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Wei X, Wang Y, Zhang S, Gu T, Steinmetz G, Yu H, Guo G, Liu X, Fan S, Wang F, Gu Y, Xin F. Structural analysis of receptor-like kinase SOBIR1 reveals mechanisms that regulate its phosphorylation-dependent activation. Plant Commun 2022; 3:100301. [PMID: 35529948 PMCID: PMC9073325 DOI: 10.1016/j.xplc.2022.100301] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/04/2021] [Accepted: 01/15/2022] [Indexed: 05/20/2023]
Abstract
Plant leucine-rich repeat (LRR) receptor-like kinases (RLKs) and LRR receptor-like proteins (RLPs) comprise a large family of cell surface receptors that play critical roles in signal perception and transduction. Both LRR-RLKs and LRR-RLPs rely on regulatory LRR-RLKs to initiate downstream signaling pathways. BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3 (BAK1/SERK3) and SUPPRESSOR OF BIR1-1 (SOBIR1) are important and extensively studied regulatory LRR-RLKs with distinct functions. Although the regulatory mechanism of BAK1 activation has been studied in detail, the activation mechanism of SOBIR1 remains poorly understood. Here, the crystal structures of the catalytically inactive kinase domain of SOBIR1 (SOBIR1-KD) from Arabidopsis thaliana were determined in complexes with AMP-PNP and Mg2+. The results show that SOBIR1-KD contains a uniquely long β3-αC loop and adopts an Src-like inactive conformation with an unusual architecture at the activation segment, which comprises three helices. Biochemical studies revealed that SOBIR1 is transphosphorylated by BAK1 following its autophosphorylation via an intermolecular mechanism, and the phosphorylation of Thr529 in the activation segment and the β3-αC loop are critical for SOBIR1 phosphorylation. Further functional analysis confirmed the importance of Thr529 and the β3-αC loop for the SOBIR1-induced cell death response in Nicotiana benthamiana. Taken together, these findings provide a structural basis for the regulatory mechanism of SOBIR1 and reveal the important elements and phosphorylation events in the special stepwise activation of SOBIR1-KD, the first such processes found in regulatory LRR-RLKs.
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Affiliation(s)
- Xue Wei
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Su Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Tianyi Gu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Gabryel Steinmetz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Haiyan Yu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guoguang Guo
- Key Laboratory of Ministry of Education for Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shilong Fan
- The Center of Protein Science, Tsinghua University, Beijing 100084, China
| | - Fengzhong Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Rehkamp A, Tänzler D, Tüting C, Kastritis PL, Iacobucci C, Ihling CH, Kipping M, Koch KW, Sinz A. First 3D-Structural Data of Full-Length Guanylyl Cyclase 1 in Rod-Outer-Segment Preparations of Bovine Retina by Cross-Linking/Mass Spectrometry. J Mol Biol 2021; 433:166947. [PMID: 33744315 DOI: 10.1016/j.jmb.2021.166947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 11/24/2022]
Abstract
The rod-outer-segment guanylyl cyclase 1 (ROS-GC1) is a key transmembrane protein for retinal phototransduction. Mutations of ROS-GC1 correlate with different retinal diseases that often lead to blindness. No structural data are available for ROS-GC1 so far. We performed a 3D-structural analysis of native ROS-GC1 from bovine retina by cross-linking/mass spectrometry (XL-MS) and computational modeling. Absolute quantification and activity measurements of native ROS-GC1 were performed by MS-based assays directly in bovine retina samples. Our data present the first 3D-structural analysis of active, full-length ROS-GC1 derived from bovine retina. We propose a novel domain organization for the intracellular domain ROS-GC1. Our XL-MS data of native ROS-GC1 from rod-outer-segment preparations of bovine retina agree with a dimeric architecture. Our integrated approach can serve as a blueprint for conducting 3D-structural studies of membrane proteins in their native environment.
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Zeng J, Platig J, Cheng TY, Ahmed S, Skaf Y, Potluri LP, Schwartz D, Steen H, Moody DB, Husson RN. Protein kinases PknA and PknB independently and coordinately regulate essential Mycobacterium tuberculosis physiologies and antimicrobial susceptibility. PLoS Pathog 2020; 16:e1008452. [PMID: 32255801 PMCID: PMC7164672 DOI: 10.1371/journal.ppat.1008452] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/17/2020] [Accepted: 03/03/2020] [Indexed: 01/28/2023] Open
Abstract
The Mycobacterium tuberculosis Ser/Thr protein kinases PknA and PknB are essential for growth and have been proposed as possible drug targets. We used a titratable conditional depletion system to investigate the functions of these kinases. Depletion of PknA or PknB or both kinases resulted in growth arrest, shortening of cells, and time-dependent loss of acid-fast staining with a concomitant decrease in mycolate synthesis and accumulation of trehalose monomycolate. Depletion of PknA and/or PknB resulted in markedly increased susceptibility to β-lactam antibiotics, and to the key tuberculosis drug rifampin. Phosphoproteomic analysis showed extensive changes in protein phosphorylation in response to PknA depletion and comparatively fewer changes with PknB depletion. These results identify candidate substrates of each kinase and suggest specific and coordinate roles for PknA and PknB in regulating multiple essential physiologies. These findings support these kinases as targets for new antituberculosis drugs and provide a valuable resource for targeted investigation of mechanisms by which protein phosphorylation regulates pathways required for growth and virulence in M. tuberculosis.
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Affiliation(s)
- Jumei Zeng
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - John Platig
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Brigham & Women’s Hospital, Harvard Medical School, Boston MA, United States of America
| | - Saima Ahmed
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Yara Skaf
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States of America
| | - Lakshmi-Prasad Potluri
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Daniel Schwartz
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States of America
| | - Hanno Steen
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - D. Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Brigham & Women’s Hospital, Harvard Medical School, Boston MA, United States of America
| | - Robert N. Husson
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States of America
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Bellinzoni M, Wehenkel AM, Durán R, Alzari PM. Novel mechanistic insights into physiological signaling pathways mediated by mycobacterial Ser/Thr protein kinases. Microbes Infect 2019; 21:222-229. [PMID: 31254628 DOI: 10.1016/j.micinf.2019.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
Protein phosphorylation is known to be one of the keystones of signal sensing and transduction in all living organisms. Once thought to be essentially confined to the eukaryotic kingdoms, reversible phosphorylation on serine, threonine and tyrosine residues, has now been shown to play a major role in many prokaryotes, where the number of Ser/Thr protein kinases (STPKs) equals or even exceeds that of two component systems. Mycobacterium tuberculosis, the etiological agent of tuberculosis, is one of the most studied organisms for the role of STPK-mediated signaling in bacteria. Driven by the interest and tractability of these enzymes as potential therapeutic targets, extensive studies revealed the remarkable conservation of protein kinases and their cognate phosphatases across evolution, and their involvement in bacterial physiology and virulence. Here, we present an overview of the current knowledge of mycobacterial STPKs structures and kinase activation mechanisms, and we then focus on PknB and PknG, two well-characterized STPKs that are essential for the intracellular survival of the bacillus. We summarize the mechanistic evidence that links PknB to the regulation of peptidoglycan synthesis in cell division and morphogenesis, and the major findings that establishes PknG as a master regulator of central carbon and nitrogen metabolism. Two decades after the discovery of STPKs in M. tuberculosis, the emerging landscape of O-phosphosignaling is starting to unveil how eukaryotic-like kinases can be engaged in unique, non-eukaryotic-like, signaling mechanisms in mycobacteria.
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Affiliation(s)
- Marco Bellinzoni
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Anne Marie Wehenkel
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Mataojo 2020, Montevideo 11400, Uruguay
| | - Pedro M Alzari
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France.
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Bellinzoni M, Wehenkel AM, Durán R, Alzari PM. Novel mechanistic insights into physiological signaling pathways mediated by mycobacterial Ser/Thr protein kinases. Genes Immun 2019; 20:383-393. [DOI: 10.1038/s41435-019-0069-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
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Sundar S, Thangamani L, Manivel G, Kumar P, Piramanayagam S. Molecular docking, molecular dynamics and MM/PBSA studies of FDA approved drugs for protein kinase a of Mycobacterium tuberculosis; application insights of drug repurposing. Informatics in Medicine Unlocked 2019; 16:100210. [DOI: 10.1016/j.imu.2019.100210] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Li P, Xu D, Ma T, Wang D, Li W, He J, Ran T, Wang W. Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism. Biochem J 2018; 475:2209-24. [DOI: 10.1042/bcj20180077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022]
Abstract
The type VI secretion system (T6SS) is a versatile and widespread export system found in many Gram-negative bacteria that delivers effector proteins into target cells. The functions of T6SSs are tightly regulated by diverse mechanisms at multiple levels, including post-translational modification through threonine phosphorylation via the Ser/Thr protein kinase (STPK) PpkA. Here, we identified that PpkA is essential for T6SS secretion in Serratia marcescens since its deletion eliminated the secretion of haemolysin co-regulated protein, while the periplasmic and transmembrane portion of PpkA was found to be disposable for T6SS secretion. We further determined the crystal structure of the kinase domain of PpkA (PpkA-294). The structure of PpkA-294 was determined in its apo form to a 1.6 Å resolution as well as in complex with ATP to a 1.41 Å resolution and with an ATP analogue AMP-PCP to a 1.45 Å resolution. The residues in the activation loop of PpkA-294 were fully determined, and the N-terminus of the loop was folded into an unprecedented inhibitory helix, revealing that the PpkA kinase domain was in an auto-inhibitory state. The ternary MgATP–PpkA-294 complex was also inactive with nucleotide ribose and phosphates in unexpected and unproductive conformations. The αC-helix in the inactive PpkA-294 adopted a conformation towards the active site but with the conserved glutamate in the helix rotated away, which we suggest to be a general conformation for all STPK kinases in the inactive form. Structural comparison of PpkA with its eukaryotic homologues reinforced the universal regulation mechanism of protein kinases.
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Khan MZ, Kaur P, Nandicoori VK. Targeting the messengers: Serine/threonine protein kinases as potential targets for antimycobacterial drug development. IUBMB Life 2018; 70:889-904. [DOI: 10.1002/iub.1871] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 04/22/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Mehak Zahoor Khan
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi India
| | - Prabhjot Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi India
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9
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Lisa MN, Wagner T, Alexandre M, Barilone N, Raynal B, Alzari PM, Bellinzoni M. The crystal structure of PknI from Mycobacterium tuberculosis shows an inactive, pseudokinase-like conformation. FEBS J 2017; 284:602-614. [PMID: 28054744 DOI: 10.1111/febs.14003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/10/2016] [Accepted: 01/04/2017] [Indexed: 11/27/2022]
Abstract
Eukaryotic-like Ser/Thr protein kinases (ePKs) have been identified in many bacterial species, where they are known to mediate signalling mechanisms that share several features with their eukaryotic counterparts. In Mycobacterium tuberculosis, PknI is one of the 11 predicted ePKs and it has been related to bacterial virulence. In order to better understand the molecular basis of its role in mycobacterial signalling, we solved the crystal structure of the PknI cytoplasmic domain. We found that even though PknI possesses most conserved elements characteristic of Hanks-type kinases, it is degraded in several motifs that are essential for the ePKs catalytic activity. Most notably, PknI presents a remarkably short activation segment lacking a peptide-substrate binding site. Consistent with this observation and similar to earlier findings for eukaryotic pseudokinases, no kinase activity was detected for the catalytic domain of PknI, against different substrates and in various experimental conditions. Based on these results, we conclude that PknI may rely on unconventional mechanism(s) for kinase activity and/or it could play alternative role(s) in mycobacterial signalling. DATABASE Atomic coordinates and structure factors for the catalytic domain of M. tuberculosis PknI are in the Protein Data Bank under the accession codes 5M06 (wild-type PknI + ADP), 5M07 (PknI_C20A), 5M08 (PknI_C20A_R136A) and 5M09 (PknI_C20A_R136N).
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Affiliation(s)
- María-Natalia Lisa
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Tristan Wagner
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Matthieu Alexandre
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Nathalie Barilone
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Bertrand Raynal
- CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris Cedex, France
| | - Pedro M Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, Paris Cedex, France.,CNRS UMR 3528 'Biologie structurale des processus cellulaires et maladies infectieuses', Institut Pasteur, Paris Cedex, France.,Sorbonne Paris Cité, Microbiologie Structurale, Université Paris Diderot, France
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Ravala SK, Singh S, Yadav GS, Kumar S, Karthikeyan S, Chakraborti PK. Evidence that phosphorylation of threonine in the GT motif triggers activation of PknA, a eukaryotic-type serine/threonine kinase from Mycobacterium tuberculosis. FEBS J 2015; 282:1419-31. [PMID: 25665034 DOI: 10.1111/febs.13230] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 12/31/2022]
Abstract
Phosphorylation of the activation loop in the catalytic domain of the RD family of bacterial eukaryotic-type Ser/Thr protein kinases (STPK) induces their conformational transition from an inactive to active state. However, mechanistic insights into the phosphorylation-mediated transition of these STPKs from an inactive to active state remain unknown. In the present study, we addressed this issue with PknA, an essential STPK from Mycobacterium tuberculosis. We found that the catalytic activity of PknA is confined within the N-terminal 283 amino acids (PknA-283). The crystal structure of PknA-283 in unphosphorylated form showed an ordered activation loop and existed in an inactive state preventing the phosphorylation of its cognate substrate(s). Peptide mass finger printing studies revealed that all activation loop threonines (Thr172, Thr174 and Thr180) were phosphorylated in the activated PknA-283 protein. Substitution of Thr180 with Ala/Asp (T180A/T180D) resulted in catalytically defective mutants, whereas a double mutant replacing Thr172 and Thr174 with Ala (T172A-T174A) was deficient in kinase activity. Analysis of PknA-283 structure, together with biochemical studies, revealed the possibility of phosphorylation of Thr180 via a cis mechanism, whereas that of Thr172 and Thr174 occurs via a trans mechanism. Moreover, unlike wild-type, these mutants did not show any drastic change in cell morphology in a phenotypic assay, implicating the role of all threonines in the activation loop towards the functionality of PknA. Thus, our findings offer a model for kinase activation showing that the phosphorylation of Thr180 triggers PknA to transphosphorylate Thr172/Thr174, thereby governing its functionality.
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