A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1

Autores
Tossounian, Maria Armineh; Hristov, Stefan Denchev; Semelak, Jonathan Alexis; Yu, Bess Yi Kun; Baczynska, Maria; Zhao, Yuhan; Estrin, Dario Ariel; Trujillo, Madia; Filonenko, Valeriy; Gouge, Jerome; Gout, Ivan
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Coenzyme A (CoA) is a key cellular metabolite which participates in diverse metabolic pathways, regulation of gene expression and the antioxidant defense mechanism. Human NME1 (hNME1), which is a moonlighting protein, was identified as a major CoA-binding protein. Biochemical studies showed that hNME1 is regulated by CoA through both covalent and non-covalent binding, which leads to a decrease in the hNME1 nucleoside diphosphate kinase (NDPK) activity. In this study, we expanded the knowledge on previous findings by focusing on the non-covalent mode of CoA binding to the hNME1. With X-ray crystallography, we solved the CoA bound structure of hNME1 (hNME1-CoA) and determined the stabilization interactions CoA forms within the nucleotide-binding site of hNME1. A hydrophobic patch stabilizing the CoA adenine ring, while salt bridges and hydrogen bonds stabilizing the phosphate groups of CoA were observed. With molecular dynamics studies, we extended our structural analysis by characterizing the hNME1-CoA structure and elucidating possible orientations of the pantetheine tail, which is absent in the X-ray structure due to its flexibility. Crystallographic studies suggested the involvement of arginine 58 and threonine 94 in mediating specific interactions with CoA. Site-directed mutagenesis and CoA-based affinity purifications showed that arginine 58 mutation to glutamate (R58E) and threonine 94 mutation to aspartate (T94D) prevent hNME1 from binding to CoA. Overall, our results reveal a unique mode by which hNME1 binds CoA, which differs significantly from that of ADP binding: the α- and β-phosphates of CoA are oriented away from the nucleotide-binding site, while 3′-phosphate faces catalytic histidine 118 (H118). The interactions formed by the CoA adenine ring and phosphate groups contribute to the specific mode of CoA binding to hNME1.
Fil: Tossounian, Maria Armineh. Colegio Universitario de Londres; Reino Unido
Fil: Hristov, Stefan Denchev. Colegio Universitario de Londres; Reino Unido
Fil: Semelak, Jonathan Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Fil: Yu, Bess Yi Kun. Colegio Universitario de Londres; Reino Unido
Fil: Baczynska, Maria. Colegio Universitario de Londres; Reino Unido
Fil: Zhao, Yuhan. Colegio Universitario de Londres; Reino Unido
Fil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Fil: Trujillo, Madia. Universidad de la República; Uruguay
Fil: Filonenko, Valeriy. Colegio Universitario de Londres; Reino Unido
Fil: Gouge, Jerome. Colegio Universitario de Londres; Reino Unido
Fil: Gout, Ivan. Colegio Universitario de Londres; Reino Unido
Materia
COALATION
COENZYME A
METASTASIS SUPPRESSOR
MOLECULAR DYNAMICS
NDPK-A STRUCTURE
NM23-H1
NME1
NUCLEOTIDE BINDING
PROTEIN-METABOLITE REGULATION
X-RAY CRYSTALLOGRAPHY
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:11336/228510
Acceder
id CONICETDig_1f7964e350fd1d318e7996a6d23c96b8
oai_identifier_str oai:ri.conicet.gov.ar:11336/228510
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1Tossounian, Maria ArminehHristov, Stefan DenchevSemelak, Jonathan AlexisYu, Bess Yi KunBaczynska, MariaZhao, YuhanEstrin, Dario ArielTrujillo, MadiaFilonenko, ValeriyGouge, JeromeGout, IvanCOALATIONCOENZYME AMETASTASIS SUPPRESSORMOLECULAR DYNAMICSNDPK-A STRUCTURENM23-H1NME1NUCLEOTIDE BINDINGPROTEIN-METABOLITE REGULATIONX-RAY CRYSTALLOGRAPHYhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1Coenzyme A (CoA) is a key cellular metabolite which participates in diverse metabolic pathways, regulation of gene expression and the antioxidant defense mechanism. Human NME1 (hNME1), which is a moonlighting protein, was identified as a major CoA-binding protein. Biochemical studies showed that hNME1 is regulated by CoA through both covalent and non-covalent binding, which leads to a decrease in the hNME1 nucleoside diphosphate kinase (NDPK) activity. In this study, we expanded the knowledge on previous findings by focusing on the non-covalent mode of CoA binding to the hNME1. With X-ray crystallography, we solved the CoA bound structure of hNME1 (hNME1-CoA) and determined the stabilization interactions CoA forms within the nucleotide-binding site of hNME1. A hydrophobic patch stabilizing the CoA adenine ring, while salt bridges and hydrogen bonds stabilizing the phosphate groups of CoA were observed. With molecular dynamics studies, we extended our structural analysis by characterizing the hNME1-CoA structure and elucidating possible orientations of the pantetheine tail, which is absent in the X-ray structure due to its flexibility. Crystallographic studies suggested the involvement of arginine 58 and threonine 94 in mediating specific interactions with CoA. Site-directed mutagenesis and CoA-based affinity purifications showed that arginine 58 mutation to glutamate (R58E) and threonine 94 mutation to aspartate (T94D) prevent hNME1 from binding to CoA. Overall, our results reveal a unique mode by which hNME1 binds CoA, which differs significantly from that of ADP binding: the α- and β-phosphates of CoA are oriented away from the nucleotide-binding site, while 3′-phosphate faces catalytic histidine 118 (H118). The interactions formed by the CoA adenine ring and phosphate groups contribute to the specific mode of CoA binding to hNME1.Fil: Tossounian, Maria Armineh. Colegio Universitario de Londres; Reino UnidoFil: Hristov, Stefan Denchev. Colegio Universitario de Londres; Reino UnidoFil: Semelak, Jonathan Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Yu, Bess Yi Kun. Colegio Universitario de Londres; Reino UnidoFil: Baczynska, Maria. Colegio Universitario de Londres; Reino UnidoFil: Zhao, Yuhan. Colegio Universitario de Londres; Reino UnidoFil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Trujillo, Madia. Universidad de la República; UruguayFil: Filonenko, Valeriy. Colegio Universitario de Londres; Reino UnidoFil: Gouge, Jerome. Colegio Universitario de Londres; Reino UnidoFil: Gout, Ivan. Colegio Universitario de Londres; Reino UnidoMultidisciplinary Digital Publishing Institute2023-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/228510Tossounian, Maria Armineh; Hristov, Stefan Denchev; Semelak, Jonathan Alexis; Yu, Bess Yi Kun; Baczynska, Maria; et al.; A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1; Multidisciplinary Digital Publishing Institute; International Journal of Molecular Sciences; 24; 11; 5-2023; 1-171422-0067CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/1422-0067/24/11/9359info:eu-repo/semantics/altIdentifier/doi/10.3390/ijms24119359info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:40:10Zoai:ri.conicet.gov.ar:11336/228510instacron: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 09:40:10.86CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
title A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
spellingShingle A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
Tossounian, Maria Armineh
COALATION
COENZYME A
METASTASIS SUPPRESSOR
MOLECULAR DYNAMICS
NDPK-A STRUCTURE
NM23-H1
NME1
NUCLEOTIDE BINDING
PROTEIN-METABOLITE REGULATION
X-RAY CRYSTALLOGRAPHY
title_short A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
title_full A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
title_fullStr A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
title_full_unstemmed A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
title_sort A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1
dc.creator.none.fl_str_mv Tossounian, Maria Armineh
Hristov, Stefan Denchev
Semelak, Jonathan Alexis
Yu, Bess Yi Kun
Baczynska, Maria
Zhao, Yuhan
Estrin, Dario Ariel
Trujillo, Madia
Filonenko, Valeriy
Gouge, Jerome
Gout, Ivan
author Tossounian, Maria Armineh
author_facet Tossounian, Maria Armineh
Hristov, Stefan Denchev
Semelak, Jonathan Alexis
Yu, Bess Yi Kun
Baczynska, Maria
Zhao, Yuhan
Estrin, Dario Ariel
Trujillo, Madia
Filonenko, Valeriy
Gouge, Jerome
Gout, Ivan
author_role author
author2 Hristov, Stefan Denchev
Semelak, Jonathan Alexis
Yu, Bess Yi Kun
Baczynska, Maria
Zhao, Yuhan
Estrin, Dario Ariel
Trujillo, Madia
Filonenko, Valeriy
Gouge, Jerome
Gout, Ivan
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv COALATION
COENZYME A
METASTASIS SUPPRESSOR
MOLECULAR DYNAMICS
NDPK-A STRUCTURE
NM23-H1
NME1
NUCLEOTIDE BINDING
PROTEIN-METABOLITE REGULATION
X-RAY CRYSTALLOGRAPHY
topic COALATION
COENZYME A
METASTASIS SUPPRESSOR
MOLECULAR DYNAMICS
NDPK-A STRUCTURE
NM23-H1
NME1
NUCLEOTIDE BINDING
PROTEIN-METABOLITE REGULATION
X-RAY CRYSTALLOGRAPHY
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Coenzyme A (CoA) is a key cellular metabolite which participates in diverse metabolic pathways, regulation of gene expression and the antioxidant defense mechanism. Human NME1 (hNME1), which is a moonlighting protein, was identified as a major CoA-binding protein. Biochemical studies showed that hNME1 is regulated by CoA through both covalent and non-covalent binding, which leads to a decrease in the hNME1 nucleoside diphosphate kinase (NDPK) activity. In this study, we expanded the knowledge on previous findings by focusing on the non-covalent mode of CoA binding to the hNME1. With X-ray crystallography, we solved the CoA bound structure of hNME1 (hNME1-CoA) and determined the stabilization interactions CoA forms within the nucleotide-binding site of hNME1. A hydrophobic patch stabilizing the CoA adenine ring, while salt bridges and hydrogen bonds stabilizing the phosphate groups of CoA were observed. With molecular dynamics studies, we extended our structural analysis by characterizing the hNME1-CoA structure and elucidating possible orientations of the pantetheine tail, which is absent in the X-ray structure due to its flexibility. Crystallographic studies suggested the involvement of arginine 58 and threonine 94 in mediating specific interactions with CoA. Site-directed mutagenesis and CoA-based affinity purifications showed that arginine 58 mutation to glutamate (R58E) and threonine 94 mutation to aspartate (T94D) prevent hNME1 from binding to CoA. Overall, our results reveal a unique mode by which hNME1 binds CoA, which differs significantly from that of ADP binding: the α- and β-phosphates of CoA are oriented away from the nucleotide-binding site, while 3′-phosphate faces catalytic histidine 118 (H118). The interactions formed by the CoA adenine ring and phosphate groups contribute to the specific mode of CoA binding to hNME1.
Fil: Tossounian, Maria Armineh. Colegio Universitario de Londres; Reino Unido
Fil: Hristov, Stefan Denchev. Colegio Universitario de Londres; Reino Unido
Fil: Semelak, Jonathan Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Fil: Yu, Bess Yi Kun. Colegio Universitario de Londres; Reino Unido
Fil: Baczynska, Maria. Colegio Universitario de Londres; Reino Unido
Fil: Zhao, Yuhan. Colegio Universitario de Londres; Reino Unido
Fil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina
Fil: Trujillo, Madia. Universidad de la República; Uruguay
Fil: Filonenko, Valeriy. Colegio Universitario de Londres; Reino Unido
Fil: Gouge, Jerome. Colegio Universitario de Londres; Reino Unido
Fil: Gout, Ivan. Colegio Universitario de Londres; Reino Unido
description Coenzyme A (CoA) is a key cellular metabolite which participates in diverse metabolic pathways, regulation of gene expression and the antioxidant defense mechanism. Human NME1 (hNME1), which is a moonlighting protein, was identified as a major CoA-binding protein. Biochemical studies showed that hNME1 is regulated by CoA through both covalent and non-covalent binding, which leads to a decrease in the hNME1 nucleoside diphosphate kinase (NDPK) activity. In this study, we expanded the knowledge on previous findings by focusing on the non-covalent mode of CoA binding to the hNME1. With X-ray crystallography, we solved the CoA bound structure of hNME1 (hNME1-CoA) and determined the stabilization interactions CoA forms within the nucleotide-binding site of hNME1. A hydrophobic patch stabilizing the CoA adenine ring, while salt bridges and hydrogen bonds stabilizing the phosphate groups of CoA were observed. With molecular dynamics studies, we extended our structural analysis by characterizing the hNME1-CoA structure and elucidating possible orientations of the pantetheine tail, which is absent in the X-ray structure due to its flexibility. Crystallographic studies suggested the involvement of arginine 58 and threonine 94 in mediating specific interactions with CoA. Site-directed mutagenesis and CoA-based affinity purifications showed that arginine 58 mutation to glutamate (R58E) and threonine 94 mutation to aspartate (T94D) prevent hNME1 from binding to CoA. Overall, our results reveal a unique mode by which hNME1 binds CoA, which differs significantly from that of ADP binding: the α- and β-phosphates of CoA are oriented away from the nucleotide-binding site, while 3′-phosphate faces catalytic histidine 118 (H118). The interactions formed by the CoA adenine ring and phosphate groups contribute to the specific mode of CoA binding to hNME1.
publishDate 2023
dc.date.none.fl_str_mv 2023-05
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/11336/228510
Tossounian, Maria Armineh; Hristov, Stefan Denchev; Semelak, Jonathan Alexis; Yu, Bess Yi Kun; Baczynska, Maria; et al.; A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1; Multidisciplinary Digital Publishing Institute; International Journal of Molecular Sciences; 24; 11; 5-2023; 1-17
1422-0067
CONICET Digital
CONICET
url http://hdl.handle.net/11336/228510
identifier_str_mv Tossounian, Maria Armineh; Hristov, Stefan Denchev; Semelak, Jonathan Alexis; Yu, Bess Yi Kun; Baczynska, Maria; et al.; A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1; Multidisciplinary Digital Publishing Institute; International Journal of Molecular Sciences; 24; 11; 5-2023; 1-17
1422-0067
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/1422-0067/24/11/9359
info:eu-repo/semantics/altIdentifier/doi/10.3390/ijms24119359
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 Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
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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score 13.070432

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