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Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases

ABSTRACT: LC-MS data of the reaction products from enzyme and nucleotide.

INSTRUMENT(S): maXis

ORGANISM(S): Bacteria

SUBMITTER: Chao-Jung Chen

PROVIDER: MSV000092570 | MassIVE | Wed Aug 02 00:17:00 BST 2023

REPOSITORIES: MassIVE

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Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases.

Project description:Purine-containing nucleotide second messengers regulate diverse cellular activities. Cyclic di-pyrimidines mediate anti-phage functions in bacteria; however, the synthesis mechanism remains elusive. Here, we determine the high-resolution structures of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases (CD-NTases) in clade E (CdnE) in its apo, substrate-, and intermediate-bound states. A conserved (R/Q)xW motif controlling the pyrimidine specificity of donor nucleotide is identified. Mutation of Trp or Arg from the (R/Q)xW motif to Ala rewires its specificity to purine nucleotides, producing mixed purine-pyrimidine cyclic dinucleotides (CDNs). Preferential binding of uracil over cytosine bases explains the product specificity of cyclic di-pyrimidine-synthesizing CdnE to cyclic di-UMP (cUU). Based on the intermediate-bound structures, a synthetic pathway for cUU containing a unique 2'3'-phosphodiester linkage through intermediate pppU[3'-5']pU is deduced. Our results provide a framework for pyrimidine selection and establish the importance of conserved residues at the C-terminal loop for the specificity determination of CD-NTases.

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Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system

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Crystal structure of 4,6-di-chloro-5-methyl-pyrimidine.

Project description:The title compound, C5H4Cl2N2, is essentially planar with an r.m.s. deviation for all non-H atoms of 0.009 Å. The largest deviation from the mean plane is 0.016 (4) Å for an N atom. In the crystal, mol-ecules are linked by pairs of C-H⋯N hydrogen bonds, forming inversion dimers, enclosing an R (2) 2(6) ring motif.

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Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system.

Project description:3',5'-cyclic uridine monophosphate (cUMP) and 3',5'-cyclic cytidine monophosphate (cCMP) have been established as bacterial second messengers in the phage defense system, named pyrimidine cyclase system for anti-phage resistance (Pycsar). This system consists of a pyrimidine cyclase and a cyclic pyrimidine receptor protein. However, the molecular mechanism underlying cyclic pyrimidine synthesis and recognition remains unclear. Herein, we determine the crystal structures of a uridylate cyclase and a cytidylate cyclase, revealing the conserved residues for cUMP and cCMP production, respectively. In addition, a distinct zinc-finger motif of the uridylate cyclase is identified to confer substantial resistance against phage infections. Furthermore, structural characterization of cUMP receptor protein PycTIR provides clear picture of specific cUMP recognition and identifies a conserved N-terminal extension that mediates PycTIR oligomerization and activation. Overall, our results contribute to the understanding of cyclic pyrimidine-mediated bacterial defense.

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Project description:In the title mol-ecule, C16H13N5, the plane of the tetra-zole ring forms dihedral angles of 16.37 (7) and 76.59 (7)° with the two phenyl rings. The dihedral angle between the phenyl rings is 68.05 (6)°. The pyrimidine ring is in a flattened boat conformation. In the crystal, mol-ecules are linked by pairs of N-H⋯N hydrogen bonds, forming inversion dimers.

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Cyclic-di-GMP and cyclic-di-AMP activate the NLRP3 inflammasome.

Project description:The cyclic dinucleotides 3'-5'diadenylate (c-diAMP) and 3'-5' diguanylate (c-diGMP) are important bacterial second messengers that have recently been shown to stimulate the secretion of type I Interferons (IFN-Is) through the c-diGMP-binding protein MPYS/STING. Here, we show that physiologically relevant levels of cyclic dinucleotides also stimulate a robust secretion of IL-1β through the NLRP3 inflammasome. Intriguingly, this response is independent of MPYS/STING. Consistent with most NLRP3 inflammasome activators, the response to c-diGMP is dependent on the mobilization of potassium and calcium ions. However, in contrast to other NLRP3 inflammasome activators, this response is not associated with significant changes in mitochondrial potential or the generation of mitochondrial reactive oxygen species. Thus, cyclic dinucleotides activate the NLRP3 inflammasome through a unique pathway that could have evolved to detect pervasive bacterial pathogen-associated molecular patterns associated with intracellular infections.

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Substrate-induced domain movement in a bifunctional protein, DcpA, regulates cyclic di-GMP turnover: Functional implications of a highly conserved motif.

Project description:In eubacteria, cyclic di-GMP (c-di-GMP) signaling is involved in virulence, persistence, motility and generally orchestrates multicellular behavior in bacterial biofilms. Intracellular c-di-GMP levels are maintained by the opposing activities of diguanylate cyclases (DGCs) and cognate phosphodiesterases (PDEs). The c-di-GMP homeostasis in Mycobacterium smegmatis is supported by DcpA, a conserved, bifunctional protein with both DGC and PDE activities. DcpA is a multidomain protein whose GAF-GGDEF-EAL domains are arranged in tandem and are required for these two activities. To gain insight into how interactions among these three domains affect DcpA activity, here we studied its domain dynamics using real-time FRET. We demonstrate that substrate binding in DcpA results in domain movement that prompts a switch from an "open" to a "closed" conformation and alters its catalytic activity. We found that a single point mutation in the conserved EAL motif (E384A) results in complete loss of the PDE activity of the EAL domain and in a significant decrease in the DGC activity of the GGDEF domain. Structural analyses revealed multiple hydrophobic and aromatic residues around Cys579 that are necessary for proper DcpA folding and maintenance of the active conformation. On the basis of these observations and taking into account additional bioinformatics analysis of EAL domain-containing proteins, we identified a critical putatively conserved motif, GCXXXQGF, that plays an important role in c-di-GMP turnover. We conclude that a substrate-induced conformational switch involving movement of a loop containing a conserved motif in the bifunctional diguanylate cyclase-phosphodiesterase DcpA controls c-di-GMP turnover in M. smegmatis.

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Crystal structure of (S)-5,7-diphenyl-4,7-di-hydro-tetra-zolo[1,5-a]pyrimidine.

Project description:The title compound, C16H13N5, was synthesized by coupling amino-tetra-zole with chalcone in the presence of an amine organocatalyst derived from chincona alkaloid. There are two mol-ecules, A and B, in the asymmetric unit. In mol-ecule A, the dihedral angles between the partly hydrogenated pyrimidine ring system (r.m.s. deviation = 0.056 Å) and the sp (2)- and sp (3)-bonded phenyl groups are 33.32 (11) and 86.53 (11)°, respectively. The equivalent data for mol-ecule B are 0.049 Å, and 27.05 (10) and 85.27 (11)°, respectively. In the crystal, A+B dimers linked by pairs of N-H⋯N hydrogen bonds generate R 2 (2)(8) loops. The dimers are linked by aromatic π-π stacking inter-actions [shortest centroid-centroid separation = 3.5367 (15) Å], which results in a three-dimensional network.

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