NMR structure of the R-module: a parallel beta-roll subunit from an Azotobacter vinelandii mannuronan C-5 epimerase.
Identifieur interne : 000140 ( Ncbi/Checkpoint ); précédent : 000139; suivant : 000141NMR structure of the R-module: a parallel beta-roll subunit from an Azotobacter vinelandii mannuronan C-5 epimerase.
Auteurs : Finn L. Aachmann [Danemark] ; Britt I G. Svanem ; Peter Güntert ; Steffen B. Petersen ; Svein Valla ; Reinhard WimmerSource :
- The Journal of biological chemistry [ 0021-9258 ] ; 2006.
Descripteurs français
- KwdFr :
- Acides aminés (), Acides hexuroniques (), Alginates (), Azotobacter vinelandii (enzymologie), Calcium (métabolisme), Carbohydrate epimerases (), Conformation des protéines, Conformation moléculaire, Données de séquences moléculaires, Ions, Liaison aux protéines, Modèles moléculaires, Modèles statistiques, Pliage des protéines, Polymères (), Spectroscopie par résonance magnétique, Structure secondaire des protéines, Structure tertiaire des protéines, Séquence d'acides aminés, Thulium ().
- MESH :
- enzymologie : Azotobacter vinelandii.
- métabolisme : Calcium.
- Acides aminés, Acides hexuroniques, Alginates, Carbohydrate epimerases, Conformation des protéines, Conformation moléculaire, Données de séquences moléculaires, Ions, Liaison aux protéines, Modèles moléculaires, Modèles statistiques, Pliage des protéines, Polymères, Spectroscopie par résonance magnétique, Structure secondaire des protéines, Structure tertiaire des protéines, Séquence d'acides aminés, Thulium.
English descriptors
- KwdEn :
- Alginates (chemistry), Amino Acid Sequence, Amino Acids (chemistry), Azotobacter vinelandii (enzymology), Calcium (metabolism), Carbohydrate Epimerases (chemistry), Hexuronic Acids (chemistry), Ions, Magnetic Resonance Spectroscopy, Models, Molecular, Models, Statistical, Molecular Conformation, Molecular Sequence Data, Polymers (chemistry), Protein Binding, Protein Conformation, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Thulium (chemistry).
- MESH :
- chemical , chemistry : Alginates, Amino Acids, Carbohydrate Epimerases, Hexuronic Acids, Polymers, Thulium.
- enzymology : Azotobacter vinelandii.
- chemical , metabolism : Calcium.
- Amino Acid Sequence, Ions, Magnetic Resonance Spectroscopy, Models, Molecular, Models, Statistical, Molecular Conformation, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary.
Abstract
In the bacterium Azotobacter vinelandii, a family of seven secreted and calcium-dependent mannuronan C-5 epimerases (AlgE1-7) has been identified. These epimerases are responsible for the epimerization of beta-d-mannuronic acid to alpha-l-guluronic acid in alginate polymers. The epimerases consist of two types of structural modules, designated A (one or two copies) and R (one to seven copies). The structure of the catalytically active A-module from the smallest epimerase AlgE4 (consisting of AR) has been solved recently. This paper describes the NMR structure of the R-module from AlgE4 and its titration with a substrate analogue and paramagnetic thulium ions. The R-module folds into a right-handed parallel beta-roll. The overall shape of the R-module is an elongated molecule with a positively charged patch that interacts with the substrate. Titration of the R-module with thulium indicated possible calcium binding sites in the loops formed by the nonarepeat sequences in the N-terminal part of the molecule and the importance of calcium binding for the stability of the R-module. Structure calculations showed that calcium ions can be incorporated in these loops without structural violations and changes. Based on the structure and the electrostatic surface potential of both the A- and R-module from AlgE4, a model for the appearance of the whole protein is proposed.
DOI: 10.1074/jbc.M510069200
PubMed: 16407237
Affiliations:
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pubmed:16407237Le document en format XML
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Aachmann</name><affiliation wicri:level="4"><nlm:affiliation>Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg</wicri:regionArea><orgName type="university">Université d'Aalborg</orgName><placeName><settlement type="city">Aalborg</settlement><region nuts="2" type="region">Jutland du Nord</region></placeName></affiliation></author><author><name sortKey="Svanem, Britt I G" sort="Svanem, Britt I G" uniqKey="Svanem B" first="Britt I G" last="Svanem">Britt I G. Svanem</name></author><author><name sortKey="Guntert, Peter" sort="Guntert, Peter" uniqKey="Guntert P" first="Peter" last="Güntert">Peter Güntert</name></author><author><name sortKey="Petersen, Steffen B" sort="Petersen, Steffen B" uniqKey="Petersen S" first="Steffen B" last="Petersen">Steffen B. Petersen</name></author><author><name sortKey="Valla, Svein" sort="Valla, Svein" uniqKey="Valla S" first="Svein" last="Valla">Svein Valla</name></author><author><name sortKey="Wimmer, Reinhard" sort="Wimmer, Reinhard" uniqKey="Wimmer R" first="Reinhard" last="Wimmer">Reinhard Wimmer</name></author></analytic><series><title level="j">The Journal of biological chemistry</title><idno type="ISSN">0021-9258</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alginates (chemistry)</term><term>Amino Acid Sequence</term><term>Amino Acids (chemistry)</term><term>Azotobacter vinelandii (enzymology)</term><term>Calcium (metabolism)</term><term>Carbohydrate Epimerases (chemistry)</term><term>Hexuronic Acids (chemistry)</term><term>Ions</term><term>Magnetic Resonance Spectroscopy</term><term>Models, Molecular</term><term>Models, Statistical</term><term>Molecular Conformation</term><term>Molecular Sequence Data</term><term>Polymers (chemistry)</term><term>Protein Binding</term><term>Protein Conformation</term><term>Protein Folding</term><term>Protein Structure, Secondary</term><term>Protein Structure, Tertiary</term><term>Thulium (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Acides aminés ()</term><term>Acides hexuroniques ()</term><term>Alginates ()</term><term>Azotobacter vinelandii (enzymologie)</term><term>Calcium (métabolisme)</term><term>Carbohydrate epimerases ()</term><term>Conformation des protéines</term><term>Conformation moléculaire</term><term>Données de séquences moléculaires</term><term>Ions</term><term>Liaison aux protéines</term><term>Modèles moléculaires</term><term>Modèles statistiques</term><term>Pliage des protéines</term><term>Polymères ()</term><term>Spectroscopie par résonance magnétique</term><term>Structure secondaire des protéines</term><term>Structure tertiaire des protéines</term><term>Séquence d'acides aminés</term><term>Thulium ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Alginates</term><term>Amino Acids</term><term>Carbohydrate Epimerases</term><term>Hexuronic Acids</term><term>Polymers</term><term>Thulium</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Azotobacter vinelandii</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Azotobacter vinelandii</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Calcium</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Calcium</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Ions</term><term>Magnetic Resonance Spectroscopy</term><term>Models, Molecular</term><term>Models, Statistical</term><term>Molecular Conformation</term><term>Molecular Sequence Data</term><term>Protein Binding</term><term>Protein Conformation</term><term>Protein Folding</term><term>Protein Structure, Secondary</term><term>Protein Structure, Tertiary</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Acides aminés</term><term>Acides hexuroniques</term><term>Alginates</term><term>Carbohydrate epimerases</term><term>Conformation des protéines</term><term>Conformation moléculaire</term><term>Données de séquences moléculaires</term><term>Ions</term><term>Liaison aux protéines</term><term>Modèles moléculaires</term><term>Modèles statistiques</term><term>Pliage des protéines</term><term>Polymères</term><term>Spectroscopie par résonance magnétique</term><term>Structure secondaire des protéines</term><term>Structure tertiaire des protéines</term><term>Séquence d'acides aminés</term><term>Thulium</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In the bacterium Azotobacter vinelandii, a family of seven secreted and calcium-dependent mannuronan C-5 epimerases (AlgE1-7) has been identified. These epimerases are responsible for the epimerization of beta-d-mannuronic acid to alpha-l-guluronic acid in alginate polymers. The epimerases consist of two types of structural modules, designated A (one or two copies) and R (one to seven copies). The structure of the catalytically active A-module from the smallest epimerase AlgE4 (consisting of AR) has been solved recently. This paper describes the NMR structure of the R-module from AlgE4 and its titration with a substrate analogue and paramagnetic thulium ions. The R-module folds into a right-handed parallel beta-roll. The overall shape of the R-module is an elongated molecule with a positively charged patch that interacts with the substrate. Titration of the R-module with thulium indicated possible calcium binding sites in the loops formed by the nonarepeat sequences in the N-terminal part of the molecule and the importance of calcium binding for the stability of the R-module. Structure calculations showed that calcium ions can be incorporated in these loops without structural violations and changes. Based on the structure and the electrostatic surface potential of both the A- and R-module from AlgE4, a model for the appearance of the whole protein is proposed.</div></front></TEI><affiliations><list><country><li>Danemark</li></country><region><li>Jutland du Nord</li></region><settlement><li>Aalborg</li></settlement><orgName><li>Université d'Aalborg</li></orgName></list><tree><noCountry><name sortKey="Guntert, Peter" sort="Guntert, Peter" uniqKey="Guntert P" first="Peter" last="Güntert">Peter Güntert</name><name sortKey="Petersen, Steffen B" sort="Petersen, Steffen B" uniqKey="Petersen S" first="Steffen B" last="Petersen">Steffen B. Petersen</name><name sortKey="Svanem, Britt I G" sort="Svanem, Britt I G" uniqKey="Svanem B" first="Britt I G" last="Svanem">Britt I G. Svanem</name><name sortKey="Valla, Svein" sort="Valla, Svein" uniqKey="Valla S" first="Svein" last="Valla">Svein Valla</name><name sortKey="Wimmer, Reinhard" sort="Wimmer, Reinhard" uniqKey="Wimmer R" first="Reinhard" last="Wimmer">Reinhard Wimmer</name></noCountry><country name="Danemark"><region name="Jutland du Nord"><name sortKey="Aachmann, Finn L" sort="Aachmann, Finn L" uniqKey="Aachmann F" first="Finn L" last="Aachmann">Finn L. Aachmann</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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