Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium
Glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium (tvGlcDH) is highly active towards D‐glucose and D‐galactose, but does not utilize aldopentoses such as D‐xylose as substrates. In the present study, the crystal structures of substrate/cofactor‐free tvGlcDH and of a tv...
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| Veröffentlicht in: | Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2014-05, Vol.70 (5), p.1271-1280 |
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| container_title | Acta crystallographica. Section D, Biological crystallography. |
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| creator | Kanoh, Yoshitaka Uehara, Seiichiroh Iwata, Hideyuki Yoneda, Kazunari Ohshima, Toshihisa Sakuraba, Haruhiko |
| description | Glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium (tvGlcDH) is highly active towards D‐glucose and D‐galactose, but does not utilize aldopentoses such as D‐xylose as substrates. In the present study, the crystal structures of substrate/cofactor‐free tvGlcDH and of a tvGlcDH T277F mutant in a binary complex with NADP and in a ternary complex with D‐glucose and nicotinic acid adenine dinucleotide phosphate, an NADP analogue, were determined at resolutions of 2.6, 2.25 and 2.33 Å, respectively. The overall structure of each monomer showed notable similarity to that of the enzyme from Sulfolobus solfataricus (ssGlcDH‐1), which accepts a broad range of C5 and C6 sugars as substrates. However, the amino‐acid residues of tvGlcDH involved in substrate binding markedly differed from those of ssGlcDH‐1. Structural comparison revealed that a decreased number of interactions between the C3‐hydroxyl group of the sugar and the enzyme are likely to be responsible for the lack of reactivity of tvGlcDH towards D‐xylose. |
| doi_str_mv | 10.1107/S1399004714002363 |
| format | Article |
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In the present study, the crystal structures of substrate/cofactor‐free tvGlcDH and of a tvGlcDH T277F mutant in a binary complex with NADP and in a ternary complex with D‐glucose and nicotinic acid adenine dinucleotide phosphate, an NADP analogue, were determined at resolutions of 2.6, 2.25 and 2.33 Å, respectively. The overall structure of each monomer showed notable similarity to that of the enzyme from Sulfolobus solfataricus (ssGlcDH‐1), which accepts a broad range of C5 and C6 sugars as substrates. However, the amino‐acid residues of tvGlcDH involved in substrate binding markedly differed from those of ssGlcDH‐1. Structural comparison revealed that a decreased number of interactions between the C3‐hydroxyl group of the sugar and the enzyme are likely to be responsible for the lack of reactivity of tvGlcDH towards D‐xylose.</description><identifier>ISSN: 1399-0047</identifier><identifier>ISSN: 0907-4449</identifier><identifier>EISSN: 1399-0047</identifier><identifier>DOI: 10.1107/S1399004714002363</identifier><identifier>PMID: 24816096</identifier><language>eng</language><publisher>5 Abbey Square, Chester, Cheshire CH1 2HU, England: International Union of Crystallography</publisher><subject>archaea ; Base Sequence ; Binding Sites ; Crystal structure ; Crystallography, X-Ray ; Enzymes ; Glucose ; Glucose - chemistry ; Glucose - metabolism ; Glucose 1-Dehydrogenase - chemistry ; Glucose 1-Dehydrogenase - genetics ; Glucose 1-Dehydrogenase - isolation & purification ; Glucose 1-Dehydrogenase - metabolism ; glucose dehydrogenase ; Models, Molecular ; Molecular Sequence Data ; Monomers ; Mutation ; NADP - analogs & derivatives ; NADP - chemistry ; NADP - metabolism ; Protein Conformation ; Residues ; Similarity ; Substrate Specificity ; Sugars ; Sulfolobus ; Sulfolobus solfataricus - enzymology ; thermophiles ; Thermoplasma - enzymology ; Thermoplasma volcanium</subject><ispartof>Acta crystallographica. 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Section D, Biological crystallography.</title><addtitle>Acta Crystallographica D</addtitle><description>Glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium (tvGlcDH) is highly active towards D‐glucose and D‐galactose, but does not utilize aldopentoses such as D‐xylose as substrates. In the present study, the crystal structures of substrate/cofactor‐free tvGlcDH and of a tvGlcDH T277F mutant in a binary complex with NADP and in a ternary complex with D‐glucose and nicotinic acid adenine dinucleotide phosphate, an NADP analogue, were determined at resolutions of 2.6, 2.25 and 2.33 Å, respectively. The overall structure of each monomer showed notable similarity to that of the enzyme from Sulfolobus solfataricus (ssGlcDH‐1), which accepts a broad range of C5 and C6 sugars as substrates. However, the amino‐acid residues of tvGlcDH involved in substrate binding markedly differed from those of ssGlcDH‐1. Structural comparison revealed that a decreased number of interactions between the C3‐hydroxyl group of the sugar and the enzyme are likely to be responsible for the lack of reactivity of tvGlcDH towards D‐xylose.</description><subject>archaea</subject><subject>Base Sequence</subject><subject>Binding Sites</subject><subject>Crystal structure</subject><subject>Crystallography, X-Ray</subject><subject>Enzymes</subject><subject>Glucose</subject><subject>Glucose - chemistry</subject><subject>Glucose - metabolism</subject><subject>Glucose 1-Dehydrogenase - chemistry</subject><subject>Glucose 1-Dehydrogenase - genetics</subject><subject>Glucose 1-Dehydrogenase - isolation & purification</subject><subject>Glucose 1-Dehydrogenase - metabolism</subject><subject>glucose dehydrogenase</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Monomers</subject><subject>Mutation</subject><subject>NADP - analogs & derivatives</subject><subject>NADP - chemistry</subject><subject>NADP - metabolism</subject><subject>Protein Conformation</subject><subject>Residues</subject><subject>Similarity</subject><subject>Substrate Specificity</subject><subject>Sugars</subject><subject>Sulfolobus</subject><subject>Sulfolobus solfataricus - enzymology</subject><subject>thermophiles</subject><subject>Thermoplasma - enzymology</subject><subject>Thermoplasma volcanium</subject><issn>1399-0047</issn><issn>0907-4449</issn><issn>1399-0047</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkUFv1DAQhS1ERcvCD-CCInHpJdRjO3F8rEppEVUR6iLEyZrYzsYliRc7Afbfk7ClQnCAgzWe8feexnqEPAP6EoDKkxvgSlEqJAhKGS_5A3K0jPJl9vC3-yF5nNItnSHG5SNyyEQFJVXlEWlvxjiZcYrYZX5IftOOcx1DtukmE5LLrGt3NoaNG3Dumhj6bGzdcmIf0Hgbtq3vvMkwmhZdGLL1z6dth6nH7GvoDA5-6p-Qgwa75J7e1RX58Pp8fXaZX727eHN2epUbUVCWs0IpxilraqwRVSltWSHlDQULBgEsKlk468qGQV0Z5xSX1DqkVW0qC5avyPHedxvDl8mlUfc-Gdd1OLgwJQ2FAAGlEvAfKBMgBSsX9MUf6G2Y4jB_ZKHYvDUrxEzBnjIxpBRdo7fR9xh3GqheEtN_JTZrnt85T3Xv7L3iV0QzoPbAN9-53b8d9emnV-z9ZbF0K5LvtT6N7vu9FuNnXUouC_3x-kIX7HotJAP9lv8A5L-xBg</recordid><startdate>201405</startdate><enddate>201405</enddate><creator>Kanoh, Yoshitaka</creator><creator>Uehara, Seiichiroh</creator><creator>Iwata, Hideyuki</creator><creator>Yoneda, Kazunari</creator><creator>Ohshima, Toshihisa</creator><creator>Sakuraba, Haruhiko</creator><general>International Union of Crystallography</general><general>Wiley Subscription Services, Inc</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QP</scope><scope>7SP</scope><scope>7SR</scope><scope>7TK</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>H8D</scope><scope>JG9</scope><scope>L7M</scope><scope>7X8</scope></search><sort><creationdate>201405</creationdate><title>Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium</title><author>Kanoh, Yoshitaka ; Uehara, Seiichiroh ; Iwata, Hideyuki ; Yoneda, Kazunari ; Ohshima, Toshihisa ; Sakuraba, Haruhiko</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4502-25992302fbabaa967d68a03f01d1ca11da975ede6f21b8cee9370dea08bc8d1d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>archaea</topic><topic>Base Sequence</topic><topic>Binding Sites</topic><topic>Crystal structure</topic><topic>Crystallography, X-Ray</topic><topic>Enzymes</topic><topic>Glucose</topic><topic>Glucose - chemistry</topic><topic>Glucose - metabolism</topic><topic>Glucose 1-Dehydrogenase - chemistry</topic><topic>Glucose 1-Dehydrogenase - genetics</topic><topic>Glucose 1-Dehydrogenase - isolation & purification</topic><topic>Glucose 1-Dehydrogenase - metabolism</topic><topic>glucose dehydrogenase</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Monomers</topic><topic>Mutation</topic><topic>NADP - analogs & derivatives</topic><topic>NADP - chemistry</topic><topic>NADP - metabolism</topic><topic>Protein Conformation</topic><topic>Residues</topic><topic>Similarity</topic><topic>Substrate Specificity</topic><topic>Sugars</topic><topic>Sulfolobus</topic><topic>Sulfolobus solfataricus - enzymology</topic><topic>thermophiles</topic><topic>Thermoplasma - enzymology</topic><topic>Thermoplasma volcanium</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kanoh, Yoshitaka</creatorcontrib><creatorcontrib>Uehara, Seiichiroh</creatorcontrib><creatorcontrib>Iwata, Hideyuki</creatorcontrib><creatorcontrib>Yoneda, Kazunari</creatorcontrib><creatorcontrib>Ohshima, Toshihisa</creatorcontrib><creatorcontrib>Sakuraba, Haruhiko</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Materials Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>Acta crystallographica. Section D, Biological crystallography.</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kanoh, Yoshitaka</au><au>Uehara, Seiichiroh</au><au>Iwata, Hideyuki</au><au>Yoneda, Kazunari</au><au>Ohshima, Toshihisa</au><au>Sakuraba, Haruhiko</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium</atitle><jtitle>Acta crystallographica. Section D, Biological crystallography.</jtitle><addtitle>Acta Crystallographica D</addtitle><date>2014-05</date><risdate>2014</risdate><volume>70</volume><issue>5</issue><spage>1271</spage><epage>1280</epage><pages>1271-1280</pages><issn>1399-0047</issn><issn>0907-4449</issn><eissn>1399-0047</eissn><abstract>Glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium (tvGlcDH) is highly active towards D‐glucose and D‐galactose, but does not utilize aldopentoses such as D‐xylose as substrates. In the present study, the crystal structures of substrate/cofactor‐free tvGlcDH and of a tvGlcDH T277F mutant in a binary complex with NADP and in a ternary complex with D‐glucose and nicotinic acid adenine dinucleotide phosphate, an NADP analogue, were determined at resolutions of 2.6, 2.25 and 2.33 Å, respectively. The overall structure of each monomer showed notable similarity to that of the enzyme from Sulfolobus solfataricus (ssGlcDH‐1), which accepts a broad range of C5 and C6 sugars as substrates. However, the amino‐acid residues of tvGlcDH involved in substrate binding markedly differed from those of ssGlcDH‐1. Structural comparison revealed that a decreased number of interactions between the C3‐hydroxyl group of the sugar and the enzyme are likely to be responsible for the lack of reactivity of tvGlcDH towards D‐xylose.</abstract><cop>5 Abbey Square, Chester, Cheshire CH1 2HU, England</cop><pub>International Union of Crystallography</pub><pmid>24816096</pmid><doi>10.1107/S1399004714002363</doi><tpages>10</tpages></addata></record> |
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| subjects | archaea Base Sequence Binding Sites Crystal structure Crystallography, X-Ray Enzymes Glucose Glucose - chemistry Glucose - metabolism Glucose 1-Dehydrogenase - chemistry Glucose 1-Dehydrogenase - genetics Glucose 1-Dehydrogenase - isolation & purification Glucose 1-Dehydrogenase - metabolism glucose dehydrogenase Models, Molecular Molecular Sequence Data Monomers Mutation NADP - analogs & derivatives NADP - chemistry NADP - metabolism Protein Conformation Residues Similarity Substrate Specificity Sugars Sulfolobus Sulfolobus solfataricus - enzymology thermophiles Thermoplasma - enzymology Thermoplasma volcanium |
| title | Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium |
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