New structural forms of a mycobacterial adenylyl cyclase Rv1625c

Barathy, D.V.; Mattoo, Rohini; Visweswariah, Sandhya S.; Suguna, K.

doi:10.1107/s2052252514016741

Cited by 8 publications

(9 citation statements)

References 34 publications

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“…Thus, it is clear that this dimer cannot be part of the catalytic cycle of the enzyme. Unusual dimer structures have been described for both the Rv1264 (24) and Rv1625 (22) adenylyl cyclases from M. tuberculosis, and in this context the domain-swapped head-to-head dimer observed for WT Rv1625 (22) shares some similarity with the head-to-head dimer we see here for GC Rho . It is unlikely that the disulfide in GC Rho would form under intracellular reducing conditions, and it seems most probable that the disulfide forms subsequent to dimerization as a consequence of a high local concentration of the two Cys residues in an oxidizing environment.…”

Section: Structure and Monomer/dimer Equilibrium Of Guanylyl Cyclasesupporting

confidence: 64%

“…To be sure, monomers of other guanylyl cyclases have been observed in solution studies (9,16), but the monomer/ dimer equilibria are more heavily shifted toward the dimer, and, as noted above, the other guanylyl cyclases all crystallized with a dimer in the asymmetric unit. There are two reports in which adenylyl cyclases crystallized as a monomer: one for a Phe to Arg mutant involving a residue in the dimer interface of the Mycobacterium tuberculosis guanylyl cyclase Rv1625c catalytic domain (22), and the other for the catalytic domains of the adenylyl cyclases, GRESAG4.1 and GRESAG4.3, from Trypanosoma brucei (23). Rv1625c forms an inactive dimer in solution (22) whereas the T. brucei enzymes display weak subunit affinity and transient formation of catalytically active dimers in solution (23).…”

Section: Discussionmentioning

confidence: 99%

“…There are two reports in which adenylyl cyclases crystallized as a monomer: one for a Phe to Arg mutant involving a residue in the dimer interface of the Mycobacterium tuberculosis guanylyl cyclase Rv1625c catalytic domain (22), and the other for the catalytic domains of the adenylyl cyclases, GRESAG4.1 and GRESAG4.3, from Trypanosoma brucei (23). Rv1625c forms an inactive dimer in solution (22) whereas the T. brucei enzymes display weak subunit affinity and transient formation of catalytically active dimers in solution (23).…”

Section: Discussionmentioning

confidence: 99%

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Structure and monomer/dimer equilibrium for the guanylyl cyclase domain of the optogenetics protein RhoGC

Kumar

Morehouse

Fofana

et al. 2017

Journal of Biological Chemistry

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RhoGC is a fusion protein from the aquatic fungus , combining a type I rhodopsin domain with a guanylyl cyclase domain. It has generated excitement as an optogenetics tool for the manipulation of cyclic nucleotide signaling pathways. To investigate the regulation of the cyclase activity, we isolated the guanylyl cyclase domain from with (GCwCC) and without (GC) the coiled-coil linker. Both constructs were constitutively active but were monomeric as determined by size-exclusion chromatography and analytical ultracentrifugation, whereas other class III nucleotidyl cyclases are functional dimers. We also observed that crystals of GC have only a monomer in an asymmetric unit. Dimers formed when crystals were grown in the presence of the non-cyclizable substrate analog 2',3'-dideoxyguanosine-5'-triphosphate, MnCl, and tartrate, but their quaternary structure did not conform to the canonical pairing expected for class III enzymes. Moreover, the structure contained a disulfide bond formed with an active-site Cys residue required for activity. We consider it unlikely that the disulfide would form under intracellular reducing conditions, raising the possibility that this unusual dimer might have a biologically relevant role in the regulation of full-length RhoGC. Although we did not observe it with direct methods, a functional dimer was identified as the active state by following the dependence of activity on total enzyme concentration. The low affinity observed for GC monomers is unusual for this enzyme class and suggests that dimer formation may contribute to light activation of the full-length protein.

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Section: Structure and Monomer/dimer Equilibrium Of Guanylyl Cyclasesupporting

confidence: 64%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Structure and monomer/dimer equilibrium for the guanylyl cyclase domain of the optogenetics protein RhoGC

Kumar

Morehouse

Fofana

et al. 2017

Journal of Biological Chemistry

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“…Dimerization is thought to bring the two halves of the enzyme together, reconstituting a mammalian AC-like fold. Attempts to describe the structure of dimeric Rv1625c in its active dimeric form so far have failed: A structure of the full-length protein is not available, and the reported structures of the catalytic domain were either captured in an inactive monomeric form ( 25 ) or in a misfolded swapped dimer configuration ( 26 ).…”

mentioning

confidence: 99%

Role of the nucleotidyl cyclase helical domain in catalytically active dimer formation

Vercellino

Rezabkova

Oliéric

et al. 2017

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

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SignificanceAdenylyl and guanylyl cyclases are at the core of cellular signaling. Although the molecular mechanisms of the reactions catalyzed by these enzymes are well established, their structures and biophysical properties remain only partially characterized. Here, we report the structure of the cytosolic domain of a mycobacterial adenylyl cyclase Cya, an evolutionary ancestor of mammalian membrane adenylyl cyclases. The structure reveals the helical domain, a highly conserved structural element that links the catalytic and transmembrane portions of Cya. We show how helical domains bring together the catalytic domains to form functionally active dimers. Our data suggest that the disease-linked mutations in human nucleotidyl cyclases may disrupt the correct assembly of the helical domain, preventing the formation of an active dimeric enzyme.

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“…In T. turnerae and T. waterburyi, none of the putative lignin peroxidases could be matched to reference templates. The two potential lignin peroxidases from T. haidensis matched with over 50 protein templates and two to three protein models for adenylate cyclases (sequence identities between 23 and 67%; QMEAN for all >−4.0) (Topal et al, 2012;Barathy et al, 2014Barathy et al, , 2015Etzl et al, 2018). Similarly, the potential lignin peroxidases from T. purpureus and T. franksiae both matched to over 50 protein templates.…”

Section: Protein Modeling Hitsmentioning

confidence: 79%

How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes

2021

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Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.

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New structural forms of a mycobacterial adenylyl cyclase Rv1625c

Abstract: Two new structural forms, a monomer and a swapped dimer, of the catalytic domain of an adenylyl cyclase from M. tuberculosis are reported.

Cited by 8 publications

References 34 publications

Structure and monomer/dimer equilibrium for the guanylyl cyclase domain of the optogenetics protein RhoGC

Structure and monomer/dimer equilibrium for the guanylyl cyclase domain of the optogenetics protein RhoGC

Role of the nucleotidyl cyclase helical domain in catalytically active dimer formation

How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes

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