1
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Canals A, Pieretti S, Muriel-Masanes M, El Yaman N, Plecha SC, Thomson JJ, Fàbrega-Ferrer M, Pérez-Luque R, Krukonis ES, Coll M. ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites. Proc Natl Acad Sci U S A 2023; 120:e2304378120. [PMID: 37428913 PMCID: PMC10629549 DOI: 10.1073/pnas.2304378120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/31/2023] [Indexed: 07/12/2023] Open
Abstract
ToxR, a Vibrio cholerae transmembrane one-component signal transduction factor, lies within a regulatory cascade that results in the expression of ToxT, toxin coregulated pilus, and cholera toxin. While ToxR has been extensively studied for its ability to activate or repress various genes in V. cholerae, here we present the crystal structures of the ToxR cytoplasmic domain bound to DNA at the toxT and ompU promoters. The structures confirm some predicted interactions, yet reveal other unexpected promoter interactions with implications for other potential regulatory roles for ToxR. We show that ToxR is a versatile virulence regulator that recognizes diverse and extensive, eukaryotic-like regulatory DNA sequences, that relies more on DNA structural elements than specific sequences for binding. Using this topological DNA recognition mechanism, ToxR can bind both in tandem and in a twofold inverted-repeat-driven manner. Its regulatory action is based on coordinated multiple binding to promoter regions near the transcription start site, which can remove the repressing H-NS proteins and prepares the DNA for optimal interaction with the RNA polymerase.
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Affiliation(s)
- Albert Canals
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028Barcelona, Spain
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, 08028Barcelona, Spain
| | - Simone Pieretti
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028Barcelona, Spain
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, 08028Barcelona, Spain
| | - Mireia Muriel-Masanes
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028Barcelona, Spain
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, 08028Barcelona, Spain
| | - Nour El Yaman
- Department of Biology, University of Detroit Mercy, Detroit, MI48221
| | - Sarah C. Plecha
- Division of Integrated Biomedical Sciences, University of Detroit Mercy School of Dentistry, Detroit, MI48208
| | - Joshua J. Thomson
- Division of Integrated Biomedical Sciences, University of Detroit Mercy School of Dentistry, Detroit, MI48208
| | - Montserrat Fàbrega-Ferrer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028Barcelona, Spain
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, 08028Barcelona, Spain
| | - Rosa Pérez-Luque
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028Barcelona, Spain
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, 08028Barcelona, Spain
| | - Eric S. Krukonis
- Division of Integrated Biomedical Sciences, University of Detroit Mercy School of Dentistry, Detroit, MI48208
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028Barcelona, Spain
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, 08028Barcelona, Spain
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2
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Fàbrega-Ferrer M, Cuervo A, Fernández FJ, Machón C, Pérez-Luque R, Pous J, Vega MC, Carrascosa JL, Coll M. Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure. Acta Crystallogr D Struct Biol 2021; 77:11-18. [PMID: 33404521 PMCID: PMC7787105 DOI: 10.1107/s2059798320015156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/13/2020] [Indexed: 11/21/2022] Open
Abstract
Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement.
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Affiliation(s)
- Montserrat Fàbrega-Ferrer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Ana Cuervo
- Centro Nacional de Biotecnología (CNB–CSIC), Darwin 3, 28049 Madrid, Spain
| | - Francisco J. Fernández
- Centro de Investigaciones Biológicas (CIB–CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - M. Cristina Vega
- Centro de Investigaciones Biológicas (CIB–CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José L. Carrascosa
- Centro Nacional de Biotecnología (CNB–CSIC), Darwin 3, 28049 Madrid, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
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3
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Vizarraga D, Kawamoto A, Matsumoto U, Illanes R, Pérez-Luque R, Martín J, Mazzolini R, Bierge P, Pich OQ, Espasa M, Sanfeliu I, Esperalba J, Fernández-Huerta M, Scheffer MP, Pinyol J, Frangakis AS, Lluch-Senar M, Mori S, Shibayama K, Kenri T, Kato T, Namba K, Fita I, Miyata M, Aparicio D. Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae. Nat Commun 2020; 11:5188. [PMID: 33057023 PMCID: PMC7560827 DOI: 10.1038/s41467-020-18777-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which form a transmembrane adhesion complex. Here we report the structure of P1, determined by X-ray crystallography and cryo-electron microscopy, and the X-ray structure of P40/P90. Contrary to what had been suggested, the binding site for sialic acid was found in P40/P90 and not in P1. Genetic and clinical variability concentrates on the N-terminal domain surfaces of P1 and P40/P90. Polyclonal antibodies generated against the mostly conserved C-terminal domain of P1 inhibited adhesion of M. pneumoniae, and serology assays with sera from infected patients were positive when tested against this C-terminal domain. P40/P90 also showed strong reactivity against human infected sera. The architectural elements determined for P1 and P40/P90 open new possibilities in vaccine development against M. pneumoniae infections.
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Affiliation(s)
- David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Akihiro Kawamoto
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - U Matsumoto
- Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan
| | - Ramiro Illanes
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Rosa Pérez-Luque
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Jesús Martín
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Rocco Mazzolini
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Paula Bierge
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Oscar Q Pich
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain.,Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Mateu Espasa
- Departament de Microbiologia, Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Isabel Sanfeliu
- Departament de Microbiologia, Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Juliana Esperalba
- Departament de Microbiologia, Hospital Universitari Vall d´Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Miguel Fernández-Huerta
- Departament de Microbiologia, Hospital Universitari Vall d´Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Jaume Pinyol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Shigetarou Mori
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Kenri
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, 558-8585, Japan.
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain.
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4
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Vizarraga D, Pérez-Luque R, Martín J, Fita I, Aparicio D. Alternative conformation of the C-domain of the P140 protein from Mycoplasma genitalium. Acta Crystallogr F Struct Biol Commun 2020; 76:508-516. [PMID: 33135669 DOI: 10.1107/s2053230x20012297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/07/2020] [Indexed: 11/10/2022]
Abstract
The human pathogen Mycoplasma genitalium is responsible for urethritis in men, and for cervicitis and pelvic inflammatory disease in women. The adherence of M. genitalium to host target epithelial cells is mediated through an adhesion complex called Nap, which is essential for infectivity. Nap is a transmembrane dimer of heterodimers of the immunodominant proteins P110 and P140. The M. genitalium genome contains multiple copies of portions that share homology with the extracellular regions of P140 and P110 encoded by the genes mg191 and mg192, respectively. Homologous recombination between the genes and the copies allows the generation of a large diversity of P140 and P110 variants to overcome surveillance by the host immune system. Interestingly, the C-terminal domain (C-domain) of the extracellular region of P140, which is essential for the function of Nap by acting as a flexible stalk anchoring the protein to the mycoplasma membrane, presents a low degree of sequence variability. In the present work, the X-ray crystal structures of two crystal forms of a construct of the P140 C-domain are reported. In both crystal forms, the construct forms a compact octamer with D4 point-group symmetry. The structure of the C-domain determined in this work presents significant differences with respect to the structure of the C-domain found recently in intact P140. The structural plasticity of the C-domain appears to be a possible mechanism that may help in the functioning of the mycoplasma adhesion complex.
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Affiliation(s)
- David Vizarraga
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Jesús Martín
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Ignacio Fita
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - David Aparicio
- Department of Structural Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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5
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Cuervo A, Fàbrega-Ferrer M, Machón C, Conesa JJ, Fernández FJ, Pérez-Luque R, Pérez-Ruiz M, Pous J, Vega MC, Carrascosa JL, Coll M. Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism. Nat Commun 2019; 10:3746. [PMID: 31431626 PMCID: PMC6702177 DOI: 10.1038/s41467-019-11705-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/18/2019] [Indexed: 12/31/2022] Open
Abstract
Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein.
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Affiliation(s)
- Ana Cuervo
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Montserrat Fàbrega-Ferrer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - José Javier Conesa
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Francisco J Fernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- Abvance Biotech srl, Ave. Reina Victoria 32, 28003, Madrid, Spain
| | - Rosa Pérez-Luque
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Mar Pérez-Ruiz
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - M Cristina Vega
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - José L Carrascosa
- Centro Nacional de Biotecnología, (CNB-CSIC), Darwin 3, 28049, Madrid, Spain.
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10, 08028, Barcelona, Spain.
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6
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Gordo V, Aparicio D, Pérez-Luque R, Benito A, Vilanova M, Usón I, Fita I, Ribó M. Structural Insights into Subunits Assembly and the Oxyester Splicing Mechanism of Neq pol Split Intein. Cell Chem Biol 2018; 25:871-879.e2. [PMID: 29754955 DOI: 10.1016/j.chembiol.2018.04.008] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/28/2018] [Accepted: 04/08/2018] [Indexed: 11/28/2022]
Abstract
Split inteins are expressed as two separated subunits (N-intein and C-intein) fused to the corresponding exteins. The specific association of both intein subunits precedes protein splicing, which results in excision of the intein subunits and in ligation, by a peptide bond, of the concomitant exteins. Catalytically active intein precursors are typically too reactive for crystallization or even isolation. Neq pol is the trans-intein of the B-type DNA polymerase I split gene from hyperthermophile Nanoarchaeum equitans. We have determined the crystal structures of both the isolated NeqN and the complex of NeqN and NeqC subunits carrying the wild-type sequences, including the essential catalytic residues Ser1 and Thr+1, in addition to seven and three residues of the N- and C-exteins, respectively. These structures provide detailed information on the unique oxyester chemistry of the splicing mechanism of Neq pol and of the extensive rearrangements that occur in NeqN during the association step.
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Affiliation(s)
- Verónica Gordo
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Antoni Benito
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - Maria Vilanova
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain
| | - Isabel Usón
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain; ICREA Lluís Companys 23, 08003 Barcelona, Spain
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri i Reixac 10, 08028 Barcelona, Spain.
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, C/ Maria Aurèlia Capmany 40, 17003 Girona, Spain; IdIBGi Hospital Universitari Josep Trueta, Girona, Spain.
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7
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Guasch A, Aranguren-Ibáñez Á, Pérez-Luque R, Aparicio D, Martínez-Høyer S, Mulero MC, Serrano-Candelas E, Pérez-Riba M, Fita I. Calcineurin Undergoes a Conformational Switch Evoked via Peptidyl-Prolyl Isomerization. PLoS One 2015; 10:e0134569. [PMID: 26248042 PMCID: PMC4527731 DOI: 10.1371/journal.pone.0134569] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/11/2015] [Indexed: 11/19/2022] Open
Abstract
A limited repertoire of PPP family of serine/threonine phosphatases with a highly conserved catalytic domain acts on thousands of protein targets to orchestrate myriad central biological roles. A major structural reorganization of human calcineurin, a ubiquitous Ser/Thr PPP regulated by calcium and calmodulin and targeted by immunosuppressant drugs cyclosporin A and FK506, is unveiled here. The new conformation involves trans- to cis-isomerization of proline in the SAPNY sequence, highly conserved across PPPs, and remodels the main regulatory site where NFATc transcription factors bind. Transitions between cis- and trans-conformations may involve peptidyl prolyl isomerases such as cyclophilin A and FKBP12, which are known to physically interact with and modulate calcineurin even in the absence of immunosuppressant drugs. Alternative conformations in PPPs provide a new perspective on interactions with substrates and other protein partners and may foster development of more specific inhibitors as drug candidates.
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Affiliation(s)
- Alicia Guasch
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Álvaro Aranguren-Ibáñez
- Human Molecular Genetics Laboratory, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de L’Hospitalet 199, L’Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Rosa Pérez-Luque
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - David Aparicio
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Sergio Martínez-Høyer
- Human Molecular Genetics Laboratory, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de L’Hospitalet 199, L’Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - M. Carmen Mulero
- Human Molecular Genetics Laboratory, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de L’Hospitalet 199, L’Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Eva Serrano-Candelas
- Human Molecular Genetics Laboratory, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de L’Hospitalet 199, L’Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Mercè Pérez-Riba
- Human Molecular Genetics Laboratory, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), Gran Via de L’Hospitalet 199, L’Hospitalet de Llobregat, 08908, Barcelona, Spain
- * E-mail: (IF); (MPR)
| | - Ignacio Fita
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic, Baldiri Reixac 10, 08028, Barcelona, Spain
- * E-mail: (IF); (MPR)
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8
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Fernández-López C, Lorenzo-Díaz F, Pérez-Luque R, Rodríguez-González L, Boer R, Lurz R, Bravo A, Coll M, Espinosa M. Nicking activity of the pMV158 MobM relaxase on cognate and heterologous origins of transfer. Plasmid 2013; 70:120-30. [DOI: 10.1016/j.plasmid.2013.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 10/27/2022]
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9
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Aparicio D, Pérez-Luque R, Carpena X, Díaz M, Ferrer JC, Loewen PC, Fita I. Structural asymmetry and disulfide bridges among subunits modulate the activity of human malonyl-CoA decarboxylase. J Biol Chem 2013; 288:11907-19. [PMID: 23482565 DOI: 10.1074/jbc.m112.443846] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Decarboxylation of malonyl-CoA to acetyl-CoA by malonyl-CoA decarboxylase (MCD; EC 4.1.1.9) is an essential facet in the regulation of fatty acid metabolism. The structure of human peroxisomal MCD reveals a molecular tetramer that is best described as a dimer of structural heterodimers, in which the two subunits present markedly different conformations. This molecular organization is consistent with half-of-the-sites reactivity. Each subunit has an all-helix N-terminal domain and a catalytic C-terminal domain with an acetyltransferase fold (GNAT superfamily). Intersubunit disulfide bridges, Cys-206-Cys-206 and Cys-243-Cys-243, can link the four subunits of the tetramer, imparting positive cooperativity to the catalytic process. The combination of a half-of-the-sites mechanism within each structural heterodimer and positive cooperativity in the tetramer produces a complex regulatory picture that is further complicated by the multiple intracellular locations of the enzyme. Transport into the peroxisome has been investigated by docking human MCD onto the peroxisomal import protein peroxin 5, which revealed interactions that extend beyond the C-terminal targeting motif.
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Affiliation(s)
- David Aparicio
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain
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10
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Pluta R, Russi S, Lorenzo-Díaz F, Pérez-Luque R, Boer DR, Espinosa M, Coll M. Structural characterization of the conjugation machinery in G+ bacteria. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311087964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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11
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Agudo R, Ferrer-Orta C, Arias A, de la Higuera I, Perales C, Pérez-Luque R, Verdaguer N, Domingo E. A multi-step process of viral adaptation to a mutagenic nucleoside analogue by modulation of transition types leads to extinction-escape. PLoS Pathog 2010; 6:e1001072. [PMID: 20865120 PMCID: PMC2928812 DOI: 10.1371/journal.ppat.1001072] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 07/26/2010] [Indexed: 01/18/2023] Open
Abstract
Resistance of viruses to mutagenic agents is an important problem for the development of lethal mutagenesis as an antiviral strategy. Previous studies with RNA viruses have documented that resistance to the mutagenic nucleoside analogue ribavirin (1-β-D-ribofuranosyl-1-H-1,2,4-triazole-3-carboxamide) is mediated by amino acid substitutions in the viral polymerase that either increase the general template copying fidelity of the enzyme or decrease the incorporation of ribavirin into RNA. Here we describe experiments that show that replication of the important picornavirus pathogen foot-and-mouth disease virus (FMDV) in the presence of increasing concentrations of ribavirin results in the sequential incorporation of three amino acid substitutions (M296I, P44S and P169S) in the viral polymerase (3D). The main biological effect of these substitutions is to attenuate the consequences of the mutagenic activity of ribavirin —by avoiding the biased repertoire of transition mutations produced by this purine analogue—and to maintain the replicative fitness of the virus which is able to escape extinction by ribavirin. This is achieved through alteration of the pairing behavior of ribavirin-triphosphate (RTP), as evidenced by in vitro polymerization assays with purified mutant 3Ds. Comparison of the three-dimensional structure of wild type and mutant polymerases suggests that the amino acid substitutions alter the position of the template RNA in the entry channel of the enzyme, thereby affecting nucleotide recognition. The results provide evidence of a new mechanism of resistance to a mutagenic nucleoside analogue which allows the virus to maintain a balance among mutation types introduced into progeny genomes during replication under strong mutagenic pressure. Viruses that have RNA as genetic material include many important human, animal and plant pathogens. A new strategy against RNA viruses consists in using mutagenic nucleotides. The objective is to provoke an excessive number of mutations, to deteriorate the viral functions to the point that the virus can not survive. One of the mutagens used in research on lethal mutagenesis is ribavirin, extensively employed in clinical practice. Unfortunately, viral mutants that are resistant to ribavirin have been selected, thus facilitating escape from lethal mutagenesis. Here we describe a new mechanism by which foot-and-mouth disease virus (FMDV) can become resistant to ribavirin. Amino acid changes in the viral polymerase, selected by ribavirin, are able to modify the types of mutations produced in the presence of ribavirin. Biochemical data indicate that the alteration of the enzyme changes the pairing behavior of ribavirin, avoiding the production of an excess of some types of mutations, supporting the hypothesis that an unbalanced mutation repertoire is detrimental to the virus. Thus, this new mechanism of resistance to ribavirin is based not as much in limiting the number of mutations in the virus genetic material but in ensuring an equilibrium among different types of mutations that favors viral survival.
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Affiliation(s)
- Rubén Agudo
- Centro de Biologia Molecular “Severo Ochoa” (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Cristina Ferrer-Orta
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Armando Arias
- Centro de Biologia Molecular “Severo Ochoa” (CSIC-UAM), Cantoblanco, Madrid, Spain
| | | | - Celia Perales
- Centro de Biologia Molecular “Severo Ochoa” (CSIC-UAM), Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Rosa Pérez-Luque
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Nuria Verdaguer
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Esteban Domingo
- Centro de Biologia Molecular “Severo Ochoa” (CSIC-UAM), Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- * E-mail:
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12
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Garces F, Fernández FJ, Gómez AM, Pérez-Luque R, Campos E, Prohens R, Aguilar J, Baldomà L, Coll M, Badía J, Vega MC. Quaternary structural transitions in the DeoR-type repressor UlaR control transcriptional readout from the L-ascorbate utilization regulon in Escherichia coli. Biochemistry 2008; 47:11424-33. [PMID: 18844374 DOI: 10.1021/bi800748x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [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
UlaR is a DNA binding protein of the DeoR family of eubacterial transcriptional repressors which maintains the utilization of the L-ascorbate ula regulon in a repressed state. The availability of L-ascorbate in the growth medium releases UlaR-mediated repression on the ula regulon, thereby activating transcription. The molecular details of this induction by L-ascorbate have remained elusive to date. Here we have identified L-ascorbate 6-phosphate as a direct effector of UlaR; using a combination of site-directed mutagenesis, gel retardation, isothermal titration calorimetry, and analytical ultracentrifugation studies, we have identified the key amino acid residues that mediate L-ascorbate 6-phosphate binding and constructed the first model of regulation of a DeoR family member, establishing the basis of the ula regulon transcription control by UlaR. In this model, specific quaternary rearrangements of the DeoR-type repressor are the molecular underpinning of the activating and repressing forms. A DNA-bound UlaR tetramer establishes repression, whereas an L-ascorbate-6-phosphate-induced breakdown of the tetrameric configuration in favor of an UlaR dimeric state results in dissociation of UlaR from DNA and allows transcription of ulaG and ula ABCDEF structural genes. Despite the fact that similar changes have been described for other unrelated repressor factors, this is the first report to demonstrate that specific oligomerization changes are responsible for the activating and repressing forms of a DeoR-type eubacterial transcriptional repressor.
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Affiliation(s)
- Fernando Garces
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
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13
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Garces F, Fernández FJ, Pérez-Luque R, Aguilar J, Baldomà L, Coll M, Badía J, Vega MC. Overproduction, crystallization and preliminary X-ray analysis of the putative L-ascorbate-6-phosphate lactonase UlaG from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 64:36-8. [PMID: 18097099 DOI: 10.1107/s1744309107065256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 12/03/2007] [Indexed: 11/10/2022]
Abstract
UlaG, the putative L-ascorbate-6-phosphate lactonase encoded by the ulaG gene from the utilization of L-ascorbate regulon in Escherichia coli, has been cloned, overexpressed, purified using standard chromatographic techniques and crystallized. Crystals were obtained by sitting-drop vapour diffusion at 293 K. Preliminary X-ray diffraction analysis revealed that the UlaG crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 104.52, b = 180.69, c = 112.88 A, beta = 103.26 degrees. The asymmetric unit is expected to contain six copies of UlaG, with a corresponding volume per protein weight of 2.16 A3 Da(-1) and a solvent content of 43%.
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Affiliation(s)
- Fernando Garces
- Structural Biology Department, Institut de Biologia Molecular de Barcelona and Institut de Recerca Biomèdica, E-08028 Barcelona, Spain
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Ferrer-Orta C, Arias A, Pérez-Luque R, Escarmís C, Domingo E, Verdaguer N. Sequential structures provide insights into the fidelity of RNA replication. Proc Natl Acad Sci U S A 2007; 104:9463-8. [PMID: 17517631 PMCID: PMC1890517 DOI: 10.1073/pnas.0700518104] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Indexed: 01/08/2023] Open
Abstract
RNA virus replication is an error-prone event caused by the low fidelity of viral RNA-dependent RNA polymerases. Replication fidelity can be decreased further by the use of mutagenic ribonucleoside analogs to a point where viral genetic information can no longer be maintained. For foot-and-mouth disease virus, the antiviral analogs ribavirin and 5-fluorouracil have been shown to be mutagenic, contributing to virus extinction through lethal mutagenesis. Here, we report the x-ray structure of four elongation complexes of foot-and-mouth disease virus polymerase 3D obtained in presence of natural substrates, ATP and UTP, or mutagenic nucleotides, ribavirin triphosphate and 5-fluorouridine triphosphate with different RNAs as template-primer molecules. The ability of these complexes to synthesize RNA in crystals allowed us to capture different successive replication events and to define the critical amino acids involved in (i) the recognition and positioning of the incoming nucleotide or analog; (ii) the positioning of the acceptor base of the template strand; and (iii) the positioning of the 3'-OH group of the primer nucleotide during RNA replication. The structures identify key interactions involved in viral RNA replication and provide insights into the molecular basis of the low fidelity of viral RNA polymerases.
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Affiliation(s)
- Cristina Ferrer-Orta
- *Institut de Biologia Molecular de Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, E-08028 Barcelona, Spain; and
| | - Armando Arias
- Centro de Biología Molecular “Severo Ochoa,” Cantoblanco, E-28049 Madrid, Spain
| | - Rosa Pérez-Luque
- *Institut de Biologia Molecular de Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, E-08028 Barcelona, Spain; and
| | - Cristina Escarmís
- Centro de Biología Molecular “Severo Ochoa,” Cantoblanco, E-28049 Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa,” Cantoblanco, E-28049 Madrid, Spain
| | - Nuria Verdaguer
- *Institut de Biologia Molecular de Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, E-08028 Barcelona, Spain; and
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Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Pérez-Luque R, Coll M, de la Cruz F. Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. J Mol Biol 2006; 358:857-69. [PMID: 16540117 DOI: 10.1016/j.jmb.2006.02.018] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 02/03/2006] [Accepted: 02/08/2006] [Indexed: 10/25/2022]
Abstract
TrwC is a DNA strand transferase that catalyzes the initial and final stages of conjugative DNA transfer. We have solved the crystal structure of the N-terminal relaxase domain of TrwC in complex with a 27 base-long DNA oligonucleotide that contains both the recognition hairpin and the scissile phosphate. In addition, a series of ternary structures of protein-DNA complexes with different divalent cations at the active site have been solved. Systematic anomalous difference analysis allowed us to determine unambiguously the nature of the metal bound. Zn2+, Ni2+ and Cu2+ were found to bind the histidine-triad metal binding site. Comparison of the structures of the different complexes suggests two pathways for the DNA to exit the active pocket. They are probably used at different steps of the conjugative DNA-processing reaction. The structural information allows us to propose (i) an enzyme mechanism where the scissile phosphate is polarized by the metal ion facilitating the nucleophilic attack of the catalytic tyrosine, and (ii) a probable sequence of events during conjugative DNA processing that explains the biological function of the relaxase.
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Affiliation(s)
- Roeland Boer
- Institut de Biologia Molecular de Barcelona (CSIC) and Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
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16
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Ferrer-Orta C, Arias A, Agudo R, Pérez-Luque R, Escarmís C, Domingo E, Verdaguer N. The structure of a protein primer-polymerase complex in the initiation of genome replication. EMBO J 2006; 25:880-8. [PMID: 16456546 PMCID: PMC1383552 DOI: 10.1038/sj.emboj.7600971] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 01/02/2006] [Indexed: 01/14/2023] Open
Abstract
Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X-ray structure of two complexes between foot-and-mouth disease virus 3D, VPg1, the substrate UTP and divalent cations, in the absence and in the presence of an oligoadenylate of 10 residues. In both complexes, VPg fits the RNA binding cleft of the polymerase and projects the key residue Tyr3 into the active site of 3D. This is achieved by multiple interactions with residues of motif F and helix alpha8 of the fingers domain and helix alpha13 of the thumb domain of the polymerase. The complex obtained in the presence of the oligoadenylate showed the product of the VPg uridylylation (VPg-UMP). Two metal ions and the catalytic aspartic acids of the polymerase active site, together with the basic residues of motif F, have been identified as participating in the priming reaction.
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Affiliation(s)
- Cristina Ferrer-Orta
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Armando Arias
- Centro de Biologia Molecular ‘Severo Ochoa' (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Rubén Agudo
- Centro de Biologia Molecular ‘Severo Ochoa' (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Rosa Pérez-Luque
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Cristina Escarmís
- Centro de Biologia Molecular ‘Severo Ochoa' (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Esteban Domingo
- Centro de Biologia Molecular ‘Severo Ochoa' (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Nuria Verdaguer
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain. Tel.: +34 93 403 49 52; Fax: +34 93 403 49 79; E-mail:
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17
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Montella C, Bellsolell L, Pérez-Luque R, Badía J, Baldoma L, Coll M, Aguilar J. Crystal structure of an iron-dependent group III dehydrogenase that interconverts L-lactaldehyde and L-1,2-propanediol in Escherichia coli. J Bacteriol 2005; 187:4957-66. [PMID: 15995211 PMCID: PMC1169507 DOI: 10.1128/jb.187.14.4957-4966.2005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The FucO protein, a member of the group III "iron-activated" dehydrogenases, catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli. The three-dimensional structure of FucO in a complex with NAD(+) was solved, and the presence of iron in the crystals was confirmed by X-ray fluorescence. The FucO structure presented here is the first structure for a member of the group III bacterial dehydrogenases shown experimentally to contain iron. FucO forms a dimer, in which each monomer folds into an alpha/beta dinucleotide-binding N-terminal domain and an all-alpha-helix C-terminal domain that are separated by a deep cleft. The dimer is formed by the swapping (between monomers) of the first chain of the beta-sheet. The binding site for Fe(2+) is located at the face of the cleft formed by the C-terminal domain, where the metal ion is tetrahedrally coordinated by three histidine residues (His200, His263, and His277) and an aspartate residue (Asp196). The glycine-rich turn formed by residues 96 to 98 and the following alpha-helix is part of the NAD(+) recognition locus common in dehydrogenases. Site-directed mutagenesis and enzyme kinetic assays were performed to assess the role of different residues in metal, cofactor, and substrate binding. In contrast to previous assumptions, the essential His267 residue does not interact with the metal ion. Asp39 appears to be the key residue for discriminating against NADP(+). Modeling L-1,2-propanediol in the active center resulted in a close approach of the C-1 hydroxyl of the substrate to C-4 of the nicotinamide ring, implying that there is a typical metal-dependent dehydrogenation catalytic mechanism.
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Affiliation(s)
- Cristina Montella
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Spain
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Arias A, Agudo R, Ferrer-Orta C, Pérez-Luque R, Airaksinen A, Brocchi E, Domingo E, Verdaguer N, Escarmís C. Mutant viral polymerase in the transition of virus to error catastrophe identifies a critical site for RNA binding. J Mol Biol 2005; 353:1021-32. [PMID: 16216271 DOI: 10.1016/j.jmb.2005.09.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Revised: 09/01/2005] [Accepted: 09/09/2005] [Indexed: 10/25/2022]
Abstract
A foot-and-mouth disease virus (FMDV) polymerase (3D) with amino acid replacements G118D, V239M and G373D (triple DMD mutant) was obtained from a molecular clone derived from a virus population treated with ribavirin, in the transition to error catastrophe (virus extinction through lethal mutagenesis). DMD 3D was expressed in Escherichia coli, purified, and its activity compared with that of wild-type enzyme and mutant enzymes with either replacement G118D, G118A or D338A (the latter affecting the catalytic motif YGDD), generated by site-directed mutagenesis. No differences among the enzymes were noted in their interaction with monoclonal antibodies specific for the FMDV polymerase. Mutant enzymes with G118D or G118A showed a 100-fold decrease in polymerization activity relative to wild-type 3D, using poly(A)/oligo(dT)15 and poly(A)/VPg as template-primers, under several reaction conditions. As expected, the activity of 3D with D338A was undetectable (<0.01 times the value for wild-type 3D). DMD and the G118 mutants showed impaired binding to template-primer RNA whereas the D338A mutant showed a binding similar to wild-type 3D. Transfection of cells with FMDV RNA encoding DMD 3D resulted in selection of revertant viruses that maintained only substitutions V239M and G373D. Consistently, when infectious transcripts encoded 3D with either G118D, G118A or D338A, viruses with reversions to the wild-type sequence were isolated. The implication of G118 in template-primer binding is supported by the location of this residue in the template-binding groove of the FMDV polymerase. In addition to identifying an amino acid residue that is critical for the binding of polymerase to RNA, the results document the presence of defective genomes in the transition of virus to error catastrophe.
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Affiliation(s)
- Armando Arias
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
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Russi S, Lucas M, Guasch A, Boer R, Pérez-Luque R, Cabezas M, Dela Cruz F, Coll M. Unveiling the DNA strand transfer-mechanism of relaxase TrwC. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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20
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Guasch A, Lucas M, Moncalián G, Cabezas M, Pérez-Luque R, Gomis-Rüth FX, de la Cruz F, Coll M. Erratum: Corrigendum: Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nat Struct Mol Biol 2004. [DOI: 10.1038/nsmb0104-102a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Guasch A, Lucas M, Moncalián G, Cabezas M, Pérez-Luque R, Gomis-Rüth FX, de la Cruz F, Coll M. Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nat Struct Mol Biol 2003; 10:1002-10. [PMID: 14625590 DOI: 10.1038/nsb1017] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2003] [Accepted: 10/30/2003] [Indexed: 02/03/2023]
Abstract
Relaxases are DNA strand transferases that catalyze the initial and final stages of DNA processing during conjugative cell-to-cell DNA transfer. Upon binding to the origin of transfer (oriT) DNA, relaxase TrwC melts the double helix. The three-dimensional structure of the relaxase domain of TrwC in complex with its cognate DNA at oriT shows a fold built on a two-layer alpha/beta sandwich, with a deep narrow cleft that houses the active site. The DNA includes one arm of an extruded cruciform, an essential feature for specific recognition. This arm is firmly embraced by the protein through a beta-ribbon positioned in the DNA major groove and a loop occupying the minor groove. It is followed by a single-stranded DNA segment that enters the active site, after a sharp U-turn forming a hydrophobic cage that traps the N-terminal methionine. Structural analysis combined with site-directed mutagenesis defines the architecture of the active site.
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Affiliation(s)
- Alicia Guasch
- Institut de Biologia Molecular de Barcelona, CSIC, Jordi Girona, 18-26, 08034 Barcelona, Spain
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Pereira PJ, Macedo-Ribeiro S, Párraga A, Pérez-Luque R, Cunningham O, Darcy K, Mantle TJ, Coll M. Structure of human biliverdin IXbeta reductase, an early fetal bilirubin IXbeta producing enzyme. Nat Struct Biol 2001; 8:215-20. [PMID: 11224564 DOI: 10.1038/84948] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biliverdin IXbeta reductase (BVR-B) catalyzes the pyridine nucleotide-dependent production of bilirubin-IXbeta, the major heme catabolite during early fetal development. BVR-B displays a preference for biliverdin isomers without propionates straddling the C10 position, in contrast to biliverdin IXalpha reductase (BVR-A), the major form of BVR in adult human liver. In addition to its tetrapyrrole clearance role in the fetus, BVR-B has flavin and ferric reductase activities in the adult. We have solved the structure of human BVR-B in complex with NADP+ at 1.15 A resolution. Human BVR-B is a monomer displaying an alpha/beta dinucleotide binding fold. The structures of ternary complexes with mesobiliverdin IValpha, biliverdin IXalpha, FMN and lumichrome show that human BVR-B has a single substrate binding site, to which substrates and inhibitors bind primarily through hydrophobic interactions, explaining its broad specificity. The reducible atom of both biliverdin and flavin substrates lies above the reactive C4 of the cofactor, an appropriate position for direct hydride transfer. BVR-B discriminates against the biliverdin IXalpha isomer through steric hindrance at the bilatriene side chain binding pockets. The structure also explains the enzyme's preference for NADP(H) and its B-face stereospecificity.
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Affiliation(s)
- P J Pereira
- Instituto de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi Girona, 18-26, 08034 Barcelona, Spain
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Gomis-Rüth FX, Moncalián G, Pérez-Luque R, González A, Cabezón E, de la Cruz F, Coll M. The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase. Nature 2001; 409:637-41. [PMID: 11214325 DOI: 10.1038/35054586] [Citation(s) in RCA: 285] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The transfer of DNA across membranes and between cells is a central biological process; however, its molecular mechanism remains unknown. In prokaryotes, trans-membrane passage by bacterial conjugation, is the main route for horizontal gene transfer. It is the means for rapid acquisition of new genetic information, including antibiotic resistance by pathogens. Trans-kingdom gene transfer from bacteria to plants or fungi and even bacterial sporulation are special cases of conjugation. An integral membrane DNA-binding protein, called TrwB in the Escherichia coli R388 conjugative system, is essential for the conjugation process. This large multimeric protein is responsible for recruiting the relaxosome DNA-protein complex, and participates in the transfer of a single DNA strand during cell mating. Here we report the three-dimensional structure of a soluble variant of TrwB. The molecule consists of two domains: a nucleotide-binding domain of alpha/beta topology, reminiscent of RecA and DNA ring helicases, and an all-alpha domain. Six equivalent protein monomers associate to form an almost spherical quaternary structure that is strikingly similar to F1-ATPase. A central channel, 20 A in width, traverses the hexamer.
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Affiliation(s)
- F X Gomis-Rüth
- Institut de Biologia Molecular de Barcelona, CSIC, Spain
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Gomis-Rüth FX, Solà M, Pérez-Luque R, Acebo P, Alda MT, González A, Espinosa M, del Solar G, Coll M. Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the pMV158-encoded plasmid transcriptional repressor protein CopG. FEBS Lett 1998; 425:161-5. [PMID: 9541028 DOI: 10.1016/s0014-5793(98)00219-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Plasmid pMV158 encodes a 45 amino acid transcriptional repressor, CopG, which is involved in copy number control. A new procedure for overproduction and purification of the protein has been developed. The CopG protein thus obtained retained its ability to specifically bind to DNA and to repress its own promoter. Purified CopG protein has been crystallized using the sitting-drop vapor diffusion method. The crystals, belonging to orthorhombic space group C222(1) (cell constants a = 67.2 A, b = 102.5 A, c = 40.2 A), were obtained from a solution containing methylpentanediol, benzamidine and sodium chloride, buffered to pH 6.7. Complete diffraction data up to 1.6 A resolution have been collected. Considerations about the Matthews parameter account for the most likely presence of three molecules in the asymmetric unit (2.27 A3/Da).
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Affiliation(s)
- F X Gomis-Rüth
- Centre d'Investigació i Desenvolupament, C.S.I.C., Barcelona, Spain.
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