arg-Leu-Lys-Asp-Leu437) including the L motif in
ttLC-FACS complex structure and the corresponding peptides are
presented as wire models (ttLC-FACS, thick violet; SC-FACS, red
violet; DhbE, blue; PheA, light green). The bound myristoyl-AMP
in the ttLC-FACS is represented as by thick green sticks, and
other bound adenylates each shown in thin colored sticks. Arg433
and Lys439 of ttLC-FACS and the corresponding residues are also
shown.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
31717-31726)
copyright 2004.
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