{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T12:47:59Z","timestamp":1785847679662,"version":"3.56.0"},"reference-count":47,"publisher":"American Chemical Society (ACS)","issue":"15","license":[{"start":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:00:00Z","timestamp":1779926400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:00:00Z","timestamp":1779926400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:00:00Z","timestamp":1779926400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"publisher","award":["CRG\/2020\/003946"],"award-info":[{"award-number":["CRG\/2020\/003946"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Bacterial infection, including that ofMycobacterium tuberculosis, leads to the accumulation of the bacterial cyclic dinucleotides (CDN), c-di-AMP and c-di-GMP, and the host cGAMP synthase-catalyzed CDN, 2\u20323\u2032-cGAMP in the cytosol, which activates STING-dependent type I interferon (IFN) and NF-\u03baB immune responses. The mycobacterial cyclic dinucleotide phosphodiesterase (CdnP) secreted into the host macrophages blunts host immunity by directly cleaving bacterial- and host-derived CDNs. The arabinose- and xylose-modified 2\u20323\u2032-cGAMP (2\u20323\u2032-(A\/X)cGAMP) analogues act as potent STING agonists and resist hydrolysis by the host-PDE ENPP1. Here, we report that 2\u20323\u2032-(A\/X)-cGAMP analogues bind to CdnP and compete with its substrate binding. Further studies revealed that these analogues inhibit the catalytic activity of CdnP. The cocrystal structure demonstrates that the arabinose-derived 2\u20323\u2032-cGAMP (AR-cGAMP) analogue is trapped in an unusual U-shaped conformation in the substrate-binding pocket, away from the catalytic residue and Mn2+, which suggests that CdnP is incompetent to hydrolyze the analogue and cannot accept the other CDN substrate for hydrolysis. Given that several bacterial and viral pathogens deploy CDN phosphodiesterase enzymes to hydrolyze both host and pathogen-derived STING agonists, sugar-modified CDNs can be used to weaken bacterial and viral defenses and stimulate the STING-mediated host immunity against these pathogens.<\/jats:p>","DOI":"10.1021\/acs.biochem.6c00106","type":"journal-article","created":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T13:45:26Z","timestamp":1779975926000},"page":"2441-2451","source":"Crossref","is-referenced-by-count":0,"title":["Structural and Biochemical Insights into the Arabinose\nand Xylose Derivatives of Cyclic-GAMP-Mediated Inhibition of\n                    <i>Mycobacterium tuberculosis<\/i>\n                    Cyclic-di-AMP Phosphodiesterase"],"prefix":"10.1021","volume":"65","author":[{"given":"Dagur Singh","family":"Hanuman","sequence":"first","affiliation":[{"name":"Indian Institute of Technology Hyderabad (IITH) , , , ,","place":["Hyderabad, Telangana, India, 502285"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Singh","family":"Neeharika","sequence":"additional","affiliation":[{"name":"Indian Institute of Technology Hyderabad (IITH) , , , ,","place":["Hyderabad, Telangana, India, 502285"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kulhar","family":"Nitin","sequence":"additional","affiliation":[{"name":"Indian Institute of Technology Hyderabad (IITH) , , , ,","place":["Hyderabad, Telangana, India, 502285"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0095-6865","authenticated-orcid":true,"given":"Suman","family":"Abhishek","sequence":"additional","affiliation":[{"name":"Indian Institute of Technology Hyderabad (IITH) , , , ,","place":["Hyderabad, Telangana, India, 502285"]},{"name":"Memorial Sloan Kettering Cancer Center , , , ,","place":["New York, New York, United States, 10065"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krishna Murari","family":"Sinha","sequence":"additional","affiliation":[{"name":"Amity University Haryana , , ,","place":["Haryana, India, 122413"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9341-0070","authenticated-orcid":true,"given":"Eerappa","family":"Rajakumara","sequence":"additional","affiliation":[{"name":"Indian Institute of Technology Hyderabad (IITH) , , , ,","place":["Hyderabad, Telangana, India, 502285"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,5,28]]},"reference":[{"key":"2026080408073169100_cit1","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1111\/j.1365-2958.2010.07514.x","article-title":"cAMP, c-di-GMP,\nc-di-AMP and now cGMP: bacteria use them all!","volume":"79","author":"Gomelsky","year":"2011","journal-title":"Mol. Microbiol."},{"key":"2026080408073169100_cit2","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1039\/C2CS35206K","article-title":"Nucleotide, c-di-GMP,\nc-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications\nin pathogenesis","volume":"42","author":"Kalia","year":"2013","journal-title":"Chem. Soc. Rev."},{"key":"2026080408073169100_cit3","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.133pe39","article-title":"Great times\nfor small molecules: c-di-AMP, a second messenger candidate in Bacteria\nand Archaea","volume":"1","author":"Ro\u0308mling","year":"2008","journal-title":"Sci. Signaling"},{"key":"2026080408073169100_cit4","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.ceb.2019.12.004","article-title":"Cyclic dinucleotides at the forefront\nof innate immunity","volume":"63","author":"Zaver","year":"2020","journal-title":"Curr. Opin. Cell Biol."},{"key":"2026080408073169100_cit5","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/nrmicro3069","article-title":"Cyclic di-AMP:\nanother second messenger enters the\nfray","volume":"11","author":"Corrigan","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"2026080408073169100_cit6","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1038\/nm.3813","article-title":"A bacterial\ncyclic dinucleotide activates\nthe cytosolic surveillance pathway and mediates innate resistance\nto tuberculosis","volume":"21","author":"Dey","year":"2015","journal-title":"Nat. Med."},{"key":"2026080408073169100_cit7","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2021.105264","article-title":"Cyclic\ndi-AMP: Small molecule with big roles in bacteria","volume":"161","author":"Mudgal","year":"2021","journal-title":"Microb. Pathog."},{"key":"2026080408073169100_cit8","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/s41594-023-00933-9","article-title":"cGAMP-activated cGAS-STING\nsignaling: its bacterial\norigins and evolutionary adaptation by metazoans","volume":"30","author":"Patel","year":"2023","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026080408073169100_cit9","doi-asserted-by":"publisher","first-page":"1366","DOI":"10.1016\/j.chembiol.2023.07.002","article-title":"Arabinose-\nand xylose-modified analogs of 2\u2032,3\u2032-cGAMP act as STING\nagonists","volume":"30","author":"Xie","year":"2023","journal-title":"Cell Chem. Biol."},{"key":"2026080408073169100_cit10","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1038\/nchembio.2254","article-title":"Inhibition of innate\nimmune cytosolic\nsurveillance by an M. tuberculosis phosphodiesterase","volume":"13","author":"Dey","year":"2017","journal-title":"Nat. Chem. Biol."},{"key":"2026080408073169100_cit11","doi-asserted-by":"publisher","first-page":"3668","DOI":"10.1074\/jbc.M115.699801","article-title":"Structural and Biochemical Insight into the Mechanism of Rv2837c\nfrom Mycobacterium tuberculosis as a c-di-NMP Phosphodiesterase","volume":"291","author":"He","year":"2016","journal-title":"J. Biol. Chem."},{"key":"2026080408073169100_cit12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0086096","article-title":"Two-step synthesis and hydrolysis of cyclic di-AMP\nin Mycobacterium tuberculosis","volume":"9","author":"Manikandan","year":"2014","journal-title":"PLoS One"},{"key":"2026080408073169100_cit13","doi-asserted-by":"publisher","DOI":"10.1093\/femspd\/fty048","article-title":"Cyclic\nnucleotide signaling in Mycobacterium tuberculosis:\nan expanding repertoire","volume":"76","author":"Johnson","year":"2018","journal-title":"Pathog. Dis."},{"key":"2026080408073169100_cit14","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02012-23","article-title":"Structure-based virtual screening and in vitro validation\nof inhibitors of cyclic dinucleotide phosphodiesterases ENPP1 and\nCdnP","volume":"12","author":"Rohilla","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"2026080408073169100_cit15","doi-asserted-by":"publisher","first-page":"1048","DOI":"10.1093\/infdis\/jiz116","article-title":"Bacillus Calmette-Gue\u0301rin\nOverexpressing an Endogenous Stimulator of Interferon Genes Agonist\nProvides Enhanced Protection Against Pulmonary Tuberculosis","volume":"221","author":"Dey","year":"2020","journal-title":"J. Infect. Dis."},{"key":"2026080408073169100_cit16","doi-asserted-by":"publisher","first-page":"1142","DOI":"10.1038\/ni.3558","article-title":"Regulation and function of the cGAS-STING pathway of\ncytosolic DNA sensing","volume":"17","author":"Chen","year":"2016","journal-title":"Nat. Immunol."},{"key":"2026080408073169100_cit17","doi-asserted-by":"publisher","first-page":"1452","DOI":"10.1038\/s43018-022-00468-w","article-title":"The cGAS-STING pathway\nand cancer","volume":"3","author":"Samson","year":"2022","journal-title":"Nat. Cancer"},{"key":"2026080408073169100_cit18","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1038\/nchembio.1661","article-title":"Hydrolysis\nof 2\u20323\u2032-cGAMP by ENPP1 and\ndesign of nonhydrolyzable analogs","volume":"10","author":"Li","year":"2014","journal-title":"Nat. Chem.\nBiol."},{"key":"2026080408073169100_cit19","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06922-7","article-title":"Structural\ninsights into cGAMP degradation by Ecto-nucleotide pyrophosphatase\nphosphodiesterase 1","volume":"9","author":"Kato","year":"2018","journal-title":"Nat. Commun."},{"key":"2026080408073169100_cit20","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijbiomac.2024.130091","article-title":"Proxy-approach in understanding the\nbisubstrate activity\nof strictosidine synthases","volume":"262","author":"Nitin","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"key":"2026080408073169100_cit21","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1007\/s00249-021-01530-8","article-title":"A standard operating\nprocedure for an enzymatic activity inhibition assay","volume":"50","author":"Smirnoviene","year":"2021","journal-title":"Eur. Biophys. J."},{"key":"2026080408073169100_cit22","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1107\/S0907444910048675","article-title":"iMOSFLM:\na new graphical interface for diffraction-image processing with MOSFLM","volume":"67","author":"Battye","year":"2011","journal-title":"Acta Crystallogr., Sect. D:Biol. Crystallogr."},{"key":"2026080408073169100_cit23","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1107\/S0907444913000061","article-title":"How good\nare my data and what is the resolution?","volume":"69","author":"Evans","year":"2013","journal-title":"Acta\nCrystallogr., Sect. D:Biol. Crystallogr."},{"key":"2026080408073169100_cit24","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1107\/S0907444909042589","article-title":"Molecular\nreplacement with MOLREP","volume":"66","author":"Vagin","year":"2010","journal-title":"Acta Crystallogr.,\nSect. D:Biol. Crystallogr."},{"key":"2026080408073169100_cit25","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1107\/S0907444911001314","article-title":"REFMAC5\nfor the refinement of macromolecular crystal structures","volume":"67","author":"Murshudov","year":"2011","journal-title":"Acta Crystallogr., Sect. D:Biol. Crystallogr."},{"key":"2026080408073169100_cit26","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development\nof Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr., Sect. D:Biol. Crystallogr."},{"key":"2026080408073169100_cit27","doi-asserted-by":"publisher","first-page":"W530","DOI":"10.1093\/nar\/gkab294","article-title":"PLIP 2021: expanding the scope of\nthe protein\u2013ligand interaction profiler to DNA and RNA","volume":"49","author":"Adasme","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2026080408073169100_cit28","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera--a visualization system\nfor exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput.\nChem."},{"key":"2026080408073169100_cit29","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1042\/BCJ20170739","article-title":"Structural\nand biochemical characterization of the catalytic domains of GdpP\nreveals a unified hydrolysis mechanism for the DHH\/DHHA1 phosphodiesterase","volume":"475","author":"Wang","year":"2018","journal-title":"Biochem. J."},{"key":"2026080408073169100_cit30","doi-asserted-by":"publisher","first-page":"1887","DOI":"10.1016\/j.str.2017.10.001","article-title":"Structural\nand Biophysical Analysis of the Soluble DHH\/DHHA1-Type Phosphodiesterase\nTM1595 from Thermotoga maritima","volume":"25","author":"Drexler","year":"2017","journal-title":"Structure"},{"key":"2026080408073169100_cit31","doi-asserted-by":"publisher","first-page":"E747","DOI":"10.1073\/pnas.1416485112","article-title":"An HD-domain\nphosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect\nbacterial growth and virulence","volume":"112","author":"Huynh","year":"2015","journal-title":"Proc. Natl.\nAcad. Sci. U.S.A."},{"key":"2026080408073169100_cit32","doi-asserted-by":"publisher","first-page":"2004","DOI":"10.1074\/jbc.M112.395491","article-title":"Cyclic di-AMP\nhomeostasis in bacillus subtilis: both\nlack and high level accumulation of the nucleotide are detrimental\nfor cell growth","volume":"288","author":"Mehne","year":"2013","journal-title":"J. Biol. Chem."},{"key":"2026080408073169100_cit33","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1016\/j.celrep.2018.04.003","article-title":"STING-Activating\nAdjuvants Elicit a Th17 Immune Response and Protect against Mycobacterium\ntuberculosis Infection","volume":"23","author":"Van Dis","year":"2018","journal-title":"Cell Rep."},{"key":"2026080408073169100_cit34","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1016\/j.str.2024.01.008","article-title":"Fluorinated\ncGAMP analogs, which act as STING agonists and are not cleavable by\npoxins: Structural basis of their function","volume":"32","author":"Klima","year":"2024","journal-title":"Structure"},{"key":"2026080408073169100_cit35","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1016\/j.molcel.2013.05.022","article-title":"Cyclic\nGMP-AMP containing mixed phosphodiester linkages\nis an endogenous high-affinity ligand for STING","volume":"51","author":"Zhang","year":"2013","journal-title":"Mol. Cell"},{"key":"2026080408073169100_cit36","doi-asserted-by":"publisher","first-page":"5153","DOI":"10.1038\/sj.emboj.7601918","article-title":"The structural basis\nof cyclic diguanylate signal transduction by PilZ domains","volume":"26","author":"Benach","year":"2007","journal-title":"EMBO J."},{"key":"2026080408073169100_cit37","doi-asserted-by":"publisher","first-page":"4936","DOI":"10.1021\/acs.biochem.5b00633","article-title":"Structural\nInsights\ninto the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK","volume":"54","author":"Chin","year":"2015","journal-title":"Biochemistry"},{"key":"2026080408073169100_cit38","doi-asserted-by":"publisher","first-page":"3333","DOI":"10.1042\/BCJ20190399","article-title":"Structures of c-di-GMP\/cGAMP\ndegrading phosphodiesterase\nVcEAL: identification of a novel conformational switch and its implication","volume":"476","author":"Yadav","year":"2019","journal-title":"Biochem. J."},{"key":"2026080408073169100_cit39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.celrep.2015.03.004","article-title":"Structural basis\nfor molecular discrimination by a 3\u2032,3\u2032-cGAMP sensing\nriboswitch","volume":"11","author":"Ren","year":"2015","journal-title":"Cell Rep."},{"key":"2026080408073169100_cit40","doi-asserted-by":"publisher","DOI":"10.1002\/anie.202207175","article-title":"Novel Poxin Stable\ncGAMP-Derivatives Are Remarkable STING Agonists","volume":"61","author":"Stazzoni","year":"2022","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026080408073169100_cit41","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1002\/1873-3468.14838","article-title":"How enzyme-centered approaches are advancing research\non cyclic oligo-nucleotides","volume":"598","author":"Wenzl","year":"2024","journal-title":"FEBS Lett."},{"key":"2026080408073169100_cit42","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/s41586-019-0928-6","article-title":"Viral and metazoan poxins are cGAMP-specific\nnucleases that restrict cGAS-STING signalling","volume":"566","author":"Eaglesham","year":"2019","journal-title":"Nature"},{"key":"2026080408073169100_cit43","doi-asserted-by":"publisher","first-page":"7894","DOI":"10.1093\/nar\/gku425","article-title":"Unique subunit packing in mycobacterial\nnanoRNase leads to alternate substrate recognitions in DHH phosphodiesterases","volume":"42","author":"Srivastav","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2026080408073169100_cit44","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1074\/jbc.M109.040238","article-title":"YybT is a signaling protein that contains a cyclic\ndinucleotide phosphodiesterase domain and a GGDEF domain with ATPase\nactivity","volume":"285","author":"Rao","year":"2010","journal-title":"J. Biol. Chem."},{"key":"2026080408073169100_cit45","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0069425","article-title":"Streptococcus pyogenes c-di-AMP phosphodiesterase, GdpP, influences\nSpeB processing and\nvirulence","volume":"8","author":"Cho","year":"2013","journal-title":"PLoS One"},{"key":"2026080408073169100_cit46","doi-asserted-by":"publisher","first-page":"5123","DOI":"10.1128\/JB.00769-13","article-title":"Two DHH subfamily\n1 proteins in Streptococcus pneumoniae possess cyclic di-AMP phosphodiesterase activity and affect bacterial\ngrowth and virulence","volume":"195","author":"Bai","year":"2013","journal-title":"J. Bacteriol."},{"key":"2026080408073169100_cit47","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.jare.2022.05.006","article-title":"STING as an\nemerging therapeutic target for drug discovery: Perspectives\nfrom the global patent landscape","volume":"44","author":"Kong","year":"2023","journal-title":"J. Adv. Res."}],"container-title":["Biochemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.biochem.6c00106","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/15\/2441\/66256902\/acs.biochem.6c00106.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/15\/2441\/66256902\/acs.biochem.6c00106.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T12:29:57Z","timestamp":1785846597000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/bichaw\/article\/65\/15\/2441\/5232456\/Structural-and-Biochemical-Insights-into-the"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,28]]},"references-count":47,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,5,28]]},"published-print":{"date-parts":[[2026,8,4]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.biochem.6c00106","relation":{},"ISSN":["0006-2960","1520-4995"],"issn-type":[{"value":"0006-2960","type":"print"},{"value":"1520-4995","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,28]]}}}