Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization.
Identifieur interne : 001F01 ( Main/Exploration ); précédent : 001F00; suivant : 001F02Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization.
Auteurs : Yuichi Nishitani [Japon] ; Riku Aono ; Akira Nakamura ; Takaaki Sato ; Haruyuki Atomi ; Tadayuki Imanaka ; Kunio MikiSource :
- Journal of molecular biology [ 1089-8638 ] ; 2013.
Descripteurs français
- KwdFr :
- AMP (métabolisme), Alignement de séquences, Chromatographie sur gel, Conformation des protéines, Cristallographie aux rayons X, Données de séquences moléculaires, Modèles biologiques, Modèles moléculaires, Multimérisation de protéines, Pentosyltransferases (), Pentosyltransferases (métabolisme), Stabilité protéique, Séquence d'acides aminés, Température, Thermococcus (), Thermococcus (enzymologie).
- MESH :
- enzymologie : Thermococcus.
- métabolisme : AMP, Pentosyltransferases.
- Alignement de séquences, Chromatographie sur gel, Conformation des protéines, Cristallographie aux rayons X, Données de séquences moléculaires, Modèles biologiques, Modèles moléculaires, Multimérisation de protéines, Pentosyltransferases, Stabilité protéique, Séquence d'acides aminés, Température, Thermococcus.
English descriptors
- KwdEn :
- Adenosine Monophosphate (metabolism), Amino Acid Sequence, Chromatography, Gel, Crystallography, X-Ray, Models, Biological, Models, Molecular, Molecular Sequence Data, Pentosyltransferases (chemistry), Pentosyltransferases (metabolism), Protein Conformation, Protein Multimerization, Protein Stability, Sequence Alignment, Temperature, Thermococcus (chemistry), Thermococcus (enzymology).
- MESH :
- chemical , chemistry : Pentosyltransferases.
- chemical , metabolism : Adenosine Monophosphate, Pentosyltransferases.
- chemistry : Thermococcus.
- enzymology : Thermococcus.
- Amino Acid Sequence, Chromatography, Gel, Crystallography, X-Ray, Models, Biological, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Multimerization, Protein Stability, Sequence Alignment, Temperature.
Abstract
AMP phosphorylase (AMPpase) catalyzes the initial reaction in a novel AMP metabolic pathway recently found in archaea, converting AMP and phosphate into adenine and ribose 1,5-bisphosphate. Gel-filtration chromatography revealed that AMPpase from Thermococcus kodakarensis (Tk-AMPpase) forms an exceptionally large macromolecular structure (>40-mers) in solution. To investigate its unique multimerization feature, we determined the first crystal structures of Tk-AMPpase, in the apo-form and in complex with substrates. Structures of two truncated forms of Tk-AMPpase (Tk-AMPpaseΔN84 and Tk-AMPpaseΔC10) clarified that this multimerization is achieved by two dimer interfaces within a single molecule: one by the central domain and the other by the C-terminal domain, which consists of an unexpected domain-swapping interaction. The N-terminal domain, characteristic of archaeal enzymes, is essential for enzymatic activity, participating in multimerization as well as domain closure of the active site upon substrate binding. Moreover, biochemical analysis demonstrated that the macromolecular assembly of Tk-AMPpase contributes to its high thermostability, essential for an enzyme from a hyperthermophile. Our findings unveil a unique archaeal nucleotide phosphorylase that is distinct in both function and structure from previously known members of the nucleoside phosphorylase II family.
DOI: 10.1016/j.jmb.2013.04.026
PubMed: 23659790
Affiliations:
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Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502</wicri:regionArea><orgName type="university">Université de Kyoto</orgName><placeName><settlement type="city">Kyoto</settlement><region type="prefecture">Région du Kansai</region></placeName></affiliation></author><author><name sortKey="Aono, Riku" sort="Aono, Riku" uniqKey="Aono R" first="Riku" last="Aono">Riku Aono</name></author><author><name sortKey="Nakamura, Akira" sort="Nakamura, Akira" uniqKey="Nakamura A" first="Akira" last="Nakamura">Akira Nakamura</name></author><author><name sortKey="Sato, Takaaki" sort="Sato, Takaaki" uniqKey="Sato T" first="Takaaki" last="Sato">Takaaki Sato</name></author><author><name sortKey="Atomi, Haruyuki" sort="Atomi, Haruyuki" uniqKey="Atomi H" first="Haruyuki" last="Atomi">Haruyuki Atomi</name></author><author><name sortKey="Imanaka, Tadayuki" sort="Imanaka, Tadayuki" uniqKey="Imanaka T" first="Tadayuki" last="Imanaka">Tadayuki Imanaka</name></author><author><name sortKey="Miki, Kunio" sort="Miki, Kunio" uniqKey="Miki K" first="Kunio" last="Miki">Kunio Miki</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="eISSN">1089-8638</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adenosine Monophosphate (metabolism)</term><term>Amino Acid Sequence</term><term>Chromatography, Gel</term><term>Crystallography, X-Ray</term><term>Models, Biological</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Pentosyltransferases (chemistry)</term><term>Pentosyltransferases (metabolism)</term><term>Protein Conformation</term><term>Protein Multimerization</term><term>Protein Stability</term><term>Sequence Alignment</term><term>Temperature</term><term>Thermococcus (chemistry)</term><term>Thermococcus (enzymology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>AMP (métabolisme)</term><term>Alignement de séquences</term><term>Chromatographie sur gel</term><term>Conformation des protéines</term><term>Cristallographie aux rayons X</term><term>Données de séquences moléculaires</term><term>Modèles biologiques</term><term>Modèles moléculaires</term><term>Multimérisation de protéines</term><term>Pentosyltransferases ()</term><term>Pentosyltransferases (métabolisme)</term><term>Stabilité protéique</term><term>Séquence d'acides aminés</term><term>Température</term><term>Thermococcus ()</term><term>Thermococcus (enzymologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Pentosyltransferases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Adenosine Monophosphate</term><term>Pentosyltransferases</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Thermococcus</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Thermococcus</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Thermococcus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>AMP</term><term>Pentosyltransferases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Chromatography, Gel</term><term>Crystallography, X-Ray</term><term>Models, Biological</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Protein Conformation</term><term>Protein Multimerization</term><term>Protein Stability</term><term>Sequence Alignment</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Chromatographie sur gel</term><term>Conformation des protéines</term><term>Cristallographie aux rayons X</term><term>Données de séquences moléculaires</term><term>Modèles biologiques</term><term>Modèles moléculaires</term><term>Multimérisation de protéines</term><term>Pentosyltransferases</term><term>Stabilité protéique</term><term>Séquence d'acides aminés</term><term>Température</term><term>Thermococcus</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">AMP phosphorylase (AMPpase) catalyzes the initial reaction in a novel AMP metabolic pathway recently found in archaea, converting AMP and phosphate into adenine and ribose 1,5-bisphosphate. Gel-filtration chromatography revealed that AMPpase from Thermococcus kodakarensis (Tk-AMPpase) forms an exceptionally large macromolecular structure (>40-mers) in solution. To investigate its unique multimerization feature, we determined the first crystal structures of Tk-AMPpase, in the apo-form and in complex with substrates. Structures of two truncated forms of Tk-AMPpase (Tk-AMPpaseΔN84 and Tk-AMPpaseΔC10) clarified that this multimerization is achieved by two dimer interfaces within a single molecule: one by the central domain and the other by the C-terminal domain, which consists of an unexpected domain-swapping interaction. The N-terminal domain, characteristic of archaeal enzymes, is essential for enzymatic activity, participating in multimerization as well as domain closure of the active site upon substrate binding. Moreover, biochemical analysis demonstrated that the macromolecular assembly of Tk-AMPpase contributes to its high thermostability, essential for an enzyme from a hyperthermophile. Our findings unveil a unique archaeal nucleotide phosphorylase that is distinct in both function and structure from previously known members of the nucleoside phosphorylase II family.</div></front></TEI><affiliations><list><country><li>Japon</li></country><region><li>Région du Kansai</li></region><settlement><li>Kyoto</li></settlement><orgName><li>Université de Kyoto</li></orgName></list><tree><noCountry><name sortKey="Aono, Riku" sort="Aono, Riku" uniqKey="Aono R" first="Riku" last="Aono">Riku Aono</name><name sortKey="Atomi, Haruyuki" sort="Atomi, Haruyuki" uniqKey="Atomi H" first="Haruyuki" last="Atomi">Haruyuki Atomi</name><name sortKey="Imanaka, Tadayuki" sort="Imanaka, Tadayuki" uniqKey="Imanaka T" first="Tadayuki" last="Imanaka">Tadayuki Imanaka</name><name sortKey="Miki, Kunio" sort="Miki, Kunio" uniqKey="Miki K" first="Kunio" last="Miki">Kunio Miki</name><name sortKey="Nakamura, Akira" sort="Nakamura, Akira" uniqKey="Nakamura A" first="Akira" last="Nakamura">Akira Nakamura</name><name sortKey="Sato, Takaaki" sort="Sato, Takaaki" uniqKey="Sato T" first="Takaaki" last="Sato">Takaaki Sato</name></noCountry><country name="Japon"><region name="Région du Kansai"><name sortKey="Nishitani, Yuichi" sort="Nishitani, Yuichi" uniqKey="Nishitani Y" first="Yuichi" last="Nishitani">Yuichi Nishitani</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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