Substrate specificity determinants of class <scp>III</scp> nucleotidyl cyclases

Bharambe, Nikhil; Barathy, D.V.; Syed, Wajeed; Visweswariah, Sandhya S.; Colaςo, Melwin; Misquith, Sandra; Suguna, K.

doi:10.1111/febs.13837

Cited by 5 publications

(12 citation statements)

References 38 publications

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“…Two divalent cations, typically magnesium or manganese, are postulated to facilitate substrate binding (ion B) and catalytic turnover (ion A) [5,30]. With a few exceptions, in ligand-and calcium-bound NC structures, only the high-affinity ion B site is occupied [4,[6][7][8]10,11,21,34,35]. This is most probably due to the significantly larger atomic radius of calcium compared to magnesium or manganese.…”

Section: Cagcágtpáca 2+ Active Sitementioning

confidence: 99%

“…Catalytic specificity for ATP in ACs is predominantly determined by two residues: Lys and Asp (or Thr), which have been shown to directly interact with N1 and N6 atoms of adenine base, respectively [5]. A few of the AC structures contain unmodified ATP [6,8,10,14]. Most of the ligandbound ACs were cocrystallized in the presence of a substrate analogue.…”

Section: Cagcágtpáca 2+ Active Sitementioning

confidence: 99%

“…They provide useful information, but also have significant limitations, for example, often contain substrate modifications that eliminate interactions critical to catalysis [4,5,33]. The Mycobacterium avium Ma1120 CHD [10] and Arthrospira platensis CyaC [4] structures are good examples of wild-type ACs crystallized with the ligand in a conformation that represents a state well aligned for the nucleophilic attack and in which both direct interactions between the specificity-determining residues and substrate are present. In GCs, Lys and Asp present in ACs are replaced by Glu and Cys (or Ser) that are believed to mediate recognition of the exocyclic amine and carbonyl group of the guanine, respectively [38].…”

Section: Cagcágtpáca 2+ Active Sitementioning

confidence: 99%

“…Mechanistic insights into the activity of class III NCs have been derived from dozens of crystal structures of AC domains in a ligand-free form or bound to substrate-based inhibitors, substrates or ATP analogues in various conformations [3][4][5][6][7][8][9][10][11]. Structural analysis suggests that the AC dimer undergoes a functional conformational change that involves 'closing' of the active site region that brings the catalytic residues distributed across the subunit interface into the proper register.…”

Section: Introductionmentioning

confidence: 99%

“…Most of the GC structures available to date represent ligand-free, atypical head-to-head or canonical head-to-tail dimers that are inactive due to misaligned active site residues [15][16][17][18][19][20]. A few reports describe crystal structures of the GC domain in the active conformation; however, they exploit enzymes of altered specificity [10,11]. Important new information has recently emerged from the 3.8 A resolution cryo-EM study of the human soluble GC (sGC) in its inactive and GMPCPP-bound NO-activated state [21], suggesting that all type III NCs undergo dynamic structural changes as part of the catalytic cycle.…”

Section: Introductionmentioning

confidence: 99%

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Molecular basis for GTP recognition by light‐activated guanylate cyclase RhGC

et al. 2019

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Cyclic guanosine 3 0 ,5 0-monophosphate (cGMP) is an intracellular signalling molecule involved in many sensory and developmental processes. Synthesis of cGMP from GTP is catalysed by guanylate cyclase (GC) in a reaction analogous to cAMP formation by adenylate cyclase (AC). Although detailed structural information is available on the catalytic region of nucleotidyl cyclases (NCs) in various states, these atomic models do not provide a sufficient explanation for the substrate selectivity between GC and AC family members. Detailed structural information on the GC domain in its active conformation is largely missing, and no crystal structure of a GTP-bound wild-type GC domain has been published to date. Here, we describe the crystal structure of the catalytic domain of rhodopsin-GC (RhGC) from Catenaria anguillulae in complex with GTP at 1.7 A resolution. Our study reveals the organization of a eukaryotic GC domain in its active conformation. We observe that the binding mode of the substrate GTP is similar to that of AC-ATP interaction, although surprisingly not all of the interactions predicted to be responsible for base recognition are present. The structure provides insights into potential mechanisms of substrate discrimination and activity regulation that may be common to all class III purine NCs. Database Structural data are available in Protein Data Bank database under the accession number 6SIR. Enzymes EC 4.6.1.2. Abbreviations AC, adenylate cyclase; ATP, adenosine-5 0-triphosphate; cAMP, cyclic 3 0 ,5 0-adenosine monophosphate; cGMP, cyclic 3 0 ,5 0-guanosine monophosphate; GC, guanylate cyclase; GTP, guanosine-5 0-triphosphate; NC, nucleotidyl cyclase; sGC, soluble guanylate cyclase.

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Section: Cagcágtpáca 2+ Active Sitementioning

confidence: 99%

Section: Cagcágtpáca 2+ Active Sitementioning

confidence: 99%

Section: Cagcágtpáca 2+ Active Sitementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular basis for GTP recognition by light‐activated guanylate cyclase RhGC

et al. 2019

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Characterization of two halophilic adenylate cyclases from Thermobifida halotolerans and Haloactinopolyspora alba

Jiang

Min

Leng

et al. 2023

Chinese Journal of Chemical Engineering

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Structural basis of adenylyl cyclase 9 activation

Lavriha

Mehta

et al. 2022

Nat Commun

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Adenylyl cyclase 9 (AC9) is a membrane-bound enzyme that converts ATP into cAMP. The enzyme is weakly activated by forskolin, fully activated by the G protein Gαs subunit and is autoinhibited by the AC9 C-terminus. Although our recent structural studies of the AC9-Gαs complex provided the framework for understanding AC9 autoinhibition, the conformational changes that AC9 undergoes in response to activator binding remains poorly understood. Here, we present the cryo-EM structures of AC9 in several distinct states: (i) AC9 bound to a nucleotide inhibitor MANT-GTP, (ii) bound to an artificial activator (DARPin C4) and MANT-GTP, (iii) bound to DARPin C4 and a nucleotide analogue ATPαS, (iv) bound to Gαs and MANT-GTP. The artificial activator DARPin C4 partially activates AC9 by binding at a site that overlaps with the Gαs binding site. Together with the previously observed occluded and forskolin-bound conformations, structural comparisons of AC9 in the four conformations described here show that secondary structure rearrangements in the region surrounding the forskolin binding site are essential for AC9 activation.

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Substrate specificity determinants of class III nucleotidyl cyclases

Abstract: Adenylyl cyclase (EC number: 4.6.1.1).

Cited by 5 publications

References 38 publications

Molecular basis for GTP recognition by light‐activated guanylate cyclase RhGC

Molecular basis for GTP recognition by light‐activated guanylate cyclase RhGC

Characterization of two halophilic adenylate cyclases from Thermobifida halotolerans and Haloactinopolyspora alba

Structural basis of adenylyl cyclase 9 activation

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