Structural basis for arginine glycosylation of host substrates by bacterial effector proteins

Jun Bae Park; Young Hun Kim; Youngki Yoo; Juyeon Kim; Sung Hoon Jun; Jin Won Cho; Samir El Qaidi; Samuel Walpole; Serena Monaco; Ana A. García-García; Miaomiao Wu; Michael P. Hays; Ramon Hurtado-Guerrero; Jesus Angulo; Philip R. Hardwidge; Jeon Soo Shin; Hyun Soo Cho

doi:10.1038/s41467-018-06680-6

Structural basis for arginine glycosylation of host substrates by bacterial effector proteins

Jun Bae Park, Young Hun Kim, Youngki Yoo, Juyeon Kim, Sung Hoon Jun, Jin Won Cho, Samir El Qaidi, Samuel Walpole, Serena Monaco, Ana A. García-García, Miaomiao Wu, Michael P. Hays, Ramon Hurtado-Guerrero, Jesus Angulo, Philip R. Hardwidge, Jeon Soo Shin, Hyun Soo Cho

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

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Abstract

The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-κB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although they differ in protein substrate specificity. Here we report that these enzymes are retaining glycosyltransferases composed of a helix-loop-helix (HLH) domain, a lid domain, and a catalytic domain. A conserved HEN motif (His-Glu-Asn) in the active site is important for enzyme catalysis and bacterial virulence. We observe differences between SseK1 and SseK2 in interactions with substrates and identify substrate residues that are critical for enzyme recognition. Long Molecular Dynamics simulations suggest that the HLH domain determines substrate specificity and the lid-domain regulates the opening of the active site. Overall, our data suggest a front-face S_Ni mechanism, explain differences in activities among these effectors, and have implications for future drug development against enteric pathogens.

Original language	English
Article number	4283
Journal	Nature communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-06680-6
Publication status	Published - 2018 Dec 1

Bibliographical note

Funding Information:
We thank the staff scientists for assistance at the beamline 5A and 1A of the Photon Factory and the beamline 5C and 7A of Pohang Light Source. This work was supported by Grants from the National Research Foundation of Korea (NRF) funded by the Korean government (MEST) (NRF-2016R1A2B2013305, 2016R1A5A1010764, 2014R1A4A1008625, 2017M3A9F6029755 and 2017R1A2B3006704), the Strategic Initiative for Microbiomes in Agriculture and Food funded by Ministry of Agriculture, Food and Rural Affairs (918012-4) and Brain Korea 21 PLUS Project for Medical Science. This work was also supported by Grants AI093913 and AI127973 from the National Institutes of Health (to P.R.H.). We also thank ARAID and MEC (CTQ2013-44367-C2-2-P, BFU2016-75633-P to R.H-G.), and the DGA (group number E34_R17) for financial support. S.M. acknowledges a postgraduate studentship from the School of Pharmacy of the University of East Anglia. J.A. and S W. acknowledge funding from BBSRC through a research grant (BB/P010660/1) and a DTP PhD studentship, respectively. We thank Dr Ridvan Nepravishta for helpful discussions and technical assistance with the NMR studies. We thank prof. Jihyun F. Kim (Yonsei University) for providing us with DNA of NleB1 and 2.

Publisher Copyright:
© 2018, The Author(s).

All Science Journal Classification (ASJC) codes

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
General
Physics and Astronomy(all)

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Park, J. B., Kim, Y. H., Yoo, Y., Kim, J., Jun, S. H., Cho, J. W., El Qaidi, S., Walpole, S., Monaco, S., García-García, A. A., Wu, M., Hays, M. P., Hurtado-Guerrero, R., Angulo, J., Hardwidge, P. R., Shin, J. S., & Cho, H. S. (2018). Structural basis for arginine glycosylation of host substrates by bacterial effector proteins. Nature communications, 9(1), [4283]. https://doi.org/10.1038/s41467-018-06680-6

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title = "Structural basis for arginine glycosylation of host substrates by bacterial effector proteins",

abstract = "The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-κB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although they differ in protein substrate specificity. Here we report that these enzymes are retaining glycosyltransferases composed of a helix-loop-helix (HLH) domain, a lid domain, and a catalytic domain. A conserved HEN motif (His-Glu-Asn) in the active site is important for enzyme catalysis and bacterial virulence. We observe differences between SseK1 and SseK2 in interactions with substrates and identify substrate residues that are critical for enzyme recognition. Long Molecular Dynamics simulations suggest that the HLH domain determines substrate specificity and the lid-domain regulates the opening of the active site. Overall, our data suggest a front-face SNi mechanism, explain differences in activities among these effectors, and have implications for future drug development against enteric pathogens.",

author = "Park, {Jun Bae} and Kim, {Young Hun} and Youngki Yoo and Juyeon Kim and Jun, {Sung Hoon} and Cho, {Jin Won} and {El Qaidi}, Samir and Samuel Walpole and Serena Monaco and Garc{\'i}a-Garc{\'i}a, {Ana A.} and Miaomiao Wu and Hays, {Michael P.} and Ramon Hurtado-Guerrero and Jesus Angulo and Hardwidge, {Philip R.} and Shin, {Jeon Soo} and Cho, {Hyun Soo}",

note = "Funding Information: We thank the staff scientists for assistance at the beamline 5A and 1A of the Photon Factory and the beamline 5C and 7A of Pohang Light Source. This work was supported by Grants from the National Research Foundation of Korea (NRF) funded by the Korean government (MEST) (NRF-2016R1A2B2013305, 2016R1A5A1010764, 2014R1A4A1008625, 2017M3A9F6029755 and 2017R1A2B3006704), the Strategic Initiative for Microbiomes in Agriculture and Food funded by Ministry of Agriculture, Food and Rural Affairs (918012-4) and Brain Korea 21 PLUS Project for Medical Science. This work was also supported by Grants AI093913 and AI127973 from the National Institutes of Health (to P.R.H.). We also thank ARAID and MEC (CTQ2013-44367-C2-2-P, BFU2016-75633-P to R.H-G.), and the DGA (group number E34_R17) for financial support. S.M. acknowledges a postgraduate studentship from the School of Pharmacy of the University of East Anglia. J.A. and S W. acknowledge funding from BBSRC through a research grant (BB/P010660/1) and a DTP PhD studentship, respectively. We thank Dr Ridvan Nepravishta for helpful discussions and technical assistance with the NMR studies. We thank prof. Jihyun F. Kim (Yonsei University) for providing us with DNA of NleB1 and 2. Publisher Copyright: {\textcopyright} 2018, The Author(s).",

year = "2018",

month = dec,

day = "1",

doi = "10.1038/s41467-018-06680-6",

language = "English",

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Park, JB, Kim, YH, Yoo, Y, Kim, J, Jun, SH, Cho, JW, El Qaidi, S, Walpole, S, Monaco, S, García-García, AA, Wu, M, Hays, MP, Hurtado-Guerrero, R, Angulo, J, Hardwidge, PR, Shin, JS & Cho, HS 2018, 'Structural basis for arginine glycosylation of host substrates by bacterial effector proteins', Nature communications, vol. 9, no. 1, 4283. https://doi.org/10.1038/s41467-018-06680-6

TY - JOUR

T1 - Structural basis for arginine glycosylation of host substrates by bacterial effector proteins

AU - Park, Jun Bae

AU - Kim, Young Hun

AU - Yoo, Youngki

AU - Kim, Juyeon

AU - Jun, Sung Hoon

AU - Cho, Jin Won

AU - El Qaidi, Samir

AU - Walpole, Samuel

AU - Monaco, Serena

AU - García-García, Ana A.

AU - Wu, Miaomiao

AU - Hays, Michael P.

AU - Hurtado-Guerrero, Ramon

AU - Angulo, Jesus

AU - Hardwidge, Philip R.

AU - Shin, Jeon Soo

AU - Cho, Hyun Soo

N1 - Funding Information: We thank the staff scientists for assistance at the beamline 5A and 1A of the Photon Factory and the beamline 5C and 7A of Pohang Light Source. This work was supported by Grants from the National Research Foundation of Korea (NRF) funded by the Korean government (MEST) (NRF-2016R1A2B2013305, 2016R1A5A1010764, 2014R1A4A1008625, 2017M3A9F6029755 and 2017R1A2B3006704), the Strategic Initiative for Microbiomes in Agriculture and Food funded by Ministry of Agriculture, Food and Rural Affairs (918012-4) and Brain Korea 21 PLUS Project for Medical Science. This work was also supported by Grants AI093913 and AI127973 from the National Institutes of Health (to P.R.H.). We also thank ARAID and MEC (CTQ2013-44367-C2-2-P, BFU2016-75633-P to R.H-G.), and the DGA (group number E34_R17) for financial support. S.M. acknowledges a postgraduate studentship from the School of Pharmacy of the University of East Anglia. J.A. and S W. acknowledge funding from BBSRC through a research grant (BB/P010660/1) and a DTP PhD studentship, respectively. We thank Dr Ridvan Nepravishta for helpful discussions and technical assistance with the NMR studies. We thank prof. Jihyun F. Kim (Yonsei University) for providing us with DNA of NleB1 and 2. Publisher Copyright: © 2018, The Author(s).

PY - 2018/12/1

Y1 - 2018/12/1

N2 - The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-κB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although they differ in protein substrate specificity. Here we report that these enzymes are retaining glycosyltransferases composed of a helix-loop-helix (HLH) domain, a lid domain, and a catalytic domain. A conserved HEN motif (His-Glu-Asn) in the active site is important for enzyme catalysis and bacterial virulence. We observe differences between SseK1 and SseK2 in interactions with substrates and identify substrate residues that are critical for enzyme recognition. Long Molecular Dynamics simulations suggest that the HLH domain determines substrate specificity and the lid-domain regulates the opening of the active site. Overall, our data suggest a front-face SNi mechanism, explain differences in activities among these effectors, and have implications for future drug development against enteric pathogens.

AB - The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-κB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although they differ in protein substrate specificity. Here we report that these enzymes are retaining glycosyltransferases composed of a helix-loop-helix (HLH) domain, a lid domain, and a catalytic domain. A conserved HEN motif (His-Glu-Asn) in the active site is important for enzyme catalysis and bacterial virulence. We observe differences between SseK1 and SseK2 in interactions with substrates and identify substrate residues that are critical for enzyme recognition. Long Molecular Dynamics simulations suggest that the HLH domain determines substrate specificity and the lid-domain regulates the opening of the active site. Overall, our data suggest a front-face SNi mechanism, explain differences in activities among these effectors, and have implications for future drug development against enteric pathogens.

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U2 - 10.1038/s41467-018-06680-6

DO - 10.1038/s41467-018-06680-6

M3 - Article

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JO - Nature Communications

JF - Nature Communications

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ER -

Structural basis for arginine glycosylation of host substrates by bacterial effector proteins

Abstract

Bibliographical note

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