Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones

Toraya, Tetsuo

doi:10.1016/j.abb.2013.11.002

Cited by 59 publications

(62 citation statements)

References 212 publications

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“…This indicates that these organisms may be able to switch between the use of compartments, depending on either the supply of the respective substrate (cho-line, ethanolamine, propanediol) or the availability of vitamin B 12 . Given that the vitamin B 12 cofactor has to be repaired or regenerated frequently (31,100) and the vitamin B 12 -dependent glycerol/ diol dehydratases as well as the ethanolamine ammonia-lyases are prone to quick inactivation during the turnover of their respective substrates, the GRE signature enzyme and the GRM BMCs may provide a relatively parsimonious alternative to their EUT and PDU BMC counterparts. Moreover, the de novo biosynthesis of vitamin B 12 is biochemically costly (80) and requires cobalt, which can be limiting.…”

Section: Prediction Of Grm Functionsmentioning

confidence: 99%

Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments

Zarzycki

Erbilgin

Kerfeld

2015

Appl Environ Microbiol

137

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Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol-and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde. Recently, it was shown that the most prevalent signature enzymes encoded by BMC loci are glycyl radical enzymes, yet little is known about the function of these BMCs. Here we characterize the glycyl radical enzyme-associated microcompartment (GRM) loci using a combination of bioinformatic analyses and active-site and structural modeling to show that the GRMs comprise five subtypes. We predict distinct functions for the GRMs, including the degradation of choline, propanediol, and fuculose phosphate. This is the first family of BMCs for which identification of the signature enzyme is insufficient for predicting function. The distinct GRM functions are also reflected in differences in shell composition and apparently different assembly pathways. The GRMs are the counterparts of the vitamin B 12 -dependent propanediol-and ethanolamine-utilizing BMCs, which are frequently associated with virulence. This study provides a comprehensive foundation for experimental investigations of the diverse roles of GRMs. Understanding this plasticity of function within a single BMC family, including characterization of differences in permeability and assembly, can inform approaches to BMC bioengineering and the design of therapeutics. In the last decade, an accumulation of countervailing evidence has overturned the long-held verdict that bacteria are primitive organisms lacking intracellular organization. In addition to membrane-bound organelles like the magnetosomes of magnetotactic bacteria (1, 2) or the anammoxosomes found in some members of the Planctomycetes, bacteria also form protein-based organelles known as bacterial microcompartments (BMCs) (3-5). The defining feature of all BMCs is a shell composed of homologous proteins containing the Pfam00936 domain. A protein with a single copy of the Pfam00936 domain that forms hexamers is referred to as BMC-H; a second type of shell protein consists of a fusion of two Pfam00936 domains and forms pseudohexameric trimers and is referred to as BMC-T. The hexamers and pseudohexamers are thought to tile into the facets of the shell (3, 6). A third type of shell protein containing the Pfam03319 domain forms pentamers that are assumed to cap the vertices of an apparently icosahedral shell and is referred to as BMC-P (3, 7). The BMC-H, BMC-T, and BMC-P oligomers are typically perforated by pores, through which metabolite exchange with the cytosol is assumed to be mediated. Residues flanking the pores are generally polar and well conserved among orthologs, and mutation of the residu...

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Section: Prediction Of Grm Functionsmentioning

confidence: 99%

Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments

Zarzycki

Erbilgin

Kerfeld

2015

Appl Environ Microbiol

137

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“…MeaB additionally remains associated with MCM during turnover and reduces the rate of oxidative inactivation (18). Notably, MeaB is structurally and mechanistically distinct from the ATP-dependent chaperones for AdoCbl-dependent eliminating enzymes, such as diol dehydratase: these chaperones, also termed reactivases, bind to inactivated enzymes and use their ATPase activity to eject damaged cofactor but do not affect AdoCbl delivery (19). An ortholog of MeaB, MeaI, is found fused to isobutyryl-CoA mutase.…”

mentioning

confidence: 99%

Visualization of a radical B ₁₂ enzyme with its G-protein chaperone

Jost¹,

Cracan

Hubbard³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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G-protein metallochaperones ensure fidelity during cofactor assembly for a variety of metalloproteins, including adenosylcobalamin (AdoCbl)-dependent methylmalonyl-CoA mutase and hydrogenase, and thus have both medical and biofuel development applications. Here, we present crystal structures of IcmF, a natural fusion protein of AdoCbl-dependent isobutyryl-CoA mutase and its corresponding G-protein chaperone, which reveal the molecular architecture of a G-protein metallochaperone in complex with its target protein.These structures show that conserved G-protein elements become ordered upon target protein association, creating the molecular pathways that both sense and report on the cofactor loading state. Structures determined of both apo-and holo-forms of IcmF depict both open and closed enzyme states, in which the cofactor-binding domain is alternatively positioned for cofactor loading and for catalysis. Notably, the G protein moves as a unit with the cofactorbinding domain, providing a visualization of how a chaperone assists in the sequestering of a precious cofactor inside an enzyme active site.

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“…OH 2 Cbl is a hallmark of inactivation in AdoCbl-dependent enzymes (23) and is characterized by an increase in absorption at 351 and 530 nm (Fig. 3C).…”

Section: Resultsmentioning

confidence: 99%

“…The susceptibility of AdoCbl-dependent radical enzymes to irreversible inactivation during catalysis necessitates their reliance on chaperones for their reactivation. In the subclass of AdoCbl-dependent enzymes to which diol dehydratase belongs, reactivating factors mediate an ATP-dependent exchange of enzyme-bound OH 2 Cbl with free AdoCbl (23,35). These reactivases have sequence similarity to DnaK and other members of the Hsp70 family of molecular chaperones and lower sequence similarity to the large subunits of corresponding mutases (23).…”

Section: Discussionmentioning

confidence: 99%

“…In the subclass of AdoCbl-dependent enzymes to which diol dehydratase belongs, reactivating factors mediate an ATP-dependent exchange of enzyme-bound OH 2 Cbl with free AdoCbl (23,35). These reactivases have sequence similarity to DnaK and other members of the Hsp70 family of molecular chaperones and lower sequence similarity to the large subunits of corresponding mutases (23). In contrast, the G-protein chaperones associated with AdoCbl-dependent acyl-CoA mutases belong to the G3E family of P-loop metallochaperones (36).…”

Section: Discussionmentioning

confidence: 99%

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Engineered and Native Coenzyme B12-dependent Isovaleryl-CoA/Pivalyl-CoA Mutase

Kitanishi

Cracan

Banerjee

2015

Journal of Biological Chemistry

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Background: IcmF exhibits low isovaleryl-CoA/pivalyl-CoA mutase (PCM) activity. Results: IcmF mutants designed to enhance PCM activity were susceptible to inactivation prompting a bioinformatics search for a "bona fide" PCM. Conclusion: A B 12 -dependent PCM was identified, cloned, and expressed and exhibited PCM activity. Significance: The newly discovered PCM could be useful in bioremediation and biosynthetic reactions.

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Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones

Cited by 59 publications

References 212 publications

Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments

Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments

Visualization of a radical B ₁₂ enzyme with its G-protein chaperone

Engineered and Native Coenzyme B12-dependent Isovaleryl-CoA/Pivalyl-CoA Mutase

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Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones

Cited by 59 publications

References 212 publications

Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments

Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments

Visualization of a radical B 12 enzyme with its G-protein chaperone

Engineered and Native Coenzyme B12-dependent Isovaleryl-CoA/Pivalyl-CoA Mutase

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Visualization of a radical B ₁₂ enzyme with its G-protein chaperone