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Ince S, Zhang P, Kutsch M, Krenczyk O, Shydlovskyi S, Herrmann C. Catalytic activity of human guanylate-binding protein 1 coupled to the release of structural restraints imposed by the C-terminal domain. FEBS J 2020; 288:582-599. [PMID: 32352209 DOI: 10.1111/febs.15348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/10/2020] [Accepted: 04/27/2020] [Indexed: 12/21/2022]
Abstract
Human guanylate-binding protein 1 (hGBP-1) shows a dimer-induced acceleration of the GTPase activity yielding GDP as well as GMP. While the head-to-head dimerization of the large GTPase (LG) domain is well understood, the role of the rest of the protein, particularly of the GTPase effector domain (GED), in dimerization and GTP hydrolysis is still obscure. In this study, with truncations and point mutations on hGBP-1 and by means of biochemical and biophysical methods, we demonstrate that the intramolecular communication between the LG domain and the GED (LG:GED) is crucial for protein dimerization and dimer-stimulated GTP hydrolysis. In the course of GTP binding and γ-phosphate cleavage, conformational changes within hGBP-1 are controlled by a chain of amino acids ranging from the region near the nucleotide-binding pocket to the distant LG:GED interface and lead to the release of the GED from the LG domain. This opening of the structure allows the protein to form GED:GED contacts within the dimer, in addition to the established LG:LG interface. After releasing the cleaved γ-phosphate, the dimer either dissociates yielding GDP as the final product or it stays dimeric to further cleave the β-phosphate yielding GMP. The second phosphate cleavage step, that is, the formation of GMP, is even more strongly coupled to structural changes and thus more sensitive to structural restraints imposed by the GED. Altogether, we depict a comprehensive mechanism of GTP hydrolysis catalyzed by hGBP-1, which provides a detailed molecular understanding of the enzymatic activity connected to large structural rearrangements of the protein. DATABASE: Structural data are available in RCSB Protein Data Bank under the accession numbers: 1F5N, 1DG3, 2B92.
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Affiliation(s)
- Semra Ince
- Physical Chemistry I, Ruhr-University, Bochum, Germany
| | - Ping Zhang
- Physical Chemistry I, Ruhr-University, Bochum, Germany
| | - Miriam Kutsch
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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Zhong X, Arnolds O, Krenczyk O, Gajewski J, Pütz S, Herrmann C, Stoll R. The Structure in Solution of Fibronectin Type III Domain 14 Reveals Its Synergistic Heparin Binding Site. Biochemistry 2018; 57:6045-6049. [PMID: 30260627 DOI: 10.1021/acs.biochem.8b00771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fibronectin is a large multidomain protein of the extracellular matrix that harbors two heparin binding sites, Hep-I and Hep-II, which support the heparin-dependent adhesion of melanoma and neuroblastoma cells [Barkalow, F. J. B., and Schwarzbauer, J. E. (1991) J. Biol. Chem. 266, 7812-7818; McCarthy, J. B., et al. (1988) Biochemistry 27, 1380-1388; Drake, S. L., et al. (1993) J. Biol. Chem. 268, 15859-15867]. The stronger heparin/HS binding site on fibronectin, Hep-II, spans fibronectin type III domains 12-14. Previous site-directed mutagenesis, nuclear magnetic resonance (NMR) chemical shift perturbation, and crystallographic structural studies all agree that the main heparin binding site is located on the surface of fibronectin type III domain 13 [Ingham, K. C., et al. (1993) Biochemistry 32, 12548-12553; Sharma, A., et al. (1999) EMBO J. 18, 1468-1479; Sachchidanand, L. O., et al. (2002) J. Biol. Chem. 277, 50629-50635]. However, the "synergy site" for heparin binding located on fibronectin type III domain 14 remained elusive because the actual binding sites could not be identified. Using NMR spectroscopy and isothermal titration calorimetry, we show here that heparin is able to bind to a cationic 'cradle' of fibronectin type III domain 14 formed by the PRARI sequence, which is involved in the integrin α4β1 interaction [Mould, A. P., and Humphries, M. J. (1991) EMBO J. 10, 4089-4095], and to the flexible loop comprising residues KNNQKSE between the last two β-strands, D and E, of FN14. Our data reveal that the individual FN14 domain binds to the sulfated sugars Dp8 and Reviparin with affinities similar to those of the individual domain FN13 [Breddin, H. K. (2002) Expert Opin. Pharmacother. 3, 173-182]. It is noteworthy that by introduction of the last β-strand of FN13 and the linker region between FN type III domains 13 and 14, the perturbation of NMR chemical shifts by heparin is significantly reduced, especially at the PRARI site. This indicates that the Hep-II binding site of fibronectin is mainly located on FN13 and the synergistic binding site on FN14 involves only the KNNQKSE sequence.
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Affiliation(s)
- Xueyin Zhong
- Ruhr-University of Bochum , Faculty of Chemistry and Biochemistry, Biomolecular NMR , Bochum 44780 , Germany
| | - Oliver Arnolds
- Ruhr-University of Bochum , Faculty of Chemistry and Biochemistry, Biomolecular NMR , Bochum 44780 , Germany
| | - Oktavian Krenczyk
- Ruhr-University of Bochum , Faculty of Chemistry and Biochemistry, Physical Chemistry I , Bochum 44780 , Germany
| | - Jana Gajewski
- Ruhr-University of Bochum , Faculty of Chemistry and Biochemistry, Biomolecular NMR , Bochum 44780 , Germany
| | - Stefanie Pütz
- Ruhr-University of Bochum , Faculty of Chemistry and Biochemistry, Biomolecular NMR , Bochum 44780 , Germany
| | - Christian Herrmann
- Ruhr-University of Bochum , Faculty of Chemistry and Biochemistry, Physical Chemistry I , Bochum 44780 , Germany
| | - Raphael Stoll
- Ruhr-University of Bochum , Faculty of Chemistry and Biochemistry, Biomolecular NMR , Bochum 44780 , Germany
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Dirkmann M, Iglesias-Fernández J, Muñoz V, Sokkar P, Rumancev C, von Gundlach A, Krenczyk O, Vöpel T, Nowack J, Schroer MA, Ebbinghaus S, Herrmann C, Rosenhahn A, Sanchez-Garcia E, Schulz F. A Multiperspective Approach to Solvent Regulation of Enzymatic Activity: HMG-CoA Reductase. Chembiochem 2017; 19:153-158. [PMID: 29139594 DOI: 10.1002/cbic.201700596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Indexed: 12/20/2022]
Abstract
3-Hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase was investigated in different organic cosolvents by means of kinetic and calorimetric measurements, molecular dynamics simulations, and small-angle X-ray scattering. The combined experimental and theoretical techniques were essential to complement each other's limitations in the investigation of the complex interaction pattern between the enzyme, different solvent types, and concentrations. In this way, the underlying mechanisms for the loss of enzyme activity in different water-miscible solvents could be elucidated. These include direct inhibitory effects onto the active center and structural distortions.
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Affiliation(s)
- Michael Dirkmann
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Javier Iglesias-Fernández
- Theoretische Chemie, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Fakultät für Biologie, Universität Duisburg-Essen, 45141, Essen, Germany
| | - Victor Muñoz
- Theoretische Chemie, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Fakultät für Biologie, Universität Duisburg-Essen, 45141, Essen, Germany
| | - Pandian Sokkar
- Theoretische Chemie, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Fakultät für Biologie, Universität Duisburg-Essen, 45141, Essen, Germany
| | - Christoph Rumancev
- Fakultät für Chemie und Biochemie, Physikalische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Andreas von Gundlach
- Fakultät für Chemie und Biochemie, Analytische Chemie-Biogrenzflächen, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Oktavian Krenczyk
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Tobias Vöpel
- Fakultät für Chemie und Biochemie, Physikalische Chemie II, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Julia Nowack
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Martin A Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Simon Ebbinghaus
- Fakultät für Chemie und Biochemie, Physikalische Chemie II, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Christian Herrmann
- Fakultät für Chemie und Biochemie, Physikalische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Axel Rosenhahn
- Fakultät für Chemie und Biochemie, Analytische Chemie-Biogrenzflächen, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
| | - Elsa Sanchez-Garcia
- Theoretische Chemie, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Fakultät für Biologie, Universität Duisburg-Essen, 45141, Essen, Germany
| | - Frank Schulz
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany
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