2 research outputs found
Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5ā²-dAdoā¢ āFree Radicalā Is Never Free
Lysine 2,3-aminomutase (LAM) is a
radical <i>S</i>-adenosyl-l-methionine (SAM) enzyme
and, like other members of this superfamily,
LAM utilizes radical-generating machinery comprising SAM anchored
to the unique Fe of a [4Fe-4S] cluster via a classical five-membered
N,O chelate ring. Catalysis is initiated by reductive cleavage of
the SAM SāC5ā² bond, which creates the highly reactive
5ā²-deoxyadenosyl radical (5ā²-dAdoā¢), the same
radical generated by homolytic CoāC bond cleavage in B<sub>12</sub> radical enzymes. The SAM surrogate <i>S</i>-3ā²,4ā²-anhydroadenosyl-l-methionine (anSAM) can replace SAM as a cofactor in the isomerization
of l-Ī±-lysine to l-Ī²-lysine by LAM,
via the stable allylic anhydroadenosyl radical (anAdoā¢). Here
electron nuclear double resonance (ENDOR) spectroscopy of the anAdoā¢
radical in the presence of <sup>13</sup>C, <sup>2</sup>H, and <sup>15</sup>N-labeled lysine completes the picture of how the active
site of LAM from <i>Clostridium subterminale</i> SB4 ātamesā the 5ā²-dAdoā¢ radical,
preventing it from carrying out harmful side reactions: this āfree
radicalā in LAM is never free. The low steric demands of the
radical-generating [4Fe-4S]/SAM construct allow the substrate target
to bind adjacent to the SāC5ā² bond, thereby enabling
the 5ā²-dAdoā¢ radical created by cleavage of this bond
to react with its partners by undergoing small motions, ā¼0.6
Ć
toward the target and ā¼1.5 Ć
overall, that are
controlled by tight van der Waals contact with its partners. We suggest
that the accessibility to substrate and ready control of the reactive
C5ā² radical, with āvan der Waals controlā of
small motions throughout the catalytic cycle, is common within the
radical SAM enzyme superfamily and is a major reason why these enzymes
are the preferred means of initiating radical reactions in nature
Electron Spin Relaxation and Biochemical Characterization of the Hydrogenase Maturase HydF: Insights into [2Fe-2S] and [4Fe-4S] Cluster Communication and Hydrogenase Activation
Nature utilizes [FeFe]-hydrogenase
enzymes to catalyze the interconversion
between H<sub>2</sub> and protons and electrons. Catalysis occurs
at the H-cluster, a carbon monoxide-, cyanide-, and dithiomethylamine-coordinated
2Fe subcluster bridged via a cysteine to a [4Fe-4S] cluster. Biosynthesis
of this unique metallocofactor is accomplished by three maturase enzymes
denoted HydE, HydF, and HydG. HydE and HydG belong to the radical <i>S</i>-adenosylmethionine superfamily of enzymes and synthesize
the nonprotein ligands of the H-cluster. These enzymes interact with
HydF, a GTPase that acts as a scaffold or carrier protein during 2Fe
subcluster assembly. Prior characterization of HydF demonstrated the
protein exists in both dimeric and tetrameric states and coordinates
both [4Fe-4S]<sup>2+/+</sup> and [2Fe-2S]<sup>2+/+</sup> clusters
[Shepard, E. M., Byer, A. S., Betz, J. N., Peters, J. W., and Broderick,
J. B. (2016) <i>Biochemistry 55</i>, 3514ā3527].
Herein, electron paramagnetic resonance (EPR) is utilized to characterize
the [2Fe-2S]<sup>+</sup> and [4Fe-4S]<sup>+</sup> clusters bound to
HydF. Examination of spin relaxation times using pulsed EPR in HydF
samples exhibiting both [4Fe-4S]<sup>+</sup> and [2Fe-2S]<sup>+</sup> cluster EPR signals supports a model in which the two cluster types
either are bound to widely separated sites on HydF or are not simultaneously
bound to a single HydF species. Gel filtration chromatographic analyses
of HydF spectroscopic samples strongly suggest the [2Fe-2S]<sup>+</sup> and [4Fe-4S]<sup>+</sup> clusters are coordinated to the dimeric
form of the protein. Lastly, we examined the 2Fe subcluster-loaded
form of HydF and showed the dimeric state is responsible for [FeFe]-hydrogenase
activation. Together, the results indicate a specific role for the
HydF dimer in the H-cluster biosynthesis pathway