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Tan J, Zhang L, Zhou X, Han S, Zhou Y, Zhu Y. Structural basis of the bacterial flagellar motor rotational switching. Cell Res 2024:10.1038/s41422-024-01017-z. [PMID: 39179739 DOI: 10.1038/s41422-024-01017-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/08/2024] [Indexed: 08/26/2024] Open
Abstract
The bacterial flagellar motor is a huge bidirectional rotary nanomachine that drives rotation of the flagellum for bacterial motility. The cytoplasmic C ring of the flagellar motor functions as the switch complex for the rotational direction switching from counterclockwise to clockwise. However, the structural basis of the rotational switching and how the C ring is assembled have long remained elusive. Here, we present two high-resolution cryo-electron microscopy structures of the C ring-containing flagellar basal body-hook complex from Salmonella Typhimurium, which are in the default counterclockwise state and in a constitutively active CheY mutant-induced clockwise state, respectively. In both complexes, the C ring consists of four subrings, but is in two different conformations. The CheY proteins are bound into an open groove between two adjacent protomers on the surface of the middle subring of the C ring and interact with the FliG and FliM subunits. The binding of the CheY protein induces a significant upward shift of the C ring towards the MS ring and inward movements of its protomers towards the motor center, which eventually remodels the structures of the FliG subunits and reverses the orientations and surface electrostatic potential of the αtorque helices to trigger the counterclockwise-to-clockwise rotational switching. The conformational changes of the FliG subunits reveal that the stator units on the motor require a relocation process in the inner membrane during the rotational switching. This study provides unprecedented molecular insights into the rotational switching mechanism and a detailed overall structural view of the bacterial flagellar motors.
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Affiliation(s)
- Jiaxing Tan
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ling Zhang
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xingtong Zhou
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Siyu Han
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zhou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Yongqun Zhu
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- Center for Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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2
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Irukuvajjula SS, Jithender Reddy G, Rao K, Vadrevu LR. Contrasting effect of ficoll on apo and holo forms of bacterial chemotaxis protein Y: Selective destabilization of the conformationally altered holo form. Int J Biol Macromol 2023; 232:123505. [PMID: 36736516 DOI: 10.1016/j.ijbiomac.2023.123505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023]
Abstract
Chemotaxis Y (CheY), upon metal binding, displays a drastic alteration in its structure and stability. This premise prompted us to study the effect of crowding on the two conformationally distinct states of the same test protein. A comparative analysis on the structure and thermal stability in the presence and absence of the macromolecular crowder, ficoll, and its monomeric unit, sucrose, revealed a contrasting effect of ficoll on the apo and holo forms. In the presence of ficoll while the thermal stability (Tm) of the apo form is enhanced, the thermal stability of the holo form is reduced. The selective lowering of Tm for the holo form in the combined presence of ficoll and sucrose and not in sucrose alone suggests that the contrasting effect is due to the macromolecular nature of ficoll. Since metal-protein interaction remains unperturbed in the presence of ficoll and Mg2+ sequestration is ruled out in a systematic manner the alternative possibility for the exclusive reduction in the thermal stability of the holo form is the ficoll-induced modulation of the relative population of apo and holo forms of CheY.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
| | - G Jithender Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State 500107, India
| | - Late Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
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3
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Hamid M, Khalid MF, Chaudhary SU, Khan S. The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS. Int J Mol Sci 2022; 23:ijms232112771. [PMID: 36361564 PMCID: PMC9659070 DOI: 10.3390/ijms232112771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction.
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Affiliation(s)
- Maham Hamid
- Biomedical Informatics and Engineering Research Laboratory (BIRL), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics and Engineering Research Laboratory (BIRL), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics and Engineering Research Laboratory (BIRL), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan
- Correspondence: (S.U.C.); (S.K.)
| | - Shahid Khan
- Syed Babar Ali School of Science & Engineering, Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Correspondence: (S.U.C.); (S.K.)
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4
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Kong L, Su M, Sang J, Huang S, Wang M, Cai Y, Xie M, Wu J, Wang S, Foster SJ, Zhang J, Han A. The W-Acidic Motif of Histidine Kinase WalK Is Required for Signaling and Transcriptional Regulation in Streptococcus mutans. Front Microbiol 2022; 13:820089. [PMID: 35558126 PMCID: PMC9087282 DOI: 10.3389/fmicb.2022.820089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
In Streptococcus mutans, we find that the histidine kinase WalK possesses the longest C-terminal tail (CTT) among all 14 TCSs, and this tail plays a key role in the interaction of WalK with its response regulator WalR. We demonstrate that the intrinsically disordered CTT is characterized by a conserved tryptophan residue surrounded by acidic amino acids. Mutation in the tryptophan not only disrupts the stable interaction, but also impairs the efficient phosphotransferase and phosphatase activities of WalRK. In addition, the tryptophan is important for WalK to compete with DNA containing a WalR binding motif for the WalR interaction. We further show that the tryptophan is important for in vivo transcriptional regulation and bacterial biofilm formation by S. mutans. Moreover, Staphylococcus aureus WalK also has a characteristic CTT, albeit relatively shorter, with a conserved W-acidic motif, that is required for the WalRK interaction in vitro. Together, these data reveal that the W-acidic motif of WalK is indispensable for its interaction with WalR, thereby playing a key role in the WalRK-dependent signal transduction, transcriptional regulation and biofilm formation.
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Affiliation(s)
- Lingyuan Kong
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingyang Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanshan Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Min Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingquan Xie
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jun Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shida Wang
- State Key Laboratory for Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Simon J Foster
- Department of Molecular Biology and Biotechnology, The Florey Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Jiaqin Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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5
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Sanchez AM, Jacewicz A, Shuman S. Fission yeast Duf89 and Duf8901 are cobalt/nickel-dependent phosphatase-pyrophosphatases that act via a covalent aspartyl-phosphate intermediate. J Biol Chem 2022; 298:101851. [PMID: 35314193 PMCID: PMC9062747 DOI: 10.1016/j.jbc.2022.101851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/02/2022] Open
Abstract
Domain of Unknown Function 89 (DUF89) proteins are metal-dependent phosphohydrolases. Exemplary DUF89 enzymes differ in their metal and phosphosubstrate preferences. Here, we interrogated the activities and structures of two DUF89 paralogs from fission yeast-Duf89 and Duf8901. We find that Duf89 and Duf8901 are cobalt/nickel-dependent phosphohydrolases adept at hydrolyzing p-nitrophenylphosphate and PPi. Crystal structures of metal-free Duf89 and Co2+-bound Duf8901 disclosed two enzyme conformations that differed with respect to the position of a three-helix module, which is either oriented away from the active site in Duf89 or forms a lid over the active site in Duf8901. Lid closure results in a 16 Å movement of Duf8901 Asp195, vis-à-vis Asp199 in Duf89, that brings Asp195 into contact with an octahedrally coordinated cobalt. Reaction of Duf8901 with BeCl2 and NaF in the presence of divalent cations Co2+, Ni2+, or Zn2+ generated covalent Duf8901-(Asp248)-beryllium trifluoride (BeF3)•Co2+, Duf8901-(Asp248)-BeF3•Ni2+, or Duf8901-(Asp248)-BeF3•Zn2+ adducts, the structures of which suggest a two-step catalytic mechanism via formation and hydrolysis of an enzyme-(aspartyl)-phosphate intermediate. Alanine mutations of Duf8901 Asp248, Asn249, Lys401, Asp286, and Asp195 that interact with BeF3•Co2+ squelched p-nitrophenylphosphatase activity. A 1.8 Å structure of a Duf8901-(Asp248)-AlF4-OH2•Co2+ transition-state mimetic suggests an associative mechanism in which Asp195 and Asp363 orient and activate the water nucleophile. Whereas deletion of the duf89 gene elicited a phenotype in which expression of phosphate homeostasis gene pho1 was derepressed, deleting duf8901 did not, thereby hinting that the DUF89 paralogs have distinct functional repertoires in vivo.
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Affiliation(s)
- Ana M Sanchez
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, New York, USA
| | - Agata Jacewicz
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
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6
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Walshe JL, Siddiquee R, Patel K, Ataide SF. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2889-2904. [PMID: 35150565 PMCID: PMC8934654 DOI: 10.1093/nar/gkac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/12/2022] [Accepted: 01/25/2022] [Indexed: 12/02/2022] Open
Abstract
Regulated transcription termination provides an efficient and responsive means to control gene expression. In bacteria, rho-independent termination occurs through the formation of an intrinsic RNA terminator loop, which disrupts the RNA polymerase elongation complex, resulting in its dissociation from the DNA template. Bacteria have a number of pathways for overriding termination, one of which is the formation of mutually exclusive RNA motifs. ANTAR domains are a class of antiterminator that bind and stabilize dual hexaloop RNA motifs within the nascent RNA chain to prevent terminator loop formation. We have determined the structures of the dimeric ANTAR domain protein EutV, from Enterococcus faecialis, in the absence of and in complex with the dual hexaloop RNA target. The structures illustrate conformational changes that occur upon RNA binding and reveal that the molecular interactions between the ANTAR domains and RNA are restricted to a single hexaloop of the motif. An ANTAR domain dimer must contact each hexaloop of the dual hexaloop motif individually to prevent termination in eubacteria. Our findings thereby redefine the minimal ANTAR domain binding motif to a single hexaloop and revise the current model for ANTAR-mediated antitermination. These insights will inform and facilitate the discovery of novel ANTAR domain RNA targets.
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Affiliation(s)
- James L Walshe
- Correspondence may also be addressed to James L. Walshe.
| | - Rezwan Siddiquee
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Karishma Patel
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Sandro F Ataide
- To whom correspondence should be addressed. Tel: +61 2 9351 7817; Fax: +61 2 9351 5858
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7
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Foster CA, Silversmith RE, Immormino RM, Vass LR, Kennedy EN, Pazy Y, Collins EJ, Bourret RB. Role of Position K+4 in the Phosphorylation and Dephosphorylation Reaction Kinetics of the CheY Response Regulator. Biochemistry 2021; 60:2130-2151. [PMID: 34167303 DOI: 10.1021/acs.biochem.1c00246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two-component signaling is a primary method by which microorganisms interact with their environments. A kinase detects stimuli and modulates autophosphorylation activity. The signal propagates by phosphotransfer from the kinase to a response regulator, eliciting a response. Response regulators operate over a range of time scales, corresponding to their related biological processes. Response regulator active site chemistry is highly conserved, but certain variable residues can influence phosphorylation kinetics. An Ala-to-Pro substitution (K+4, residue 113) in the Escherichia coli response regulator CheY triggers a constitutively active phenotype; however, the A113P substitution is too far from the active site to directly affect phosphochemistry. To better understand the activating mechanism(s) of the substitution, we analyzed receiver domain sequences to characterize the evolutionary role of the K+4 position. Although most featured Pro, Leu, Ile, and Val residues, chemotaxis-related proteins exhibited atypical Ala, Gly, Asp, and Glu residues at K+4. Structural and in silico analyses revealed that CheY A113P adopted a partially active configuration. Biochemical data showed that A113P shifted CheY toward a more activated state, enhancing autophosphorylation. By characterizing CheY variants, we determined that this functionality was transmitted through a hydrophobic network bounded by the β5α5 loop and the α1 helix of CheY. This region also interacts with the phosphodonor CheAP1, suggesting that binding generates an activating perturbation similar to the A113P substitution. Atypical residues like Ala at the K+4 position likely serve two purposes. First, restricting autophosphorylation may minimize background noise generated by intracellular phosphodonors such as acetyl phosphate. Second, optimizing interactions with upstream partners may help prime the receiver domain for phosphorylation.
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Affiliation(s)
- Clay A Foster
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ruth E Silversmith
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Robert M Immormino
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Luke R Vass
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Emily N Kennedy
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yael Pazy
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edward J Collins
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Robert B Bourret
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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8
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Evidence for Pentapeptide-Dependent and Independent CheB Methylesterases. Int J Mol Sci 2020; 21:ijms21228459. [PMID: 33187094 PMCID: PMC7698151 DOI: 10.3390/ijms21228459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 12/22/2022] Open
Abstract
Many bacteria possess multiple chemosensory pathways that are composed of homologous signaling proteins. These pathways appear to be functionally insulated from each other, but little information is available on the corresponding molecular basis. We report here a novel mechanism that contributes to pathway insulation. We show that, of the four CheB paralogs of Pseudomonas aeruginosa PAO1, only CheB2 recognizes a pentapeptide at the C-terminal extension of the McpB (Aer2) chemoreceptor (KD = 93 µM). McpB is the sole chemoreceptor that stimulates the Che2 pathway, and CheB2 is the methylesterase of this pathway. Pectobacterium atrosepticum SCRI1043 has a single CheB, CheB_Pec, and 19 of its 36 chemoreceptors contain a C-terminal pentapeptide. The deletion of cheB_Pec abolished chemotaxis, but, surprisingly, none of the pentapeptides bound to CheB_Pec. To determine the corresponding structural basis, we solved the 3D structure of CheB_Pec. Its structure aligned well with that of the pentapeptide-dependent enzyme from Salmonella enterica. However, no electron density was observed in the CheB_Pec region corresponding to the pentapeptide-binding site in the Escherichia coli CheB. We hypothesize that this structural disorder is associated with the failure to bind pentapeptides. Combined data show that CheB methylesterases can be divided into pentapeptide-dependent and independent enzymes.
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9
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Paithankar KS, Enderle M, Wirthensohn DC, Miller A, Schlesner M, Pfeiffer F, Rittner A, Grininger M, Oesterhelt D. Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation. Acta Crystallogr F Struct Biol Commun 2019; 75:576-585. [PMID: 31475924 PMCID: PMC6718144 DOI: 10.1107/s2053230x19010896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/04/2019] [Indexed: 12/15/2022] Open
Abstract
Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection.
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Affiliation(s)
- Karthik Shivaji Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Mathias Enderle
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - David C. Wirthensohn
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Arthur Miller
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Schlesner
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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10
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Gaviard C, Broutin I, Cosette P, Dé E, Jouenne T, Hardouin J. Lysine Succinylation and Acetylation in Pseudomonas aeruginosa. J Proteome Res 2018; 17:2449-2459. [DOI: 10.1021/acs.jproteome.8b00210] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Isabelle Broutin
- LCRB, UMR 8015, CNRS, University Paris Descartes, Sorbonne Paris City, 75270 Paris Cedex 06, France
| | - Pascal Cosette
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000 Rouen, France
- PISSARO Proteomic Facility, IRIB, 76821 Mont-Saint-Aignan, France
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11
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Alam N, Goldstein O, Xia B, Porter KA, Kozakov D, Schueler-Furman O. High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PLoS Comput Biol 2017; 13:e1005905. [PMID: 29281622 PMCID: PMC5760072 DOI: 10.1371/journal.pcbi.1005905] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 01/09/2018] [Accepted: 11/29/2017] [Indexed: 11/24/2022] Open
Abstract
Peptide-protein interactions contribute a significant fraction of the protein-protein interactome. Accurate modeling of these interactions is challenging due to the vast conformational space associated with interactions of highly flexible peptides with large receptor surfaces. To address this challenge we developed a fragment based high-resolution peptide-protein docking protocol. By streamlining the Rosetta fragment picker for accurate peptide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge of accurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy, as validated on a small but representative set of peptide-protein complex structures well resolved by X-ray crystallography. Our approach opens up the way to high-resolution modeling of many more peptide-protein interactions and to the detailed study of peptide-protein association in general. PIPER-FlexPepDock is freely available to the academic community as a server at http://piperfpd.furmanlab.cs.huji.ac.il. Peptide-protein interactions are crucial components of various important biological processes in living cells. High-resolution structural information of such interactions provides insight about the underlying biophysical principles governing the interactions, and a starting point for their targeted manipulations. Accurate docking algorithms can help fill the gap between the vast number of these interactions and the small number of experimentally solved structures. However, the accuracies of the existing protocols have been limited, in particular for ab initio docking when no information about the peptide beyond its sequence is available. Here we introduce PIPER-FlexPepDock, a fragment-based global docking protocol for high-resolution modeling of peptide-protein interactions. Integration of accurate and efficient representation of the peptide using fragment ensembles, their fast and exhaustive rigid-body docking, and their subsequent accurate flexible refinement, enables peptide-protein docking of remarkable accuracy. The validation on a representative benchmark set of crystallographically solved high-resolution peptide-protein complexes demonstrates significantly improved performance over all existing docking protocols. This opens up the way to the modeling of many more peptide-protein interactions, and to a more detailed study of peptide-protein association in general.
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Affiliation(s)
- Nawsad Alam
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Oriel Goldstein
- School of Computer Sciences and Engineering, The Hebrew University, Jerusalem, Israel
| | - Bing Xia
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Kathryn A. Porter
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America
- Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail: (OSF); (DK)
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
- * E-mail: (OSF); (DK)
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12
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Otrusinová O, Demo G, Padrta P, Jaseňáková Z, Pekárová B, Gelová Z, Szmitkowska A, Kadeřávek P, Jansen S, Zachrdla M, Klumpler T, Marek J, Hritz J, Janda L, Iwaï H, Wimmerová M, Hejátko J, Žídek L. Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. J Biol Chem 2017; 292:17525-17540. [PMID: 28860196 DOI: 10.1074/jbc.m117.790212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/28/2017] [Indexed: 11/06/2022] Open
Abstract
Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1RD) from Arabidopsis thaliana We observed that the crystal structures of free, Mg2+-bound, and beryllofluoridated CKI1RD (a stable analogue of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2+ binding and beryllofluoridation alter the conformational equilibrium of the β3-α3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the β3-α3 loop while keeping the active-site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the β3-α3 loop directly interacts with the ATP-binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the β3-α3 loop of CKI1RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic β3-α3 loop of CKI1RD, the corresponding loop of the ETR1 receiver domain (ETR1RD) exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1RD is involved in phosphorylation-independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MSP.
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Affiliation(s)
- Olga Otrusinová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Gabriel Demo
- From the Central European Institute of Technology and
| | - Petr Padrta
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Jaseňáková
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Blanka Pekárová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Gelová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Agnieszka Szmitkowska
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Pavel Kadeřávek
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Séverine Jansen
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Milan Zachrdla
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | | | - Jaromír Marek
- From the Central European Institute of Technology and
| | - Jozef Hritz
- From the Central European Institute of Technology and
| | - Lubomír Janda
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Hideo Iwaï
- the Institute of Biotechnology, University of Helsinki, Viikinkaari 1 (P. O. Box 65), 00014 Helsinki, Finland
| | - Michaela Wimmerová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Jan Hejátko
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Lukáš Žídek
- From the Central European Institute of Technology and .,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
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13
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Liao JM, Wang YT, Lin CLS. A fragment-based docking simulation for investigating peptide–protein bindings. Phys Chem Chem Phys 2017; 19:10436-10442. [DOI: 10.1039/c6cp07136h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We developed a fragment-based docking strategy for long peptide docking simulations, which separates a long peptide into halves for docking, and then recombined to rebuild whole-peptide docking conformations. With further screening, optimizations and MM/GBSA scoring, our method was capable of efficiently predicting the near-native peptide binding conformations.
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Affiliation(s)
- Jun-min Liao
- Graduate School of Medicine
- Kaohsiung Medical University
- Taiwan
| | - Yeng-Tseng Wang
- Department of Biochemistry
- Kaohsiung Medical University
- Taiwan
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14
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Foster CA, West AH. Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems. Proteins 2016; 85:155-176. [PMID: 27802580 PMCID: PMC5242315 DOI: 10.1002/prot.25207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023]
Abstract
Two‐component signaling (TCS) is the primary means by which bacteria, as well as certain plants and fungi, respond to external stimuli. Signal transduction involves stimulus‐dependent autophosphorylation of a sensor histidine kinase and phosphoryl transfer to the receiver domain of a downstream response regulator. Phosphorylation acts as an allosteric switch, inducing structural and functional changes in the pathway's components. Due to their transient nature, phosphorylated receiver domains are challenging to characterize structurally. In this work, we provide a methodology for simulating receiver domain phosphorylation to predict conformations that are nearly identical to experimental structures. Using restrained molecular dynamics, phosphorylated conformations of receiver domains can be reliably sampled on nanosecond timescales. These simulations also provide data on conformational dynamics that can be used to identify regions of functional significance related to phosphorylation. We first validated this approach on several well‐characterized receiver domains and then used it to compare the upstream and downstream components of the fungal Sln1 phosphorelay. Our results demonstrate that this technique provides structural insight, obtained in the absence of crystallographic or NMR information, regarding phosphorylation‐induced conformational changes in receiver domains that regulate the output of their associated signaling pathway. To our knowledge, this is the first time such a protocol has been described that can be broadly applied to TCS proteins for predictive purposes. Proteins 2016; 85:155–176. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Clay A Foster
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Ann H West
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
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15
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Fernández I, Otero LH, Klinke S, Carrica MDC, Goldbaum FA. Snapshots of Conformational Changes Shed Light into the NtrX Receiver Domain Signal Transduction Mechanism. J Mol Biol 2015; 427:3258-3272. [DOI: 10.1016/j.jmb.2015.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/11/2015] [Accepted: 06/17/2015] [Indexed: 11/29/2022]
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16
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Ben-Shimon A, Niv MY. AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking. Structure 2015; 23:929-940. [PMID: 25914054 DOI: 10.1016/j.str.2015.03.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 03/20/2015] [Accepted: 03/22/2015] [Indexed: 12/18/2022]
Abstract
The huge conformational space stemming from the inherent flexibility of peptides is among the main obstacles to successful and efficient computational modeling of protein-peptide interactions. Current peptide docking methods typically overcome this challenge using prior knowledge from the structure of the complex. Here we introduce AnchorDock, a peptide docking approach, which automatically targets the docking search to the most relevant parts of the conformational space. This is done by precomputing the free peptide's structure and by computationally identifying anchoring spots on the protein surface. Next, a free peptide conformation undergoes anchor-driven simulated annealing molecular dynamics simulations around the predicted anchoring spots. In the challenging task of a completely blind docking test, AnchorDock produced exceptionally good results (backbone root-mean-square deviation ≤ 2.2Å, rank ≤15) for 10 of 13 unbound cases tested. The impressive performance of AnchorDock supports a molecular recognition pathway that is driven via pre-existing local structural elements.
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Affiliation(s)
- Avraham Ben-Shimon
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment and The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Rehovot 76100, Israel
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment and The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Rehovot 76100, Israel.
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17
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Li YC, Chang CK, Chang CF, Cheng YH, Fang PJ, Yu T, Chen SC, Li YC, Hsiao CD, Huang TH. Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element. Nucleic Acids Res 2014; 42:8777-88. [PMID: 24990372 PMCID: PMC4117788 DOI: 10.1093/nar/gku572] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein-DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.
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Affiliation(s)
- Yi-Chuan Li
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Ya-Hsin Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Pei-Ju Fang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Tsunai Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Sheng-Chia Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Yi-Ching Li
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Tai-huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC Department of Physics, National Taiwan Normal University, Taipei 116, Taiwan, ROC
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18
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Chemosensory regulation of a HEAT-repeat protein couples aggregation and sporulation in Myxococcus xanthus. J Bacteriol 2014; 196:3160-8. [PMID: 24957622 DOI: 10.1128/jb.01866-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Chemosensory systems are complex, highly modified two-component systems (TCS) used by bacteria to control various biological functions ranging from motility to sporulation. Chemosensory systems and TCS both modulate phosphorelays comprised of histidine kinases and response regulators, some of which are single-domain response regulators (SD-RRs) such as CheY. In this study, we have identified and characterized the Che7 chemosensory system of Myxococcus xanthus, a common soil bacterium which displays multicellular development in response to stress. Both genetic and biochemical analyses indicate that the Che7 system regulates development via a direct interaction between the SD-RR CheY7 and a HEAT repeat domain-containing protein, Cpc7. Phosphorylation of the SD-RR affects the interaction with its target, and residues within the α4-β5-α5 fold of the REC domain govern this interaction. The identification of the Cpc7 interaction with CheY7 extends the diversity of known targets for SD-RRs in biological systems.
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19
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Sircar R, Greenswag AR, Bilwes AM, Gonzalez-Bonet G, Crane BR. Structure and activity of the flagellar rotor protein FliY: a member of the CheC phosphatase family. J Biol Chem 2013; 288:13493-502. [PMID: 23532838 PMCID: PMC3650386 DOI: 10.1074/jbc.m112.445171] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND FliY is a flagellar rotor protein of the CheC phosphatase family. RESULTS The FliY structure resembles that of the rotor protein FliM but contains two active centers for CheY dephosphorylation. CONCLUSION FliY incorporates properties of the FliM/FliN rotor proteins and the CheC/CheX phosphatases to serve multiple functions in the flagellar switch. SIGNIFICANCE FliY distinguishes flagellar architecture and function in different types of bacteria. Rotating flagella propel bacteria toward favorable environments. Sense of rotation is determined by the intracellular response regulator CheY, which when phosphorylated (CheY-P) interacts directly with the flagellar motor. In many different types of bacteria, the CheC/CheX/FliY (CXY) family of phosphatases terminates the CheY-P signal. Unlike CheC and CheX, FliY is localized in the flagellar switch complex, which also contains the stator-coupling protein FliG and the target of CheY-P, FliM. The 2.5 Å resolution crystal structure of the FliY catalytic domain from Thermotoga maritima bears strong resemblance to the middle domain of FliM. Regions of FliM that mediate contacts within the rotor compose the phosphatase active sites in FliY. Despite the similarity between FliY and FliM, FliY does not bind FliG and thus is unlikely to be a substitute for FliM in the center of the switch complex. Solution studies indicate that FliY dimerizes through its C-terminal domains, which resemble the Escherichia coli switch complex component FliN. FliY differs topologically from the E. coli chemotaxis phosphatase CheZ but appears to utilize similar structural motifs for CheY dephosphorylation in close analogy to CheX. Recognition properties and phosphatase activities of site-directed mutants identify two pseudosymmetric active sites in FliY (Glu(35)/Asn(38) and Glu(132)/Asn(135)), with the second site (Glu(132)/Asn(135)) being more active. A putative N-terminal CheY binding domain conserved with FliM is not required for binding CheY-P or phosphatase activity.
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Affiliation(s)
- Ria Sircar
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Anna R. Greenswag
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Alexandrine M. Bilwes
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Gabriela Gonzalez-Bonet
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Brian R. Crane
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, To whom correspondence should be addressed: Dept. of Chemistry and Chemical Biology Cornell University, Ithaca, NY 14850. Tel.: 607-254-8634; E-mail:
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20
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Bauer J, Reiss K, Veerabagu M, Heunemann M, Harter K, Stehle T. Structure-function analysis of Arabidopsis thaliana histidine kinase AHK5 bound to its cognate phosphotransfer protein AHP1. MOLECULAR PLANT 2013; 6:959-970. [PMID: 23132142 DOI: 10.1093/mp/sss126] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The multi-step phosphorelay (MSP) system defines a key signal transduction pathway in plants and many eukaryotes. In this system, external stimuli first lead to the activation of a histidine kinase, followed by transfer of a phosphoryl group from the receiver domain of the kinase (HK(RD)) to downstream, cytosolic phosphotransfer proteins (HPs). In order to establish the determinants of specificity for this signaling relay system, we have solved the first crystal structure of a plant HK(RD), AHK5(RD), in complex with one of its cognate HPs, AHP1. AHP1 binds AHK5(RD) via a prominent hydrogen bond docking ridge and a hydrophobic patch. These features are conserved among all AHP proteins, but differ significantly from other structurally characterized prokaryotic and eukaryotic HPs. Surface plasmon resonance experiments show that AHK5(RD) binds to AHP1-3 with similar, micromolar affinity, consistent with the transient nature of this signaling complex. Our correlation of structural and functional data provide the first insight, at the atomic level as well as with quantitative affinity data, into the molecular recognition events governing the MSP in plants.
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Affiliation(s)
- Johannes Bauer
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076 Tübingen, Germany
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21
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Sheftic SR, Garcia PP, White E, Robinson VL, Gage DJ, Alexandrescu AT. Nuclear magnetic resonance structure and dynamics of the response regulator Sma0114 from Sinorhizobium meliloti. Biochemistry 2012; 51:6932-41. [PMID: 22880754 DOI: 10.1021/bi300922z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Receiver domains control intracellular responses triggered by signal transduction in bacterial two-component systems. Here, we report the solution nuclear magnetic resonance structure and dynamics of Sma0114 from the bacterium Sinorhizobium meliloti, the first such characterization of a receiver domain from the HWE-kinase family of two-component systems. The structure of Sma0114 adopts a prototypical α(5)/β(5) Rossman fold but has features that set it apart from other receiver domains. The fourth β-strand of Sma0114 houses a PFxFATGY sequence motif, common to many HWE-kinase-associated receiver domains. This sequence motif in Sma0114 may substitute for the conserved Y-T coupling mechanism, which propagates conformational transitions in the 455 (α4-β5-α5) faces of receiver domains, to prime them for binding downstream effectors once they become activated by phosphorylation. In addition, the fourth α-helix of the consensus 455 face in Sma0114 is replaced with a segment that shows high flexibility on the pico- to nanosecond time scale by (15)N relaxation data. Secondary structure prediction analysis suggests that the absence of helix α4 may be a conserved property of the HWE-kinase-associated family of receiver domains to which Sma0114 belongs. In spite of these differences, Sma0114 has a conserved active site, binds divalent metal ions such as Mg(2+) and Ca(2+) that are required for phosphorylation, and exhibits micro- to millisecond active-site dynamics similar to those of other receiver domains. Taken together, our results suggest that Sma0114 has a conserved active site but differs from typical receiver domains in the structure of the 455 face that is used to effect signal transduction following activation.
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Affiliation(s)
- Sarah R Sheftic
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT 06269, USA
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22
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McDonald LR, Boyer JA, Lee AL. Segmental motions, not a two-state concerted switch, underlie allostery in CheY. Structure 2012; 20:1363-73. [PMID: 22727815 PMCID: PMC3552614 DOI: 10.1016/j.str.2012.05.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 05/11/2012] [Accepted: 05/12/2012] [Indexed: 11/30/2022]
Abstract
The switch between an inactive and active conformation is an important transition for signaling proteins, yet the mechanisms underlying such switches are not clearly understood. Escherichia coli CheY, a response regulator protein from the two-component signal transduction system that regulates bacterial chemotaxis, is an ideal protein for the study of allosteric mechanisms. By using 15N CPMG relaxation dispersion experiments, we monitored the inherent dynamic switching of unphosphorylated CheY. We show that CheY does not undergo a two-state concerted switch between the inactive and active conformations. Interestingly, partial saturation of Mg2+ enhances the intrinsic allosteric motions. Taken together with chemical shift perturbations, these data indicate that the μs-ms timescale motions underlying CheY allostery are segmental in nature. We propose an expanded allosteric network of residues, including W58, that undergo asynchronous, local switching between inactive and active-like conformations as the primary basis for the allosteric mechanism.
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Affiliation(s)
- Leanna R McDonald
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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23
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Sinorhizobium meliloti CheA complexed with CheS exhibits enhanced binding to CheY1, resulting in accelerated CheY1 dephosphorylation. J Bacteriol 2011; 194:1075-87. [PMID: 22194454 DOI: 10.1128/jb.06505-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Retrophosphorylation of the histidine kinase CheA in the chemosensory transduction chain is a widespread mechanism for efficient dephosphorylation of the activated response regulator. First discovered in Sinorhizobium meliloti, the main response regulator CheY2-P shuttles its phosphoryl group back to CheA, while a second response regulator, CheY1, serves as a sink for surplus phosphoryl groups from CheA-P. We have identified a new component in this phospho-relay system, a small 97-amino-acid protein named CheS. CheS has no counterpart in enteric bacteria but revealed distinct similarities to proteins of unknown function in other members of the α subgroup of proteobacteria. Deletion of cheS causes a phenotype similar to that of a cheY1 deletion strain. Fluorescence microscopy revealed that CheS is part of the polar chemosensory cluster and that its cellular localization is dependent on the presence of CheA. In vitro binding, as well as coexpression and copurification studies, gave evidence of CheA/CheS complex formation. Using limited proteolysis coupled with mass spectrometric analyses, we defined CheA(163-256) to be the CheS binding domain, which overlaps with the N-terminal part of the CheY2 binding domain (CheA(174-316)). Phosphotransfer experiments using isolated CheA-P showed that dephosphorylation of CheY1-P but not CheY2-P is increased in the presence of CheS. As determined by surface plasmon resonance spectroscopy, CheY1 binds ∼100-fold more strongly to CheA/CheS than to CheA. We propose that CheS facilitates signal termination by enhancing the interaction of CheY1 and CheA, thereby promoting CheY1-P dephosphorylation, which results in a more efficient drainage of the phosphate sink.
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Pekárová B, Klumpler T, Třísková O, Horák J, Jansen S, Dopitová R, Borkovcová P, Papoušková V, Nejedlá E, Sklenář V, Marek J, Zídek L, Hejátko J, Janda L. Structure and binding specificity of the receiver domain of sensor histidine kinase CKI1 from Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:827-839. [PMID: 21569135 DOI: 10.1111/j.1365-313x.2011.04637.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Multistep phosphorelay (MSP) signaling mediates responses to a variety of important stimuli in plants. In Arabidopsis MSP, the signal is transferred from sensor histidine kinase (HK) via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. In contrast to ancestral two-component signaling in bacteria, protein interactions in plant MSP are supposed to be rather nonspecific. Here, we show that the C-terminal receiver domain of HK CKI1 (CKI1(RD) ) is responsible for the recognition of CKI1 downstream signaling partners, and specifically interacts with AHP2, AHP3 and AHP5 with different affinities. We studied the effects of Mg²⁺, the co-factor necessary for signal transduction via MSP, and phosphorylation-mimicking BeF₃⁻ on CKI1(RD) in solution, and determined the crystal structure of free CKI1(RD) and CKI1(RD) in a complex with Mg²⁺. We found that the structure of CKI1(RD) shares similarities with the only known structure of plant HK, ETR1(RD) , with the main differences being in loop L3. Magnesium binding induces the rearrangement of some residues around the active site of CKI1(RD) , as was determined by both X-ray crystallography and NMR spectroscopy. Collectively, these results provide initial insights into the nature of molecular mechanisms determining the specificity of MSP signaling and MSP catalysis in plants.
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Affiliation(s)
- Blanka Pekárová
- Department of Functional Genomics and Proteomics, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic
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25
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Action at a distance: amino acid substitutions that affect binding of the phosphorylated CheY response regulator and catalysis of dephosphorylation can be far from the CheZ phosphatase active site. J Bacteriol 2011; 193:4709-18. [PMID: 21764922 DOI: 10.1128/jb.00070-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two-component regulatory systems, in which phosphorylation controls the activity of a response regulator protein, provide signal transduction in bacteria. For example, the phosphorylated CheY response regulator (CheYp) controls swimming behavior. In Escherichia coli, the chemotaxis phosphatase CheZ stimulates the dephosphorylation of CheYp. CheYp apparently binds first to the C terminus of CheZ and then binds to the active site where dephosphorylation occurs. The phosphatase activity of the CheZ(2) dimer exhibits a positively cooperative dependence on CheYp concentration, apparently because the binding of the first CheYp to CheZ(2) is inhibited compared to the binding of the second CheYp. Thus, CheZ phosphatase activity is reduced at low CheYp concentrations. The CheZ21IT gain-of-function substitution, located far from either the CheZ active site or C-terminal CheY binding site, enhances CheYp binding and abolishes cooperativity. To further explore mechanisms regulating CheZ activity, we isolated 10 intragenic suppressor mutations of cheZ21IT that restored chemotaxis. The suppressor substitutions were located along the central portion of CheZ and were not allele specific. Five suppressor mutants tested biochemically diminished the binding of CheYp and/or the catalysis of dephosphorylation, even when the suppressor substitutions were distant from the active site. One suppressor mutant also restored cooperativity to CheZ21IT. Consideration of results from this and previous studies suggests that the binding of CheYp to the CheZ active site (not to the C terminus) is rate limiting and leads to cooperative phosphatase activity. Furthermore, amino acid substitutions distant from the active site can affect CheZ catalytic activity and CheYp binding, perhaps via the propagation of structural or dynamic perturbations through a helical bundle.
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26
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Raveh B, London N, Zimmerman L, Schueler-Furman O. Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS One 2011; 6:e18934. [PMID: 21572516 PMCID: PMC3084719 DOI: 10.1371/journal.pone.0018934] [Citation(s) in RCA: 211] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Accepted: 03/12/2011] [Indexed: 11/18/2022] Open
Abstract
Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions.
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Affiliation(s)
- Barak Raveh
- Department of Microbiology and Molecular Genetics, Hadassah Medical School, Institute for Medical Research Israel-Canada, The Hebrew University, Jerusalem, Israel
- The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Nir London
- Department of Microbiology and Molecular Genetics, Hadassah Medical School, Institute for Medical Research Israel-Canada, The Hebrew University, Jerusalem, Israel
| | - Lior Zimmerman
- Department of Microbiology and Molecular Genetics, Hadassah Medical School, Institute for Medical Research Israel-Canada, The Hebrew University, Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Hadassah Medical School, Institute for Medical Research Israel-Canada, The Hebrew University, Jerusalem, Israel
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27
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Barbieri CM, Mack TR, Robinson VL, Miller MT, Stock AM. Regulation of response regulator autophosphorylation through interdomain contacts. J Biol Chem 2010; 285:32325-35. [PMID: 20702407 PMCID: PMC2952233 DOI: 10.1074/jbc.m110.157164] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 07/29/2010] [Indexed: 11/17/2022] Open
Abstract
DNA-binding response regulators (RRs) of the OmpR/PhoB subfamily alternate between inactive and active conformational states, with the latter having enhanced DNA-binding affinity. Phosphorylation of an aspartate residue in the receiver domain, usually via phosphotransfer from a cognate histidine kinase, stabilizes the active conformation. Many of the available structures of inactive OmpR/PhoB family proteins exhibit extensive interfaces between the N-terminal receiver and C-terminal DNA-binding domains. These interfaces invariably involve the α4-β5-α5 face of the receiver domain, the locus of the largest differences between inactive and active conformations and the surface that mediates dimerization of receiver domains in the active state. Structures of receiver domain dimers of DrrB, DrrD, and MtrA have been determined, and phosphorylation kinetics were analyzed. Analysis of phosphotransfer from small molecule phosphodonors has revealed large differences in autophosphorylation rates among OmpR/PhoB RRs. RRs with substantial domain interfaces exhibit slow rates of phosphorylation. Rates are greatly increased in isolated receiver domain constructs. Such differences are not observed between autophosphorylation rates of full-length and isolated receiver domains of a RR that lacks interdomain interfaces, and they are not observed in histidine kinase-mediated phosphotransfer. These findings suggest that domain interfaces restrict receiver domain conformational dynamics, stabilizing an inactive conformation that is catalytically incompetent for phosphotransfer from small molecule phosphodonors. Inhibition of phosphotransfer by domain interfaces provides an explanation for the observation that some RRs cannot be phosphorylated by small molecule phosphodonors in vitro and provides a potential mechanism for insulating some RRs from small molecule-mediated phosphorylation in vivo.
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Affiliation(s)
- Christopher M. Barbieri
- From the Center for Advanced Biotechnology and Medicine
- the Department of Biochemistry
- the Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635 and
| | - Timothy R. Mack
- From the Center for Advanced Biotechnology and Medicine
- the Department of Biochemistry
- the Graduate School of Biomedical Sciences, and
| | - Victoria L. Robinson
- From the Center for Advanced Biotechnology and Medicine
- the Department of Biochemistry
- the Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635 and
| | - Matthew T. Miller
- From the Center for Advanced Biotechnology and Medicine
- the Department of Chemistry, Rutgers University, Piscataway, New Jersey 08854-8066
| | - Ann M. Stock
- From the Center for Advanced Biotechnology and Medicine
- the Department of Biochemistry
- the Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635 and
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28
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Liarzi O, Barak R, Bronner V, Dines M, Sagi Y, Shainskaya A, Eisenbach M. Acetylation represses the binding of CheY to its target proteins. Mol Microbiol 2010; 76:932-43. [PMID: 20398208 DOI: 10.1111/j.1365-2958.2010.07148.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability of CheY, the response regulator of bacterial chemotaxis, to generate clockwise rotation is regulated by two covalent modifications - phosphorylation and acetylation. While the function and signal propagation of the former are widely understood, the mechanism and role of the latter are still obscure. To obtain information on the function of this acetylation, we non-enzymatically acetylated CheY to a level similar to that found in vivo, and examined its binding to its kinase CheA, its phosphatase CheZ and the switch protein FliM - its target at the flagellar switch complex. Acetylation repressed the binding to all three proteins. These results suggest that both phosphorylation and acetylation determine CheY's ability to bind to its target proteins, thus providing two levels of regulation, fast and slow respectively. The fast level is modulated by environmental signals (e.g. chemotactic and thermotactic stimuli). The slow one is regulated by the metabolic state of the cell and it determines, at each metabolic state, the fraction of CheY molecules that can participate in signalling.
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Affiliation(s)
- Orna Liarzi
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
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29
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Silversmith RE. Auxiliary phosphatases in two-component signal transduction. Curr Opin Microbiol 2010; 13:177-83. [PMID: 20133180 DOI: 10.1016/j.mib.2010.01.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/05/2010] [Accepted: 01/07/2010] [Indexed: 11/18/2022]
Abstract
Signal termination in two-component systems occurs by loss of the phosphoryl group from the response regulator protein. This review explores our current understanding of the structures, catalytic mechanisms and means of regulation of the known families of phosphatases that catalyze response regulator dephosphorylation. The CheZ and CheC/CheX/FliY families, despite different overall structures, employ identical catalytic strategies using an amide side chain to orient a water molecule for in-line attack of the aspartyl phosphate. Spo0E phosphatases contain sequence and structural features that suggest a strategy similar to the chemotaxis phosphatases but the mechanism used by the Rap phosphatases is not yet elucidated. Identification of features shared by phosphatase families may aid in the identification of currently unrecognized classes of response regulator phosphatases.
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Affiliation(s)
- Ruth E Silversmith
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA.
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30
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Mack TR, Gao R, Stock AM. Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB. J Mol Biol 2009; 389:349-64. [PMID: 19371748 DOI: 10.1016/j.jmb.2009.04.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Revised: 04/08/2009] [Accepted: 04/08/2009] [Indexed: 12/28/2022]
Abstract
Structural analysis of the Escherichia coli response regulator transcription factor PhoB indicates that the protein dimerizes in two different orientations that are both mediated by the receiver domain. The two dimers exhibit 2-fold rotational symmetry: one involves the alpha 4-beta 5-alpha 5 surface and the other involves the alpha1/alpha 5 surface. The alpha 4-beta 5-alpha 5 dimer is observed when the protein is crystallized in the presence of the phosphoryl analog BeF(3)(-), while the alpha1/alpha 5 dimer is observed in its absence. From these studies, a model of the inactive and active states of PhoB has been proposed that involves the formation of two distinct dimers. In order to gain further insight into the roles of these dimers, we have engineered a series of mutations in PhoB intended to perturb each of them selectively. Our results indicate that perturbation of the alpha 4-beta 5-alpha 5 surface disrupts phosphorylation-dependent dimerization and DNA binding as well as PhoB-mediated transcriptional activation of phoA, while perturbations to the alpha1/alpha 5 surface do not. Furthermore, experiments with a GCN4 leucine zipper/PhoB chimera protein indicate that PhoB is activated through an intermolecular mechanism. Together, these results support a model of activation of PhoB in which phosphorylation promotes dimerization via the alpha 4-beta 5-alpha 5 face, which enhances DNA binding and thus the ability of PhoB to regulate transcription.
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Affiliation(s)
- Timothy R Mack
- Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854, USA
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31
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McAdams K, Casper ES, Matthew Haas R, Santarsiero BD, Eggler AL, Mesecar A, Halkides CJ. The structures of T87I phosphono-CheY and T87I/Y106W phosphono-CheY help to explain their binding affinities to the FliM and CheZ peptides. Arch Biochem Biophys 2008; 479:105-13. [PMID: 18801331 DOI: 10.1016/j.abb.2008.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 08/19/2008] [Accepted: 08/20/2008] [Indexed: 10/21/2022]
Abstract
CheY is a response regulator in bacterial chemotaxis. Escherichia coli CheY mutants T87I and T87I/Y106W CheY are phosphorylatable on Asp57 but unable to generate clockwise rotation of the flagella. To understand this phenotype in terms of structure, stable analogs of the two CheY-P mutants were synthesized: T87I phosphono-CheY and T87I phosphono-CheY. Dissociation constants for peptides derived from flagellar motor protein FliM and phosphatase CheZ were determined for phosphono-CheY and the two mutants. The peptides bind phosphono-CheY almost as strongly as CheY-P; however, they do not bind T87I phosphono-CheY or T87I/Y106W phosphono-CheY, implying that the mutant proteins cannot bind FliM or CheZ tightly in vivo. The structures of T87I phosphono-CheY and T87I/Y106W phosphono-CheY were solved to resolutions of 1.8 and 2.4A, respectively. The increased bulk of I87 forces the side-chain of Y106 or W106, into a more solvent-accessible conformation, which occludes the peptide-binding site.
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Affiliation(s)
- Kenneth McAdams
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC 28403, USA
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32
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Diaz AR, Stephenson S, Green JM, Levdikov VM, Wilkinson AJ, Perego M. Functional Role for a Conserved Aspartate in the Spo0E Signature Motif Involved in the Dephosphorylation of the Bacillus subtilis Sporulation Regulator Spo0A. J Biol Chem 2008; 283:2962-72. [DOI: 10.1074/jbc.m709032200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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33
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Silversmith RE, Levin MD, Schilling E, Bourret RB. Kinetic Characterization of Catalysis by the Chemotaxis Phosphatase CheZ. J Biol Chem 2008; 283:756-65. [DOI: 10.1074/jbc.m704400200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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34
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Abstract
Chemotaxis, a means for motile bacteria to sense the environment and achieve directed swimming, is controlled by flagellar rotation. The primary output of the chemotaxis machinery is the phosphorylated form of the response regulator CheY (P-CheY). The steady-state level of P-CheY dictates the direction of rotation of the flagellar motor. The chemotaxis signal in the form of P-CheY is terminated by the phosphatase CheZ. Efficient dephosphorylation of CheY by CheZ requires two distinct protein-protein interfaces: one involving the strongly conserved C-terminal helix of CheZ (CheZ(C)) tethering the two proteins together and the other constituting an active site for catalytic dephosphorylation. In a previous work (J. Guhaniyogi, V. L. Robinson, and A. M. Stock, J. Mol. Biol. 359:624-645, 2006), we presented high-resolution crystal structures of CheY in complex with the CheZ(C) peptide that revealed alternate binding modes subject to the conformational state of CheY. In this study, we report biochemical and structural data that support the alternate-binding-mode hypothesis and identify key recognition elements in the CheY-CheZ(C) interaction. In addition, we present kinetic studies of the CheZ(C)-associated effect on CheY phosphorylation with its physiologically relevant phosphodonor, the histidine kinase CheA. Our results indicate mechanistic differences in phosphotransfer from the kinase CheA versus that from small-molecule phosphodonors, explaining a modest twofold increase of CheY phosphorylation with the former, observed in this study, relative to a 10-fold increase previously documented with the latter.
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35
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Fraser JS, Merlie JP, Echols N, Weisfield SR, Mignot T, Wemmer DE, Zusman DR, Alber T. An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS. Mol Microbiol 2007; 65:319-32. [PMID: 17573816 PMCID: PMC1974792 DOI: 10.1111/j.1365-2958.2007.05785.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Myxococcus xanthus FrzS protein transits from pole-to-pole within the cell, accumulating at the pole that defines the direction of movement in social (S) motility. Here we show using atomic-resolution crystallography and NMR that the FrzS receiver domain (RD) displays the conserved switch Tyr102 in an unusual conformation, lacks the conserved Asp phosphorylation site, and fails to bind Mg(2+) or the phosphoryl analogue, Mg(2+) x BeF(3). Mutation of Asp55, closest to the canonical site of RD phosphorylation, showed no motility phenotype in vivo, demonstrating that phosphorylation at this site is not necessary for domain function. In contrast, the Tyr102Ala and His92Phe substitutions on the canonical output face of the FrzS RD abolished S-motility in vivo. Single-cell fluorescence microscopy measurements revealed a striking mislocalization of these mutant FrzS proteins to the trailing cell pole in vivo. The crystal structures of the mutants suggested that the observed conformation of Tyr102 in the wild-type FrzS RD is not sufficient for function. These results support the model that FrzS contains a novel 'pseudo-receiver domain' whose function requires recognition of the RD output face but not Asp phosphorylation.
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Affiliation(s)
- James S Fraser
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA 94720-3320, USA.
- *For correspondence. E-mail ; Tel. (+1) 510 642 8758; Fax (+1) 510 643 9290
| | - John P Merlie
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA 94720-3320, USA.
| | - Nathaniel Echols
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA 94720-3320, USA.
| | - Shellie R Weisfield
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA 94720-3320, USA.
| | - Tâm Mignot
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA 94720-3320, USA.
| | - David E Wemmer
- Department of Chemistry, University of California and Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA 94720-1460, USA.
| | - David R Zusman
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA 94720-3320, USA.
| | - Tom Alber
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA 94720-3320, USA.
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36
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Gao R, Mack TR, Stock AM. Bacterial response regulators: versatile regulatory strategies from common domains. Trends Biochem Sci 2007; 32:225-34. [PMID: 17433693 PMCID: PMC3655528 DOI: 10.1016/j.tibs.2007.03.002] [Citation(s) in RCA: 246] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 02/07/2007] [Accepted: 03/15/2007] [Indexed: 01/29/2023]
Abstract
Response regulators (RRs) comprise a major family of signaling proteins in prokaryotes. A modular architecture that consists of a conserved receiver domain and a variable effector domain enables RRs to function as phosphorylation-regulated switches that couple a wide variety of cellular behaviors to environmental cues. Recently, advances have been made in understanding RR functions both at genome-wide and molecular levels. Global techniques have been developed to analyze RR input and output, expanding the scope of characterization of these versatile components. Meanwhile, structural studies have revealed that, despite common structures and mechanisms of function within individual domains, a range of interactions between receiver and effector domains confer great diversity in regulatory strategies, optimizing individual RRs for the specific regulatory needs of different signaling systems.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Howard Hughes Medical Institute, Piscataway, NJ 08854, USA
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37
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Affiliation(s)
- Ann M Stock
- Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854-5627, USA.
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38
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Musial-Siwek M, Rusch SL, Kendall DA. Selective photoaffinity labeling identifies the signal peptide binding domain on SecA. J Mol Biol 2006; 365:637-48. [PMID: 17084862 PMCID: PMC1851904 DOI: 10.1016/j.jmb.2006.10.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Revised: 10/02/2006] [Accepted: 10/08/2006] [Indexed: 11/26/2022]
Abstract
SecA, an ATPase crucial to the Sec-dependent translocation machinery in Escherichia coli, recognizes and directly binds the N-terminal signal peptide of an exported preprotein. This interaction plays a central role in the targeting and transport of preproteins via the SecYEG channel. Here we identify the signal peptide binding groove (SPBG) on SecA addressing a key issue regarding the SecA-preprotein interaction. We employ a synthetic signal peptide containing the photoreactive benzoylphenylalanine to efficiently and specifically label SecA containing a unique Factor Xa site. Comparison of the photolabeled fragment from the subsequent proteolysis of several SecAs, which vary only in the location of the Factor Xa site, reveals one 53 residue segment in common with the entire series. The covalently modified SecA segment produced is the same in aqueous solution and in lipid vesicles. This spans amino acid residues 269 to 322 of the E. coli protein, which is distinct from a previously proposed signal peptide binding site, and contributes to a hydrophobic peptide binding groove evident in molecular models of SecA.
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Affiliation(s)
| | | | - Debra A. Kendall
- *Corresponding author. Department of Molecular and Cell Biology, 91 North Eagleville Road, University of Connecticut, Storrs, Connecticut 06269-3125, USA; Tel.: (860) 486-1891; Fax: (860) 486-4331; E-mail: ()
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39
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Dyer CM, Dahlquist FW. Switched or not?: the structure of unphosphorylated CheY bound to the N terminus of FliM. J Bacteriol 2006; 188:7354-63. [PMID: 17050923 PMCID: PMC1636273 DOI: 10.1128/jb.00637-06] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 07/26/2006] [Indexed: 11/20/2022] Open
Abstract
Phosphorylation of Escherichia coli CheY increases its affinity for its target, FliM, 20-fold. The interaction between BeF(3)(-)-CheY, a phosphorylated CheY (CheY approximately P) analog, and the FliM sequence that it binds has been described previously in molecular detail. Although the conformation that unphosphorylated CheY adopts in complex with FliM was unknown, some evidence suggested that it is similar to that of CheY approximately P. To resolve the issue, we have solved the crystallographic structure of unphosphorylated, magnesium(II)-bound CheY in complex with a synthetic peptide corresponding to the target region of FliM (the 16 N-terminal residues of FliM [FliM(16)]). While the peptide conformation and binding site are similar to those of the BeF(3)(-)-CheY-FliM(16) complex, the inactive CheY conformation is largely retained in the unphosphorylated Mg(2+)-CheY-FliM(16) complex. Communication between the target binding site and the phosphorylation site, observed previously in biochemical experiments, is enabled by a network of conserved side chain interactions that partially mimic those observed in BeF(3)(-)-activated CheY. This structure makes clear the active role that the beta4-alpha4 loop plays in the Tyr(87)-Tyr(106) coupling mechanism that enables allosteric communication between the phosphorylation site and the target binding surface. Additionally, this structure provides a high-resolution view of an intermediate conformation of a response regulator protein, which had been generally assumed to be two state.
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Affiliation(s)
- Collin M Dyer
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, 93106, USA
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