Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution
Autor(a) principal: | |
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Data de Publicação: | 1995 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/S0969-2126(01)00270-2 http://hdl.handle.net/11449/64662 |
Resumo: | Background: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldose-ketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. Results: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 Å resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. Conclusions: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger. |
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Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolutionα/β open structureAldose-ketose isomeraseAllosteric enzymeNAD-binding domain2 deoxy 2 aminoglucitol 6 phosphate2-deoxy-2-aminoglucitol-6-phosphatebacterial proteindrug derivativeenzyme inhibitorepimerasefructose 6 phosphatefructose phosphatefructose-6-phosphateglucosamineglucosamine 6 phosphateglucosamine 6 phosphate isomeraseglucosamine 6-phosphateglucosamine-6-phosphate isomeraseglucose 6 phosphateglucose phosphateisomerasenicotinamide adenine dinucleotidephosphatesorbitolsugar phosphateallosterismbinding sitebiosynthesiscatalysischemical structurechemistrydrug antagonismenzymologyEscherichia colimacromoleculemetabolismprotein conformationX ray crystallographyAldose-Ketose IsomerasesAllosteric RegulationBacterial ProteinsBinding SitesCarbohydrate EpimerasesCatalysisCrystallography, X-RayEnzyme InhibitorsFructosephosphatesGlucosamineGlucose-6-PhosphateGlucosephosphatesMacromolecular SubstancesModels, MolecularNADPhosphatesProtein ConformationSorbitolSugar PhosphatesBacteria (microorganisms)Background: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldose-ketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. Results: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 Å resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. Conclusions: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger.Inst. de Fisica de São Carlos Universidade de São Paulo, São Carlos, SP, 13560-970Departamento de Bioquímica Facultad de Medicina Univ. Nac. Auton. de México, 04510, México, D.F.Depto. de Fis. e Biofísica IB-UNESP, CP 510, Botucatu, 18618-000Depto. Reconocimiento Molec. y B. Instituto de Biotecnología Univ. Nac. Auton. de México, PO Box 510-3, Cuernavaca, MOR, 62250Depto. de Fis. e Biofísica IB-UNESP, CP 510, Botucatu, 18618-000Universidade de São Paulo (USP)Univ. Nac. Auton. de MéxicoUniversidade Estadual Paulista (Unesp)Oliva, GlauciusFontes, Marcos R.M. [UNESP]Garratt, Richard C.Altamirano, Myriam M.Calcagno, Mario L.Horjales, Eduardo2014-05-27T11:18:02Z2014-05-27T11:18:02Z1995-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1323-1332application/pdfhttp://dx.doi.org/10.1016/S0969-2126(01)00270-2Structure, v. 3, n. 12, p. 1323-1332, 1995.0969-2126http://hdl.handle.net/11449/6466210.1016/S0969-2126(01)00270-22-s2.0-00296460952-s2.0-0029646095.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengStructure4.9073,554info:eu-repo/semantics/openAccess2023-12-15T06:22:28Zoai:repositorio.unesp.br:11449/64662Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-12-15T06:22:28Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution |
title |
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution |
spellingShingle |
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution Oliva, Glaucius α/β open structure Aldose-ketose isomerase Allosteric enzyme NAD-binding domain 2 deoxy 2 aminoglucitol 6 phosphate 2-deoxy-2-aminoglucitol-6-phosphate bacterial protein drug derivative enzyme inhibitor epimerase fructose 6 phosphate fructose phosphate fructose-6-phosphate glucosamine glucosamine 6 phosphate glucosamine 6 phosphate isomerase glucosamine 6-phosphate glucosamine-6-phosphate isomerase glucose 6 phosphate glucose phosphate isomerase nicotinamide adenine dinucleotide phosphate sorbitol sugar phosphate allosterism binding site biosynthesis catalysis chemical structure chemistry drug antagonism enzymology Escherichia coli macromolecule metabolism protein conformation X ray crystallography Aldose-Ketose Isomerases Allosteric Regulation Bacterial Proteins Binding Sites Carbohydrate Epimerases Catalysis Crystallography, X-Ray Enzyme Inhibitors Fructosephosphates Glucosamine Glucose-6-Phosphate Glucosephosphates Macromolecular Substances Models, Molecular NAD Phosphates Protein Conformation Sorbitol Sugar Phosphates Bacteria (microorganisms) |
title_short |
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution |
title_full |
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution |
title_fullStr |
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution |
title_full_unstemmed |
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution |
title_sort |
Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution |
author |
Oliva, Glaucius |
author_facet |
Oliva, Glaucius Fontes, Marcos R.M. [UNESP] Garratt, Richard C. Altamirano, Myriam M. Calcagno, Mario L. Horjales, Eduardo |
author_role |
author |
author2 |
Fontes, Marcos R.M. [UNESP] Garratt, Richard C. Altamirano, Myriam M. Calcagno, Mario L. Horjales, Eduardo |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) Univ. Nac. Auton. de México Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Oliva, Glaucius Fontes, Marcos R.M. [UNESP] Garratt, Richard C. Altamirano, Myriam M. Calcagno, Mario L. Horjales, Eduardo |
dc.subject.por.fl_str_mv |
α/β open structure Aldose-ketose isomerase Allosteric enzyme NAD-binding domain 2 deoxy 2 aminoglucitol 6 phosphate 2-deoxy-2-aminoglucitol-6-phosphate bacterial protein drug derivative enzyme inhibitor epimerase fructose 6 phosphate fructose phosphate fructose-6-phosphate glucosamine glucosamine 6 phosphate glucosamine 6 phosphate isomerase glucosamine 6-phosphate glucosamine-6-phosphate isomerase glucose 6 phosphate glucose phosphate isomerase nicotinamide adenine dinucleotide phosphate sorbitol sugar phosphate allosterism binding site biosynthesis catalysis chemical structure chemistry drug antagonism enzymology Escherichia coli macromolecule metabolism protein conformation X ray crystallography Aldose-Ketose Isomerases Allosteric Regulation Bacterial Proteins Binding Sites Carbohydrate Epimerases Catalysis Crystallography, X-Ray Enzyme Inhibitors Fructosephosphates Glucosamine Glucose-6-Phosphate Glucosephosphates Macromolecular Substances Models, Molecular NAD Phosphates Protein Conformation Sorbitol Sugar Phosphates Bacteria (microorganisms) |
topic |
α/β open structure Aldose-ketose isomerase Allosteric enzyme NAD-binding domain 2 deoxy 2 aminoglucitol 6 phosphate 2-deoxy-2-aminoglucitol-6-phosphate bacterial protein drug derivative enzyme inhibitor epimerase fructose 6 phosphate fructose phosphate fructose-6-phosphate glucosamine glucosamine 6 phosphate glucosamine 6 phosphate isomerase glucosamine 6-phosphate glucosamine-6-phosphate isomerase glucose 6 phosphate glucose phosphate isomerase nicotinamide adenine dinucleotide phosphate sorbitol sugar phosphate allosterism binding site biosynthesis catalysis chemical structure chemistry drug antagonism enzymology Escherichia coli macromolecule metabolism protein conformation X ray crystallography Aldose-Ketose Isomerases Allosteric Regulation Bacterial Proteins Binding Sites Carbohydrate Epimerases Catalysis Crystallography, X-Ray Enzyme Inhibitors Fructosephosphates Glucosamine Glucose-6-Phosphate Glucosephosphates Macromolecular Substances Models, Molecular NAD Phosphates Protein Conformation Sorbitol Sugar Phosphates Bacteria (microorganisms) |
description |
Background: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldose-ketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. Results: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 Å resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. Conclusions: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger. |
publishDate |
1995 |
dc.date.none.fl_str_mv |
1995-12-01 2014-05-27T11:18:02Z 2014-05-27T11:18:02Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/S0969-2126(01)00270-2 Structure, v. 3, n. 12, p. 1323-1332, 1995. 0969-2126 http://hdl.handle.net/11449/64662 10.1016/S0969-2126(01)00270-2 2-s2.0-0029646095 2-s2.0-0029646095.pdf |
url |
http://dx.doi.org/10.1016/S0969-2126(01)00270-2 http://hdl.handle.net/11449/64662 |
identifier_str_mv |
Structure, v. 3, n. 12, p. 1323-1332, 1995. 0969-2126 10.1016/S0969-2126(01)00270-2 2-s2.0-0029646095 2-s2.0-0029646095.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Structure 4.907 3,554 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
1323-1332 application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1803649997577650176 |