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PDBsum entry 2c00
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Enzyme class:
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E.C.6.3.4.14
- biotin carboxylase.
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Reaction:
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N6-biotinyl-L-lysyl-[protein] + hydrogencarbonate + ATP = N6- carboxybiotinyl-L-lysyl-[protein] + ADP + phosphate + H+
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N(6)-biotinyl-L-lysyl-[protein]
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+
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hydrogencarbonate
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+
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ATP
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=
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N(6)- carboxybiotinyl-L-lysyl-[protein]
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+
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ADP
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+
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phosphate
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Protein Sci
17:1706-1718
(2008)
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PubMed id:
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Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
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I.Mochalkin,
J.R.Miller,
A.Evdokimov,
S.Lightle,
C.Yan,
C.K.Stover,
G.L.Waldrop.
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ABSTRACT
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Bacterial acetyl-CoA carboxylase is a multifunctional biotin-dependent enzyme
that consists of three separate proteins: biotin carboxylase (BC), biotin
carboxyl carrier protein (BCCP), and carboxyltransferase (CT). Acetyl-CoA
carboxylase is a potentially attractive target for novel antibiotics because it
catalyzes the first committed step in fatty acid biosynthesis. In the first
half-reaction, BC catalyzes the ATP-dependent carboxylation of BCCP. In the
second half-reaction, the carboxyl group is transferred from carboxybiotinylated
BCCP to acetyl-CoA to produce malonyl-CoA. A series of structures of BC from
several bacteria crystallized in the presence of various ATP analogs is
described that addresses three major questions concerning the catalytic
mechanism. The structure of BC bound to AMPPNP and the two catalytically
essential magnesium ions resolves inconsistencies between the kinetics of
active-site BC mutants and previously reported BC structures. Another structure
of AMPPNP bound to BC shows the polyphosphate chain folded back on itself, and
not in the correct (i.e., extended) conformation for catalysis. This provides
the first structural evidence for the hypothesis of substrate-induced synergism,
which posits that ATP binds nonproductively to BC in the absence of biotin. The
BC homodimer has been proposed to exhibit half-sites reactivity where the active
sites alternate or "flip-flop" their catalytic cycles. A crystal structure of BC
showed the ATP analog AMPPCF(2)P bound to one subunit while the other subunit
was unliganded. The liganded subunit was in the closed or catalytic conformation
while the unliganded subunit was in the open conformation. This provides the
first structural evidence for half-sites reactivity in BC.
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Selected figure(s)
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Figure 4.
Figure 4. Stereoview of superimposed AMPPNP in SaBC and
EcBC crystal structures. SaBC/AMPPNP structure is colored in
red. EcBC/AMPPNP structure is colored in blue. SaBC residues
involved in interactions with the ligand are shown in sticks
with the following atom colors: carbon, yellow; nitrogen, blue;
oxygen, red. Images were prepared using PyMOL molecular graphics
systems (DeLano Scientific).
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Figure 5.
Figure 5. View of octahedrally coordinated magnesium ions
in BC crystal structures. Nucleotide molecules and protein
residues are shown in sticks with the following atom colors:
carbon, green; nitrogen, blue; oxygen, red; phosphorus, orange.
Magnesium ions and water molecules are shown as green and red
spheres. (A) View of two magnesium-binding sites in the
SaBC/AMPPNP structure. (B) View of one magnesium-binding site in
the PaBC/AMPCP structure.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2008,
17,
1706-1718)
copyright 2008.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Adina-Zada,
R.Hazra,
C.Sereeruk,
S.Jitrapakdee,
T.N.Zeczycki,
M.S.Maurice,
W.W.Cleland,
J.C.Wallace,
and
P.V.Attwood
(2011).
Probing the allosteric activation of pyruvate carboxylase using 2',3'-O-(2,4,6-trinitrophenyl) adenosine 5'-triphosphate as a fluorescent mimic of the allosteric activator acetyl CoA.
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Arch Biochem Biophys,
509,
117-126.
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B.R.Novak,
D.Moldovan,
G.L.Waldrop,
and
M.S.de Queiroz
(2011).
Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations.
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Proteins,
79,
622-632.
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U.Pieper,
B.M.Webb,
D.T.Barkan,
D.Schneidman-Duhovny,
A.Schlessinger,
H.Braberg,
Z.Yang,
E.C.Meng,
E.F.Pettersen,
C.C.Huang,
R.S.Datta,
P.Sampathkumar,
M.S.Madhusudhan,
K.Sjölander,
T.E.Ferrin,
S.K.Burley,
and
A.Sali
(2011).
ModBase, a database of annotated comparative protein structure models, and associated resources.
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Nucleic Acids Res,
39,
D465-D474.
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C.T.Walsh,
and
M.A.Fischbach
(2009).
Repurposing libraries of eukaryotic protein kinase inhibitors for antibiotic discovery.
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Proc Natl Acad Sci U S A,
106,
1689-1690.
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C.Y.Chou,
L.P.Yu,
and
L.Tong
(2009).
Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.
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J Biol Chem,
284,
11690-11697.
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PDB codes:
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J.R.Miller,
S.Dunham,
I.Mochalkin,
C.Banotai,
M.Bowman,
S.Buist,
B.Dunkle,
D.Hanna,
H.J.Harwood,
M.D.Huband,
A.Karnovsky,
M.Kuhn,
C.Limberakis,
J.Y.Liu,
S.Mehrens,
W.T.Mueller,
L.Narasimhan,
A.Ogden,
J.Ohren,
J.V.Prasad,
J.A.Shelly,
L.Skerlos,
M.Sulavik,
V.H.Thomas,
S.VanderRoest,
L.Wang,
Z.Wang,
A.Whitton,
T.Zhu,
and
C.K.Stover
(2009).
A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore.
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Proc Natl Acad Sci U S A,
106,
1737-1742.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
