Metallocofactor assembly for [FeFe]-hydrogenases

Dinis, Pedro; Wieckowski, Beata M.; Roach, Peter L.

doi:10.1016/j.sbi.2016.06.004

Cited by 15 publications

(7 citation statements)

References 44 publications

(76 reference statements)

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“…The original set of 650 sequences has now grown over 150-fold (not counting sequences from the large compilations of metagenomic data now coming available). Known functions reveal that RSS enzymes catalyze a dizzying array of disparate and essential chemistries that range from the formation of complex metal cofactors (Dinis, Wieckowski, & Roach, 2016) (e.g. the formation of the [FeFe]-hydrogenase metallocofactor in HydG (Pilet et al, 2009) and HydE (Nicolet et al, 2008)) to the formation of more than half of the over two dozen known organic cofactors (for example, biotin (Lotierzo, Tse Sum Bui, Florentin, Escalettes, & Marquet, 2005; Reyda, Dippold, Dotson, & Jarrett, 2008), lipoic acid (Cicchillo, Lee, et al, 2004; Miller et al, 2000), menaquinone (vitamin K) (Hiratsuka et al, 2008) and pyrroloquinonoline quinone (PQQ) (Barr et al, 2016; Puehringer, Metlitzky, & Schwarzenbacher, 2008)).…”

Section: Introduction: Overview Of the Radical Sam Superfamilymentioning

confidence: 99%

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug and Play” Domain

Holliday

Akiva

Meng

et al. 2018

Methods in Enzymology

109

113

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The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5'-deoxyadenosyl radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure-function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.

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Section: Introduction: Overview Of the Radical Sam Superfamilymentioning

confidence: 99%

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug and Play” Domain

Holliday

Akiva

Meng

et al. 2018

Methods in Enzymology

109

113

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“…26,28−31 Recent spectroscopic and structural work has shown that the accessory cluster site in HydG is occupied by a [4Fe-4S][(κ 3 -Cys)Fe] moiety that is proposed to be the site of Fe(CO) 2 (CN)Cys synthon formation, although the precise mechanistic details of DHG breakdown at this site require further clarification. 24,28,32−36 …”

mentioning

confidence: 99%

Electron Spin Relaxation and Biochemical Characterization of the Hydrogenase Maturase HydF: Insights into [2Fe-2S] and [4Fe-4S] Cluster Communication and Hydrogenase Activation

et al. 2017

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Nature utilizes [FeFe]-hydrogenase enzymes to catalyze the interconversion between H2 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 S-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]2+/+ and [2Fe-2S]2+/+ clusters [Shepard, E. M., Byer, A. S., Betz, J. N., Peters, J. W., and Broderick, J. B. (2016) Biochemistry 55, 3514–3527]. Herein, electron paramagnetic resonance (EPR) is utilized to characterize the [2Fe-2S]+ and [4Fe-4S]+ clusters bound to HydF. Examination of spin relaxation times using pulsed EPR in HydF samples exhibiting both [4Fe-4S]+ and [2Fe-2S]+ 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]+ and [4Fe-4S]+ 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.

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“…These systems function similarly, but they are biochemically discrete. Additional systems have been described for building more complex Fe-S clusters such as those found in dinitrogenase reductases and hydrogenases (reviewed in references 14 and 15 ).…”

Section: Building Iron-sulfur Clustersmentioning

confidence: 99%