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Hernández-Rocamora VM, Molina R, Alba A, Carrasco-López C, Rojas-Altuve A, Panjikar S, Medina A, Usón I, Alfonso C, Galán B, Rivas G, Hermoso JA, Sanz JM. Structural characterization of PaaX, the main repressor of the phenylacetate degradation pathway in Escherichia coli W: A novel fold of transcription regulator proteins. Int J Biol Macromol 2024; 254:127935. [PMID: 37949283 DOI: 10.1016/j.ijbiomac.2023.127935] [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: 07/20/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
PaaX is a transcriptional repressor of the phenylacetic acid (PAA) catabolic pathway, a central route for bacterial aerobic degradation of aromatic compounds. Induction of the route is achieved through the release of PaaX from its promoter sequences by the first compound of the pathway, phenylacetyl-coenzyme A (PA-CoA). We report the crystal structure of PaaX from Escherichia coli W. PaaX displays a novel type of fold for transcription regulators, showing a dimeric conformation where the monomers present a three-domain structure: an N-terminal winged helix-turn-helix domain, a dimerization domain similar to the Cas2 protein and a C-terminal domain without structural homologs. The domains are separated by a crevice amenable to harbour a PA-CoA molecule. The biophysical characterization of the protein in solution confirmed several hints predicted from the structure, i.e. its dimeric conformation, a modest importance of cysteines and a high dependence of solubility and thermostability on ionic strength. At a moderately acidic pH, the protein formed a stable folding intermediate with remaining α-helical structure, a disrupted tertiary structure and exposed hydrophobic patches. Our results provide valuable information to understand the stability and mechanism of PaaX and pave the way for further analysis of other regulators with similar structural configurations.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Av. Universidad, s/n, E-03202 Elche, Alicante, Spain; Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alejandra Alba
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Alzoray Rojas-Altuve
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia; Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Baldiri Reixach 15, 08028 Barcelona, Spain; ICREA: Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain.
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.
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Medina A, Jiménez E, Caballero I, Castellví A, Triviño Valls J, Alcorlo M, Molina R, Hermoso JA, Sammito MD, Borges R, Usón I. Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER. Acta Crystallogr D Struct Biol 2022; 78:1283-1293. [PMID: 36322413 PMCID: PMC9629495 DOI: 10.1107/s2059798322009706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/03/2022] [Indexed: 11/23/2022] Open
Abstract
Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios.
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Affiliation(s)
- Ana Medina
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Elisabet Jiménez
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Iracema Caballero
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Albert Castellví
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Josep Triviño Valls
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Martin Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, Spanish National Research Council (CSIC), Madrid, Spain
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, Spanish National Research Council (CSIC), Madrid, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, Spanish National Research Council (CSIC), Madrid, Spain
| | - Massimo D. Sammito
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Rafael Borges
- Department of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
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Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway. BIOLOGY 2015; 4:424-42. [PMID: 26075354 PMCID: PMC4498308 DOI: 10.3390/biology4020424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/25/2015] [Accepted: 05/29/2015] [Indexed: 11/17/2022]
Abstract
Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism—coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and β-oxidation of fatty acids.
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