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De Bruyn P, Prolič-Kalinšek M, Vandervelde A, Malfait M, Sterckx YGJ, Sobott F, Hadži S, Pardon E, Steyaert J, Loris R. Nanobody-aided crystallization of the transcription regulator PaaR2 from Escherichia coli O157:H7. Acta Crystallogr F Struct Biol Commun 2021; 77:374-384. [PMID: 34605442 PMCID: PMC8488858 DOI: 10.1107/s2053230x21009006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 08/30/2021] [Indexed: 11/10/2022] Open
Abstract
paaR2-paaA2-parE2 is a three-component toxin-antitoxin module found in prophage CP-993P of Escherichia coli O157:H7. Transcription regulation of this module occurs via the 123-amino-acid regulator PaaR2, which forms a large oligomeric structure. Despite appearing to be well folded, PaaR2 withstands crystallization, as does its N-terminal DNA-binding domain. Native mass spectrometry was used to screen for nanobodies that form a unique complex and stabilize the octameric structure of PaaR2. One such nanobody, Nb33, allowed crystallization of the protein. The resulting crystals belong to space group F432, with unit-cell parameter a = 317 Å, diffract to 4.0 Å resolution and are likely to contain four PaaR2 monomers and four nanobody monomers in the asymmetric unit. Crystals of two truncates containing the N-terminal helix-turn-helix domain also interact with Nb33, and the corresponding co-crystals diffracted to 1.6 and 1.75 Å resolution.
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Affiliation(s)
- Pieter De Bruyn
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Maruša Prolič-Kalinšek
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexandra Vandervelde
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Milan Malfait
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Yann G.-J. Sterckx
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
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2
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Madigan JP, Hou F, Ye L, Hu J, Dong A, Tempel W, Yohe ME, Randazzo PA, Jenkins LMM, Gottesman MM, Tong Y. The tuberous sclerosis complex subunit TBC1D7 is stabilized by Akt phosphorylation-mediated 14-3-3 binding. J Biol Chem 2018; 293:16142-16159. [PMID: 30143532 DOI: 10.1074/jbc.ra118.003525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/13/2018] [Indexed: 01/19/2023] Open
Abstract
The tuberous sclerosis complex (TSC) is a negative regulator of mTOR complex 1, a signaling node promoting cellular growth in response to various nutrients and growth factors. However, several regulators in TSC signaling still await discovery and characterization. Using pulldown and MS approaches, here we identified the TSC complex member, TBC1 domain family member 7 (TBC1D7), as a binding partner for PH domain and leucine-rich repeat protein phosphatase 1 (PHLPP1), a negative regulator of Akt kinase signaling. Most TBC domain-containing proteins function as Rab GTPase-activating proteins (RabGAPs), but the crystal structure of TBC1D7 revealed that it lacks residues critical for RabGAP activity. Sequence analysis identified a putative site for both Akt-mediated phosphorylation and 14-3-3 binding at Ser-124, and we found that Akt phosphorylates TBC1D7 at Ser-124. However, this phosphorylation had no effect on the binding of TBC1D7 to TSC1, but stabilized TBC1D7. Moreover, 14-3-3 protein both bound and stabilized TBC1D7 in a growth factor-dependent manner, and a phospho-deficient substitution, S124A, prevented this interaction. The crystal structure of 14-3-3ζ in complex with a phospho-Ser-124 TBC1D7 peptide confirmed the direct interaction between 14-3-3 and TBC1D7. The sequence immediately upstream of Ser-124 aligned with a canonical β-TrCP degron, and we found that the E3 ubiquitin ligase β-TrCP2 ubiquitinates TBC1D7 and decreases its stability. Our findings reveal that Akt activity determines the phosphorylation status of TBC1D7 at the phospho-switch Ser-124, which governs binding to either 14-3-3 or β-TrCP2, resulting in increased or decreased stability of TBC1D7, respectively.
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Affiliation(s)
| | - Feng Hou
- the Structural Genomics Consortium and
| | - Linlei Ye
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada, and
| | | | | | | | | | - Paul A Randazzo
- Laboratory of Cell and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | | | | | - Yufeng Tong
- the Structural Genomics Consortium and .,the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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Luo Z, Pederick VG, Paton JC, McDevitt CA, Kobe B. Structural characterisation of the HT3 motif of the polyhistidine triad protein D from Streptococcus pneumoniae. FEBS Lett 2018; 592:2341-2350. [PMID: 29856892 DOI: 10.1002/1873-3468.13122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 01/12/2023]
Abstract
The bacterium Streptococcus pneumoniae (the pneumococcus) is a major human pathogen that requires Zn2+ for its survival and virulence in the host environment. Polyhistidine triad protein D (PhtD) has a known role in pneumococcal Zn2+ homeostasis. However, the mechanistic basis of PhtD function remains unclear, partly due to a lack of structural information. Here, we determined the crystal structure of the fragment PhtD269-339 , containing the third Zn2+ -binding histidine triad (HT) motif of the protein. Analysis of the structure suggests that Zn2+ binding occurs at the surface of the protein and that all five HT motifs in the protein bind Zn2+ and share similar structures. These new structural insights aid in our understanding of how the Pht proteins facilitate pneumococcal Zn2+ acquisition.
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Affiliation(s)
- Zhenyao Luo
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Victoria G Pederick
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
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New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins. Sci Rep 2015; 5:15660. [PMID: 26489670 PMCID: PMC4614863 DOI: 10.1038/srep15660] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/29/2015] [Indexed: 02/08/2023] Open
Abstract
Roquins are a family of highly conserved RNA-binding proteins that also contain a RING-type E3 ubiquitin ligase domain. They repress constitutive decay elements containing mRNAs and play a critical role in RNA homeostasis and immunological self-tolerance. Here we present the crystal structures of the RNA-binding region of Roquin paralog RC3H2 in both apo- and RNA-bound forms. The RNA-binding region has a bipartite architecture composed of ROQ and HEPN domains, and can bind to stem-loop and double-stranded RNAs simultaneously. The two domains undergo a large orientation change to accommodate RNA duplex binding. We profiled E2 ubiquitin-conjugating enzymes that pair with Roquins and found that RC3H1 and RC3H2 interact with two sets of overlapping but not identical E2 enzymes to drive the assembly of polyubiquitin chains of different linkages. Crystal structures, small-angle X-ray scattering, and E2 profiling revealed that while the two paralogs are highly homologous, RC3H2 and RC3H1 are different in their structures and functions. We also demonstrated that RNA duplex binding to RC3H2 cross-talks with its E3 ubiquitin ligase function using an in vitro auto-ubiquitination assay.
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