Intermediates in the catalytic cycle of methyl coenzyme M reductase: Isotope exchange is consistent with formation of a σ-Alkane-Nickel Complex

Article abstract of DOI:10.1002/anie.201003214

The key nickel enzyme for methanogenesis (MCR) catalyzes the formation of CH₃D and CH₂D₂ in a deuterated medium. CH ₂D₂ is formed by an exchange of deuterium into the S-methyl group of the substrate. Deuterium is incorporated at both carbon atoms of the S-ethyl group of ethyl coenzyme M, and a ¹³C label is rapidly scrambled within the ethyl group (see scheme). Thus, at least one intermediate is formed and the isotope exchange pattern is consistent with formation of a σ-alkane-nickel complex.

Full text of DOI:10.1002/anie.201003214

Communications
DOI: 10.1002/anie.201003214
À
Enzymatic C H Activation
Intermediates in the Catalytic Cycle of Methyl Coenzyme M
Reductase: Isotope Exchange is Consistent with Formation of a
s-Alkane–Nickel Complex**
Silvan Scheller, Meike Goenrich, Stefan Mayr, Rudolf K. Thauer, and Bernhard Jaun*
[6]
[7]
[8]
À
À
À
Methyl coenzyme M reductase (MCR) is the key enzyme that
catalyzes the last step of methane formation in all methano-
genic archaea.[1] It converts the two substrates methyl
coenzyme M (CH3-S-CoM) and coenzyme B (CoB-SH) into
methane and the corresponding heterodisulfide (CoB-S-S-
CoM) (Scheme 1).
containing Ni H, Ni C, and Ni S bonds have been
characterized by EPR spectroscopy. However, no intermedi-
ates along the catalytic pathway could be observed to date,
and the reaction mechanism is thus still unknown.
Herein, we report that MCR catalyzes the incorporation
of deuterium from the medium not only into the product
methane but also into the substrate. Studies with stable
isotopes show the existence of an intermediate in which the
carbon–sulfur bond is broken and through which the carbon-
bound hydrogen atoms of the S-alkyl group of the substrate
can exchange with solvent-derived deuterium.
Methane generated in assays with purified enzyme
(MCR-I), CH3-S-CoM, and CoB-SH in deuterated medium
1
was analyzed by H NMR spectroscopy. We found that not
only CH3D (the expected isotopologue), but also a significant
amount of CH2D2 was formed (see the Supporting Informa-
tion, Figure S1.1).[5c,9] To determine whether this double
labeling was the consequence of deuterium incorporation
into the substrate, the remaining CH3-S-CoM was analyzed by
1H NMR spectroscopy before full conversion. We found that
deuterium is indeed introduced into the methyl group of
methyl coenzyme M. After 54% conversion (for conditions
and spectra, see the Supporting Information, Section 1.2), the
remaining substrate contained 4.8% CH2D-S-CoM.[10]
(Scheme 2).
Scheme 1. The reaction catalyzed by methyl coenzyme M reductase in
methanogens and the structure of the prosthetic group F430. The
natural substrate, methyl coenzyme M, is converted into methane, and
the non-natural substrate ethyl coenzyme M into ethane.
MCR consists of three protein chains arranged in a
C2-symmetric a2b2g2 complex[2] with two active sites, each
containing one molecule of the nickel hydrocorphinate F430
(1).[3] The nickel center must be in the nickel(I) oxidation
state for the enzyme to be active,[4] and the fourth hydrogen of
the product CH4 originates from the medium.[5] With sub-
strate analogues and inhibitors, different enzyme states
Scheme 2. Double incorporation of deuterium into the product meth-
ane and exchange of deuterium into the remaining substrate methyl
coenzyme M catalyzed by MCR in D2O.
[*] S. Scheller, Dr. S. Mayr, Prof. B. Jaun
Laboratory of Organic Chemistry, ETH Zurich
Wolfgang-Pauli-Strasse 10, 8093 Zurich (Switzerland)
Fax: (+41)44-632-1475
The non-natural substrate ethyl coenzyme M is converted
by MCR, giving ethane,[11] although about 200 times[11c] more
slowly than the natural substrate Me-S-CoM gives methane.
Investigation of deuterium incorporation into Et-S-CoM
under the conditions used for Me-S-CoM revealed that
deuterium is introduced at both carbon centers of the S-
ethyl group. After 2 min reaction time, only about 1% of the
substrate had been converted into ethane, but the remaining
substrate contained 9.0% of CH3CHD-S-CoM and 15.2%
CH2DCH2-S-CoM. After 32 min, a mixture of 11 isotopo-
logues could be detected (containing, for example, 10.8%
CHD2CD2-S-CoM and 4.9% CD3CHD-S-CoM). Figure 1
E-mail: jaun@org.chem.ethz.ch
Dr. M. Goenrich, Prof. R. K. Thauer
Max-Planck-Institute for Terrestrial Microbiology
Karl-von-Frisch-Strasse 10, 35403 Marburg (Germany)
[**] This work was supported by the Swiss National Science Foundation
(S.S., S.M., and B.J.; grant no. 200020-119752), the Max Planck
Society, and the Fonds der Chemischen Industrie (M.G. and R.K.T.).
We thank Reinhard Bꢀcher for technical assistance and Dr. Marc-
Olivier Ebert for his help with specialized NMR techniques.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201003214.
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Chemie
the ethyl ligand was observed whereby the deuterium
remained attached to the labeled carbon during the vicinal
bond shift (Scheme 3).
Scheme 3. Bond shifts via a s-complex as proposed by Bergman[12] for
a [(H)(Et)RhCp*PMe3] complex and consistent with the pattern of
isotope exchange with CH313CH2S-CoM in D2O catalyzed by MCR.
Figure 1. Formation of the 11 isotopologues of ethyl-S-CoM that are
detectable by 1H NMR spectroscopy as a function of incubation time
with MCR-I in deuterated medium at 608C. Molar fractions were
1
determined from H{2H} NMR spectra. CD3CD2SCoM is not observed
in the 1H NMR spectrum. (See the Supporting Information for
experimental conditions.)
We have recently shown that the MCR-catalyzed reaction
is indeed reversible.[13] In a competitive experiment, methane
was converted into Me-S-CoM with 0.011 UmgÀ1, whereas
ethane was converted into Et-S-CoM with 0.00074 UmgÀ1
(for details, see the Supporting Information). These reverse
reactions are much slower than the isotope exchange
described herein (ca. 1 UmgÀ1 for Me-S-CoM and
10 UmgÀ1 for Et-S-CoM). Therefore, the formation of
CH2D2 from Me-S-CoM in D2O is mainly due to deuterium
exchange into the substrate. Isotope exchange occurs along
the catalytic pathway before the products are formed and at
least one intermediate must exist, which either reacts back to
the substrates (with the possibility of isotope exchange) or
forward to give the products. Scheme 4 illustrates the minimal
reaction profile taking into account the ratio of substrate
deuteration versus product formation for the two substrates.
shows the molar fractions of Et-S-CoM isotopologues as a
function of time.
As direct deuterium incorporation into the methyl group
of ethyl-S-CoM was considered to be mechanistically unrea-
sonable, we tested for putative scrambling of the two carbon
centers within the ethyl group using a 13C label. In experi-
ments with CH313CH2-S-CoM in non-deuterated medium, the
13C label was nearly statistically distributed within the ethyl
group after incubation for 32 min. The scrambling process
showed apparent first-order kinetics, with a half-life time of
about 4 min (see the Supporting Information, Figure S1.3).
To correlate deuterium incorporation with carbon scram-
bling, experiments with CH313CH2-S-CoM were run in
deuterated medium. Analysis after 2 min reaction time
showed the following molar fractions of monodeuterated
isotopologues: CH313CHDS-CoM (8.2%); CH2D13CH2-S-
CoM (0.0%); 13CH3CHD-S-CoM (0.0%); 13CH2DCH2-S-
CoM (12.9%). After 8 minutes, the doubly deuterated species
were found at molar fractions of CH313CD2-S-CoM (1.18%),
13CHD2CH2-S-CoM (3.43%), and 13CH2DCHD-S-CoM
(4.71%), CH2D13CHD-S-CoM (4.84%), which is close to
the statistically expected ratios of 1:3 and 1:1, respectively
(Supporting Information, Figure S1.5).
This distribution demonstrates that deuterium is intro-
duced only at the carbon center bound to sulfur in the
substrate and that deuterium incorporation into the methyl
group is a consequence of the carbon scrambling. (A plot
showing the time dependence of all observed isotopologues of
the 13C-labeled substrate is given in the Supporting Informa-
tion, Figure S1.4.)
The same pattern of isotope exchange has been observed
by Periana and Bergman with a hydridoethylrhodium com-
plex [Cp*(PMe3)Rh(Et)(D)].[12] They found that the
[1-13C]ethyl deuteride rearranges to the [1-13C, 1-2H]ethyl
hydride upon warming to À808C. On further warming to
À258C, rearrangement of the a-13C label to the b carbon of
À
In the intermediate ternary complex, the C S bond is
[14]
À
À
replaced by a C D bond and therefore all C H(D) bonds
of the prospective alkane are already set up, although the
exact binding mode is not known. However, our experimental
findings are consistent with the formation of a s-coordinated
alkane as an intermediate (Scheme 5). In contrast to the
mechanisms proposed earlier,[1a,15] which assumed involve-
ment of a single axial coordination site on the nickel, a
mechanism via nickel(hydrido)(alkyl) and nickel(s-alkane)
intermediates such as proposed herein requires the availabil-
ity of two adjacent coordination sites. From EPR studies with
substrate analogues, it is known that the enzyme undergoes a
major conformational change upon binding of the second
substrate,[16] and MCR-species with a hydride and a thiolate
coordinated to the nickel center along with the coordinatively
distorted hydrocorphin ligand have been characterized.[6,8]
Therefore, a second adjacent coordination site may well be
accessible.
À
In the reverse reaction, the activation of the strong C H
bond of methane, a nickel(s-alkane) complex as the first
intermediate is more in line with chemical precedence for
[17]
À
C H activation at transition metals than, for example, the
very endothermal abstraction (70 kJmolÀ1) of a hydrogen
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S-alkyl group of the substrate can exchange with solvent-
derived deuterium according to a pattern that has also been
observed in [(H)(alkyl)RhCp*(L)] complexes. This reactivity
is the case for both the native substrate and the non-natural
substrate ethyl-S-CoM. We propose considering (s-alkane)-
NiF430 and (H)(alkyl)NiF430 complexes as intermediates
for both methane formation and anaerobic methane activa-
tion (Scheme 5). However, with the exception of the CH4
activation by Ni(H)(OH)+ in the gas phase observed by
Schlangen and Schwarz,[19] no non-enzymatic example of this
type of reactivity catalyzed by a late transition metal with an
odd number of electrons (such as nickel(I), d9) is currently
known. Hopefully, the biological importance of the MCR-
À
catalyzed reactions and the current interest in mild C H
activation will prompt in-depth chemical studies of this type
of odd-electron transition metal centers as catalysts.
Received: May 27, 2010
Published online: September 20, 2010
Scheme 4. Reaction profiles of a) methyl coenzyme M and b) the non-
À
Keywords: C H activation · isotope exchange ·
methyl coenzyme M reductase · nickel enzymes ·
natural substrate ethyl coenzyme M. From the ratio of deuterium
incorporation versus product formation, the indicated energy differ-
ences are calculated.
.
s-alkane ligands
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in red) in deuterated medium. The ligand of coenzyme F430 is shown schematically as bold
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ate in which the carbon–sulfur bond of the substrate is broken
and through which the carbon-bound hydrogen atoms of the
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Angewandte
Chemie
[9] The formation of CH2D2 in methanogensis was reported earlier
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reported herein depends on the magnitude of 3H and 2H kinetic
À
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