Loss of iron–sulfur clusters from biotin synthase as a result of catalysis promotes unfolding and degradation

Reyda, Michael R.; Dippold, Rachael P.; Dotson, Michael E.; Jarrett, Joseph T.

doi:10.1016/j.abb.2007.12.001

Cited by 19 publications

(18 citation statements)

References 29 publications

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“…If not, the protein molecule perishes and must be re-synthesized de novo . More recent work done in vitro has shown that loss of iron-sulfur clusters from BioB as a result of catalysis promotes unfolding and degradation (75). Hence, some BioB molecules may catalyze only one or a few turnovers in their lifetimes whereas others may complete >100 turnovers.…”

Section: The Pathway and Proteins Of Biotin Synthesismentioning

confidence: 99%

Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation

Cronan

2014

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Summary Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as “swinging arms” that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well-described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like “arm” of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise and the BioH esterase for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyl transferase followed by sulfur insertion at carbons C6 and C8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized and thus there is no transcriptional control of the synthetic genes. In contrast transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA a dual function protein that both represses biotin operon transcription and ligates biotin to its cognate protein.

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Section: The Pathway and Proteins Of Biotin Synthesismentioning

confidence: 99%

Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation

Cronan

2014

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“…It described a homologous group of enzymes united by their utilization of SAM in a radical mechanism (Sofia, Chen, Hetzler, Reyes-Spindola, & Miller, 2001). The original sequence set came from 126 species representing all Kingdoms of life and included many of the first RSS enzymes to be characterized: lysine 2,3-aminomutase (LAM), (Moss & Frey, 1987), biotin synthase (BioB) (Lotierzo, Tse Sum Bui, Florentin, Escalettes, & Marquet, 2005; Reyda, Dippold, Dotson, & Jarrett, 2008) lipoyl synthase (LipA) (Cicchillo, Iwig, et al, 2004; Miller et al, 2000), pyruvate-formate lyase activase (PflA) (Knappe & Sawers, 1990; Vey et al, 2008), and anaerobic ribonucleoside-triphosphate reductase activase (NrdG) (Padovani, Thomas, Trautwein, Mulliez, & Fontecave, 2001). From a chemical perspective, to be considered a member of the RSS, Sofia defined three characteristics that were minimally required:…”

Section: Introduction: Overview Of the Radical Sam Superfamilymentioning

confidence: 99%

“…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)). They are also involved in the modification of nucleic acids, often via methylation of aromatic carbon centers, repair of DNA dimers (as in spore photoproduct lyase (SPL) (Benjdia, Heil, Barends, Carell, & Schlichting, 2012; Yang & Li, 2015)), the formation of the wybutosine base on tRNA (Young & Bandarian, 2011), and the formation of complex natural products such as antibiotics (Mahanta, Hudson, & Mitchell, 2017a, 2017b) (for example nosiheptide (LaMattina et al, 2017; Yu et al, 2009) and bleomycin (Tao et al, 2007)).…”

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

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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“…In the case of those with labile FeS clusters, their steady state abundance relies on the operation of cluster repair mechanisms, and these are sensitive to Fe availability (Garland et al, 1999;Jensen and Culotta, 2000;Djaman et al, 2004). In Fe deficiency, the apoproteins would not be remetallated, making them susceptible to proteases (Reyda et al, 2008). For other Fe proteins, a recognition mechanism is not obvious, but their degradation might be a consequence of oxidative stress damage from reaction of the active site Fe with H 2 O 2 (Halliwell and Gutteridge, 1984;reviewed in Imlay, 2008).…”

Section: Maintenance Of Fesodmentioning

confidence: 99%