Crystal structures of porcine STINGCBD–CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins

Xiaoyan Cong; Zenglin Yuan; Yijun Du; Bo Wu; Defen Lu; Xiangju Wu; Youjia Zhang; Feng Li; Bin Wei; Jun Li; Jiaqiang Wu; Sujuan Xu; Jinbao Wang; Jing Qi; Guijun Shang; Lichuan Gu

doi:10.1074/jbc.RA119.007367

Crystal structures of porcine STING^CBD–CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins

Xiaoyan Cong, Zenglin Yuan, Yijun Du, Bo Wu, Defen Lu, Xiangju Wu, Youjia Zhang, Feng Li, Bin Wei, Jun Li, Jiaqiang Wu, Sujuan Xu, Jinbao Wang, Jing Qi, Guijun Shang, Lichuan Gu

Veterinary Science

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

The cyclic dinucleotide (CDN)-stimulator of interferon genes (STING) pathway plays an important role in the detection of viral and bacterial pathogens in animals. Previous studies have shown that the metazoan second messenger cyclic [G(2,5)pA(3,5)p] (2,3-cGAMP) generated by cyclic GMP-AMP synthase cGAS binds STING with high affinity compared with bacterial CDNs such as c-di-GMP, c-di-AMP, and 3,3-cGAMP. Despite recent progress indicating that the CDN-binding domain (CBD) of dimeric STING binds asymmetric 2,3-cGAMP preferentially over symmetric 3,3-CDNs, it remains an open question whether STING molecules, such as human STING, adopt a symmetric dimeric conformation to efficiently engage its asymmetric ligand. Here, structural studies of the CBD from porcine STING (STING^CBD) in complex with CDNs at 1.76 –2.6 Å resolution revealed that porcine STING^CBD, unlike its human and mouse counterparts, can adopt an asymmetric ligand-binding pocket to accommodate the CDNs. We observed that the extensive interactions and shape complementarity between asymmetric 2,3-cGAMP and the ligand-binding pocket make it the most preferred ligand for porcine STING and that geometry constraints limit the binding between symmetric 3,3-CDN and porcine STING. The ligand-discrimination mechanism of porcine STING observed here expands our understanding of how the CDN–STING pathway is activated and of its role in antiviral defense.

Original language	English
Pages (from-to)	11420-11432
Number of pages	13
Journal	Journal of Biological Chemistry
Volume	294
Issue number	30
DOIs	https://doi.org/10.1074/jbc.RA119.007367
State	Published - Jul 26 2019

Bibliographical note

Funding Information:
This work was supported by National Natural Science Foundation of China Grants 31470732 (to L. G.), 31502051 (to X. C.), 31672609 (to J. Q.) and 21673244 (to Bo. W.) and the National Key Research and Development Program of China Grant 2016YFD0501505 (to Y. D.). The authors declare that they have no conflicts of interest with the contents of this article. This article contains Figs. S1 and S2 and Table S1. The atomic coordinates and structure factors (codes 6A03, 6A04, 6A05, 6A06, and 6IYF) have been deposited in the Protein Data Bank (http://wwpdb.org/). † Deceased September 25, 2018. 1 Both authors contributed equally to this work. 2To whom correspondence may be addressed. E-mail: qj-happy2008@ 163.com. 3 To whom correspondence may be addressed. E-mail: gjshang@gmail.com. 4 To whom correspondence may be addressed. E-mail: lcgu@sdu.edu.cn.

Funding Information:
This work was supported by National Natural Science Foundation of China Grants 31470732 (to L. G.), 31502051 (to X. C.), 31672609 (to J. Q.) and 21673244 (to Bo. W.) and the National Key Research and Development Program of China Grant 2016YFD0501505 (to Y. D.). The authors declare that they have no conflicts of interest with the contents of this article. We thank the staff of beamlines BL17U1 and BL19U at the Shanghai Synchrotron Radiation Facility (SSRF) for their support in the data collection. We also thank Dr. Xuewu Zhang for critical reading and editing of this manuscript.

Publisher Copyright:
© 2019 Cong et al.

ASJC Scopus subject areas

Biochemistry
Molecular Biology
Cell Biology

Access to Document

10.1074/jbc.RA119.007367

Cite this

Cong, X., Yuan, Z., Du, Y., Wu, B., Lu, D., Wu, X., Zhang, Y., Li, F., Wei, B., Li, J., Wu, J., Xu, S., Wang, J., Qi, J., Shang, G., & Gu, L. (2019). Crystal structures of porcine STING^CBD–CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins. Journal of Biological Chemistry, 294(30), 11420-11432. https://doi.org/10.1074/jbc.RA119.007367

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title = "Crystal structures of porcine STINGCBD–CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins",

abstract = "The cyclic dinucleotide (CDN)-stimulator of interferon genes (STING) pathway plays an important role in the detection of viral and bacterial pathogens in animals. Previous studies have shown that the metazoan second messenger cyclic [G(2,5)pA(3,5)p] (2,3-cGAMP) generated by cyclic GMP-AMP synthase cGAS binds STING with high affinity compared with bacterial CDNs such as c-di-GMP, c-di-AMP, and 3,3-cGAMP. Despite recent progress indicating that the CDN-binding domain (CBD) of dimeric STING binds asymmetric 2,3-cGAMP preferentially over symmetric 3,3-CDNs, it remains an open question whether STING molecules, such as human STING, adopt a symmetric dimeric conformation to efficiently engage its asymmetric ligand. Here, structural studies of the CBD from porcine STING (STINGCBD) in complex with CDNs at 1.76 –2.6 {\AA} resolution revealed that porcine STINGCBD, unlike its human and mouse counterparts, can adopt an asymmetric ligand-binding pocket to accommodate the CDNs. We observed that the extensive interactions and shape complementarity between asymmetric 2,3-cGAMP and the ligand-binding pocket make it the most preferred ligand for porcine STING and that geometry constraints limit the binding between symmetric 3,3-CDN and porcine STING. The ligand-discrimination mechanism of porcine STING observed here expands our understanding of how the CDN–STING pathway is activated and of its role in antiviral defense.",

author = "Xiaoyan Cong and Zenglin Yuan and Yijun Du and Bo Wu and Defen Lu and Xiangju Wu and Youjia Zhang and Feng Li and Bin Wei and Jun Li and Jiaqiang Wu and Sujuan Xu and Jinbao Wang and Jing Qi and Guijun Shang and Lichuan Gu",

note = "Funding Information: This work was supported by National Natural Science Foundation of China Grants 31470732 (to L. G.), 31502051 (to X. C.), 31672609 (to J. Q.) and 21673244 (to Bo. W.) and the National Key Research and Development Program of China Grant 2016YFD0501505 (to Y. D.). The authors declare that they have no conflicts of interest with the contents of this article. This article contains Figs. S1 and S2 and Table S1. The atomic coordinates and structure factors (codes 6A03, 6A04, 6A05, 6A06, and 6IYF) have been deposited in the Protein Data Bank (http://wwpdb.org/). † Deceased September 25, 2018. 1 Both authors contributed equally to this work. 2To whom correspondence may be addressed. E-mail: qj-happy2008@ 163.com. 3 To whom correspondence may be addressed. E-mail: gjshang@gmail.com. 4 To whom correspondence may be addressed. E-mail: lcgu@sdu.edu.cn. Funding Information: This work was supported by National Natural Science Foundation of China Grants 31470732 (to L. G.), 31502051 (to X. C.), 31672609 (to J. Q.) and 21673244 (to Bo. W.) and the National Key Research and Development Program of China Grant 2016YFD0501505 (to Y. D.). The authors declare that they have no conflicts of interest with the contents of this article. We thank the staff of beamlines BL17U1 and BL19U at the Shanghai Synchrotron Radiation Facility (SSRF) for their support in the data collection. We also thank Dr. Xuewu Zhang for critical reading and editing of this manuscript. Publisher Copyright: {\textcopyright} 2019 Cong et al.",

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Cong, X, Yuan, Z, Du, Y, Wu, B, Lu, D, Wu, X, Zhang, Y, Li, F, Wei, B, Li, J, Wu, J, Xu, S, Wang, J, Qi, J, Shang, G & Gu, L 2019, 'Crystal structures of porcine STING^CBD–CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins', Journal of Biological Chemistry, vol. 294, no. 30, pp. 11420-11432. https://doi.org/10.1074/jbc.RA119.007367

TY - JOUR

T1 - Crystal structures of porcine STINGCBD–CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins

AU - Cong, Xiaoyan

AU - Yuan, Zenglin

AU - Du, Yijun

AU - Wu, Bo

AU - Lu, Defen

AU - Wu, Xiangju

AU - Zhang, Youjia

AU - Li, Feng

AU - Wei, Bin

AU - Li, Jun

AU - Wu, Jiaqiang

AU - Xu, Sujuan

AU - Wang, Jinbao

AU - Qi, Jing

AU - Shang, Guijun

AU - Gu, Lichuan

N1 - Funding Information: This work was supported by National Natural Science Foundation of China Grants 31470732 (to L. G.), 31502051 (to X. C.), 31672609 (to J. Q.) and 21673244 (to Bo. W.) and the National Key Research and Development Program of China Grant 2016YFD0501505 (to Y. D.). The authors declare that they have no conflicts of interest with the contents of this article. This article contains Figs. S1 and S2 and Table S1. The atomic coordinates and structure factors (codes 6A03, 6A04, 6A05, 6A06, and 6IYF) have been deposited in the Protein Data Bank (http://wwpdb.org/). † Deceased September 25, 2018. 1 Both authors contributed equally to this work. 2To whom correspondence may be addressed. E-mail: qj-happy2008@ 163.com. 3 To whom correspondence may be addressed. E-mail: gjshang@gmail.com. 4 To whom correspondence may be addressed. E-mail: lcgu@sdu.edu.cn. Funding Information: This work was supported by National Natural Science Foundation of China Grants 31470732 (to L. G.), 31502051 (to X. C.), 31672609 (to J. Q.) and 21673244 (to Bo. W.) and the National Key Research and Development Program of China Grant 2016YFD0501505 (to Y. D.). The authors declare that they have no conflicts of interest with the contents of this article. We thank the staff of beamlines BL17U1 and BL19U at the Shanghai Synchrotron Radiation Facility (SSRF) for their support in the data collection. We also thank Dr. Xuewu Zhang for critical reading and editing of this manuscript. Publisher Copyright: © 2019 Cong et al.

PY - 2019/7/26

Y1 - 2019/7/26

N2 - The cyclic dinucleotide (CDN)-stimulator of interferon genes (STING) pathway plays an important role in the detection of viral and bacterial pathogens in animals. Previous studies have shown that the metazoan second messenger cyclic [G(2,5)pA(3,5)p] (2,3-cGAMP) generated by cyclic GMP-AMP synthase cGAS binds STING with high affinity compared with bacterial CDNs such as c-di-GMP, c-di-AMP, and 3,3-cGAMP. Despite recent progress indicating that the CDN-binding domain (CBD) of dimeric STING binds asymmetric 2,3-cGAMP preferentially over symmetric 3,3-CDNs, it remains an open question whether STING molecules, such as human STING, adopt a symmetric dimeric conformation to efficiently engage its asymmetric ligand. Here, structural studies of the CBD from porcine STING (STINGCBD) in complex with CDNs at 1.76 –2.6 Å resolution revealed that porcine STINGCBD, unlike its human and mouse counterparts, can adopt an asymmetric ligand-binding pocket to accommodate the CDNs. We observed that the extensive interactions and shape complementarity between asymmetric 2,3-cGAMP and the ligand-binding pocket make it the most preferred ligand for porcine STING and that geometry constraints limit the binding between symmetric 3,3-CDN and porcine STING. The ligand-discrimination mechanism of porcine STING observed here expands our understanding of how the CDN–STING pathway is activated and of its role in antiviral defense.

AB - The cyclic dinucleotide (CDN)-stimulator of interferon genes (STING) pathway plays an important role in the detection of viral and bacterial pathogens in animals. Previous studies have shown that the metazoan second messenger cyclic [G(2,5)pA(3,5)p] (2,3-cGAMP) generated by cyclic GMP-AMP synthase cGAS binds STING with high affinity compared with bacterial CDNs such as c-di-GMP, c-di-AMP, and 3,3-cGAMP. Despite recent progress indicating that the CDN-binding domain (CBD) of dimeric STING binds asymmetric 2,3-cGAMP preferentially over symmetric 3,3-CDNs, it remains an open question whether STING molecules, such as human STING, adopt a symmetric dimeric conformation to efficiently engage its asymmetric ligand. Here, structural studies of the CBD from porcine STING (STINGCBD) in complex with CDNs at 1.76 –2.6 Å resolution revealed that porcine STINGCBD, unlike its human and mouse counterparts, can adopt an asymmetric ligand-binding pocket to accommodate the CDNs. We observed that the extensive interactions and shape complementarity between asymmetric 2,3-cGAMP and the ligand-binding pocket make it the most preferred ligand for porcine STING and that geometry constraints limit the binding between symmetric 3,3-CDN and porcine STING. The ligand-discrimination mechanism of porcine STING observed here expands our understanding of how the CDN–STING pathway is activated and of its role in antiviral defense.

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