Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase

Autores
Gonzalez, Javier Marcelo; Martí Arbona, Ricardo; Chen, Julian; Broom Peltz, Brian; Unkefer, Clifford
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD+-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an α-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.Crystal structures of apo malate dehydrogenase (MDH) from Methylobacterium extorquens, MDH bound to NAD+, and MDH with oxaloacetate and ADP-ribose revealed conformational changes, closing the active site upon coenzyme and substrate binding. In the ternary complex, His284 is in position to donate a proton in the formation of (2S)-malate.
Fil: Gonzalez, Javier Marcelo. Universidad Nacional de Santiago del Estero. Instituto de Bionanotecnología del Noa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Bionanotecnología del Noa; Argentina
Fil: Marti Arbona, R.. Bioscience Division, Los Alamos National Laboratory; Estados Unidos
Fil: Chen, J. C. H.. Bioscience Division, Los Alamos National Laboratory; Estados Unidos
Fil: Broom Peltz, B.. Bioscience Division, Los Alamos National Laboratory; Estados Unidos
Fil: Unkefer, C. J.. Bioscience Division, Los Alamos National Laboratory; Estados Unidos
Materia
BIOFUELS
MALATE DEHYDROGENASE
METHYLOBACTERIUM EXTORQUENS
METHYLOTROPHS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/92464

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network_name_str CONICET Digital (CONICET)
spelling Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenaseGonzalez, Javier MarceloMartí Arbona, RicardoChen, JulianBroom Peltz, BrianUnkefer, CliffordBIOFUELSMALATE DEHYDROGENASEMETHYLOBACTERIUM EXTORQUENSMETHYLOTROPHShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD+-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an α-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.Crystal structures of apo malate dehydrogenase (MDH) from Methylobacterium extorquens, MDH bound to NAD+, and MDH with oxaloacetate and ADP-ribose revealed conformational changes, closing the active site upon coenzyme and substrate binding. In the ternary complex, His284 is in position to donate a proton in the formation of (2S)-malate.Fil: Gonzalez, Javier Marcelo. Universidad Nacional de Santiago del Estero. Instituto de Bionanotecnología del Noa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Bionanotecnología del Noa; ArgentinaFil: Marti Arbona, R.. Bioscience Division, Los Alamos National Laboratory; Estados UnidosFil: Chen, J. C. H.. Bioscience Division, Los Alamos National Laboratory; Estados UnidosFil: Broom Peltz, B.. Bioscience Division, Los Alamos National Laboratory; Estados UnidosFil: Unkefer, C. J.. Bioscience Division, Los Alamos National Laboratory; Estados UnidosInternational Union of Crystallography2018-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/92464Gonzalez, Javier Marcelo; Martí Arbona, Ricardo; Chen, Julian; Broom Peltz, Brian; Unkefer, Clifford; Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase; International Union of Crystallography; Acta Crystallographica Section F: Structural Biology Communications; 74; 10; 10-2018; 610-6162053-230XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1107/S2053230X18011809info:eu-repo/semantics/altIdentifier/url/http://scripts.iucr.org/cgi-bin/paper?S2053230X18011809info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168771/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:00:50Zoai:ri.conicet.gov.ar:11336/92464instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:00:50.577CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
title Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
spellingShingle Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
Gonzalez, Javier Marcelo
BIOFUELS
MALATE DEHYDROGENASE
METHYLOBACTERIUM EXTORQUENS
METHYLOTROPHS
title_short Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
title_full Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
title_fullStr Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
title_full_unstemmed Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
title_sort Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase
dc.creator.none.fl_str_mv Gonzalez, Javier Marcelo
Martí Arbona, Ricardo
Chen, Julian
Broom Peltz, Brian
Unkefer, Clifford
author Gonzalez, Javier Marcelo
author_facet Gonzalez, Javier Marcelo
Martí Arbona, Ricardo
Chen, Julian
Broom Peltz, Brian
Unkefer, Clifford
author_role author
author2 Martí Arbona, Ricardo
Chen, Julian
Broom Peltz, Brian
Unkefer, Clifford
author2_role author
author
author
author
dc.subject.none.fl_str_mv BIOFUELS
MALATE DEHYDROGENASE
METHYLOBACTERIUM EXTORQUENS
METHYLOTROPHS
topic BIOFUELS
MALATE DEHYDROGENASE
METHYLOBACTERIUM EXTORQUENS
METHYLOTROPHS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD+-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an α-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.Crystal structures of apo malate dehydrogenase (MDH) from Methylobacterium extorquens, MDH bound to NAD+, and MDH with oxaloacetate and ADP-ribose revealed conformational changes, closing the active site upon coenzyme and substrate binding. In the ternary complex, His284 is in position to donate a proton in the formation of (2S)-malate.
Fil: Gonzalez, Javier Marcelo. Universidad Nacional de Santiago del Estero. Instituto de Bionanotecnología del Noa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Bionanotecnología del Noa; Argentina
Fil: Marti Arbona, R.. Bioscience Division, Los Alamos National Laboratory; Estados Unidos
Fil: Chen, J. C. H.. Bioscience Division, Los Alamos National Laboratory; Estados Unidos
Fil: Broom Peltz, B.. Bioscience Division, Los Alamos National Laboratory; Estados Unidos
Fil: Unkefer, C. J.. Bioscience Division, Los Alamos National Laboratory; Estados Unidos
description Three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP-ribose occupying the pyridine nucleotide-binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate-binding site is accessible in the enzyme resting state or NAD+-bound forms, the substrate-bound form exhibits a closed conformation. This conformational change involves the transition of an α-helix to a 310-helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)-malate.Crystal structures of apo malate dehydrogenase (MDH) from Methylobacterium extorquens, MDH bound to NAD+, and MDH with oxaloacetate and ADP-ribose revealed conformational changes, closing the active site upon coenzyme and substrate binding. In the ternary complex, His284 is in position to donate a proton in the formation of (2S)-malate.
publishDate 2018
dc.date.none.fl_str_mv 2018-10
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/92464
Gonzalez, Javier Marcelo; Martí Arbona, Ricardo; Chen, Julian; Broom Peltz, Brian; Unkefer, Clifford; Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase; International Union of Crystallography; Acta Crystallographica Section F: Structural Biology Communications; 74; 10; 10-2018; 610-616
2053-230X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/92464
identifier_str_mv Gonzalez, Javier Marcelo; Martí Arbona, Ricardo; Chen, Julian; Broom Peltz, Brian; Unkefer, Clifford; Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase; International Union of Crystallography; Acta Crystallographica Section F: Structural Biology Communications; 74; 10; 10-2018; 610-616
2053-230X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1107/S2053230X18011809
info:eu-repo/semantics/altIdentifier/url/http://scripts.iucr.org/cgi-bin/paper?S2053230X18011809
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168771/
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv International Union of Crystallography
publisher.none.fl_str_mv International Union of Crystallography
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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