Biochemistry of Methyl-Coenzyme M Reductase: The Nickel Metalloenzyme that Catalyzes the Final Step in Synthesis and the First Step in Anaerobic Oxidation of the Greenhouse Gas Methane - The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment - page 129

Å

The nickel ions in the two F 430 -containing active sites are separated by 50 .

Each active site is accessible from the surface only through a 50 Å long channel,

which is 25 Å in diameter at the protein surface and narrows to 8 Å over the last

Å

16 of the tunnel that leads to a pocket at the base of the channel where F 430 binds

(Figure 2b ). The side chain oxygen of Gln ʱ ' 147 binds to the nickel atom of F 430 on
its bottom face. The protein fold, the conformation, and the binding modes of F 430
are well conserved in all structures that have been reported, including those of the
Ni(II) [ 54 ] and methyl-Ni(III) forms of the enzyme [ 51 ].
In MCR ox1 -silent state, CoMS binds almost parallel to the tetrapyrrole plane,
with its negatively charged sulfonate group interacting with an Arg residue.
CoBSH binds perpendicular to CoMSH, with its threonine phosphate moiety
interacting with residues near the lip of the tunnel and the seven-carbon mercapto-
heptanoyl chain threaded through the hydrophobic tunnel, ending with its
thiolate sulfur of CoBSH 8.6 fromtheNi.Theheterodisulfideproductofthe

MCR reaction, CoBS-SCoM, binds with the CoBSH moiety in the same position
as CoBS and one of its sulfonate oxygens of CoMS axially coordinated to
nickel.
Because binding of CoBSH would block binding of methyl-CoM, an ordered
mechanism was proposed in which methyl-SCoM binds first, then CoBSH, with a
conformational change induced by substrate binding to bring the two substrates in
appropriate position to react [ 52 ]. The ordered mechanism was demonstrated by
steady-state and presteady-state kinetic studies [ 55 ]. A CoMSH-induced conforma-
tional change was indicated by the MCR red1 -silent structure [ 52 ], yet elegant NMR,
EPR, and 19 F-ENDOR studies from the groups of Thauer and Jaun using CoMSH
and the S-CF 3 analog of CoBSH demonstrated that binding of the second substrate
to either the Ni(I) or Ni(II) states of MCR induces a 2

Å

movement of CoBSH
closer to the Ni [ 56 ]. A structural comparison of MCR in the presence of various
mercaptoalkanoyl analogs of CoBSH supports this concept and suggests
that rearrangement of the Tyr residues near the Ni center might trigger deeper
penetration of CoBSH into MCR [ 53 ].
High-resolution crystal structures revealed that MCR contains five posttrans-
lationally modified amino acids,

Å

including 1-N-methylhistidine ( ʱ 257),

5-( S )-methylarginine ( ʱ 271), 2-( S )-methylglutamine ( ʱ 400), S-methylcysteine

( subunits within the substrate channel

[ 57 ]. The methyl groups were shown to be introduced by S-adenosylmethionine
(SAM)-dependent reactions [ 58 ]. Mass spectrometric studies revealed that, while
thioglycine (from Gly ʱ 445) has been found in all methanogens in which it has
been examined and proposed to play a redox role during catalysis [ 52 ], various
organisms (including MCR I and MCR II from M. marburgensis ,MCRIfrom
Methanocaldococcus jannaschii ,and Methanoculleus thermophilus ,MCR
from Methanococcus voltae , Methanopyrus kandleri, and Methanosarcina
barkeri , and two MCRs of the ANME-1 methanotrophic archaea cluster isolated
from Black Sea mats) contain different modified methylated residues [ 59 ].

ʱ 452), and thioglycine ( ʱ 445) from the ʱ