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PDBsum entry 2i2x
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Contents |
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(+ 2 more)
459 a.a.
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(+ 2 more)
258 a.a.
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References listed in PDB file
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Key reference
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Title
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Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-Cobalamin methyltransferase complex.
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Authors
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C.H.Hagemeier,
M.Krer,
R.K.Thauer,
E.Warkentin,
U.Ermler.
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Ref.
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Proc Natl Acad Sci U S A, 2006,
103,
18917-18922.
[DOI no: ]
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PubMed id
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Abstract
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Some methanogenic and acetogenic microorganisms have the catalytic capability to
cleave heterolytically the C O bond of methanol. To obtain insight into the
elusive enzymatic mechanism of this challenging chemical reaction we have
investigated the methanol-activating MtaBC complex from Methanosarcina barkeri
composed of the zinc-containing MtaB and the
5-hydroxybenzimidazolylcobamide-carrying MtaC subunits. Here we report the 2.5-A
crystal structure of this complex organized as a (MtaBC)(2) heterotetramer. MtaB
folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at
the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to
two cysteinyl sulfurs (Cys-220 and Cys-269) and one carboxylate oxygen
(Glu-164). MtaC is structurally related to the cobalamin-binding domain of
methionine synthase. Its corrinoid cofactor at the top of the Rossmann domain
reaches deeply into the funnel of MtaB, defining a region between zinc(II) and
the corrinoid cobalt that must be the binding site for methanol. The active site
geometry supports a S(N)2 reaction mechanism, in which the C O bond in methanol
is activated by the strong electrophile zinc(II) and cleaved because of an
attack of the supernucleophile cob(I)amide. The environment of zinc(II) is
characterized by an acidic cluster that increases the charge density on the
zinc(II), polarizes methanol, and disfavors deprotonation of the methanol
hydroxyl group. Implications of the MtaBC structure for the second step of the
reaction, in which the methyl group is transferred to coenzyme M, are discussed.
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Figure 1.
The MtaBC structure. (A) In the (MtaBC)[2] heterotetramer (in
stereo) each MtaBC unit (MtaB in blue and MtaC in red) is
related to its partner unit (in light blue and red) by a twofold
noncrystallographic axis. The (MtaBC)[2] complex has a size of
62 Å × 55 Å × 52 Å and forms two
active sites separated by a distance of 38 Å. The
corrinoids are shown as stick models, and the zinc(II) ions are
depicted by green spheres. The contact loops between the two
active sites are highlighted in black. For oligomeric assembly
the interactions between the N-terminal extension of MtaC (in
green) and the counter MtaB are essential. (B) In the MtaBC unit
the Rossmann domain (orange) of MtaC is only loosely associated
with its helical domain (red) and MtaB (blue). MtaB is
subdivided into a TIM barrel core (dark blue) and a helical
layer (light blue). The active site is located between the
corrinoid cobalt and zinc(II).
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Figure 3.
Proposed mechanism of methanol activation. (A) Scheme of a
unique acidic cluster that flanks the zinc and methanol-binding
site. The acidic residues (in red) might play a crucial role in
polarizing zinc(II) and methanol. The unclear peak X was
tentatively assigned as a potassium ion. Methanol is modeled
into the protein, and its distance to the corrinoid Co is
estimated based on the distance between the zinc(II) and
methanol oxygen of 2 Å. (B) S[N]2 mechanism for the
methylation of 5-hydroxybenzimidazolyl cob(I)amide with
methanol. The methanol is activated by the strong electrophile
zinc(II) and attacked by the supernucleophile cob(I)amide.
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