Crystal structure of cis‐biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase from a PCB degrader at 2.0 Å resolution
cis‐Biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+‐enzyme complex was determined by molecular replacement and refined to an R‐value of 17.9% at 2.0 Å. As a member of the short‐chain al...
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| Veröffentlicht in: | Protein science 1998-06, Vol.7 (6), p.1286-1293 |
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| container_title | Protein science |
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| creator | Hülsmeyer, Martin Hecht, Hans‐Jürgen Niefind, Karsten Schomburg, Dietmar Hofer, Bernd Timmis, Kenneth N. Eltis, Lindsay D. |
| description | cis‐Biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+‐enzyme complex was determined by molecular replacement and refined to an R‐value of 17.9% at 2.0 Å. As a member of the short‐chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two‐step reaction mechanism is proposed for cis‐dihydrodiol dehydrogenases. |
| doi_str_mv | 10.1002/pro.5560070603 |
| format | Article |
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The crystal structure of the NAD+‐enzyme complex was determined by molecular replacement and refined to an R‐value of 17.9% at 2.0 Å. As a member of the short‐chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two‐step reaction mechanism is proposed for cis‐dihydrodiol dehydrogenases.</description><identifier>ISSN: 0961-8368</identifier><identifier>EISSN: 1469-896X</identifier><identifier>DOI: 10.1002/pro.5560070603</identifier><identifier>PMID: 9655331</identifier><language>eng</language><publisher>Bristol: Cold Spring Harbor Laboratory Press</publisher><subject>Asparagine ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Hydrogen Bonding ; Macromolecular Substances ; Models, Molecular ; NAD - metabolism ; NAD‐dependent oxidoreductase ; Oxidoreductases - chemistry ; Oxidoreductases - metabolism ; PCB degradation ; Polychlorinated Biphenyls - metabolism ; Protein Folding ; short‐chain alcohol dehydrogenase ; substrate docking ; Substrate Specificity ; X‐ray crystallography</subject><ispartof>Protein science, 1998-06, Vol.7 (6), p.1286-1293</ispartof><rights>Copyright © 1998 The Protein Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4163-21bc7732f546735f161e1834fa5ed5915d5820ab506882eabc06ff20bd3d22b33</citedby><cites>FETCH-LOGICAL-c4163-21bc7732f546735f161e1834fa5ed5915d5820ab506882eabc06ff20bd3d22b33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144030/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144030/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,1417,1433,27924,27925,45574,45575,46409,46833,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/9655331$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hülsmeyer, Martin</creatorcontrib><creatorcontrib>Hecht, Hans‐Jürgen</creatorcontrib><creatorcontrib>Niefind, Karsten</creatorcontrib><creatorcontrib>Schomburg, Dietmar</creatorcontrib><creatorcontrib>Hofer, Bernd</creatorcontrib><creatorcontrib>Timmis, Kenneth N.</creatorcontrib><creatorcontrib>Eltis, Lindsay D.</creatorcontrib><title>Crystal structure of cis‐biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase from a PCB degrader at 2.0 Å resolution</title><title>Protein science</title><addtitle>Protein Sci</addtitle><description>cis‐Biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+‐enzyme complex was determined by molecular replacement and refined to an R‐value of 17.9% at 2.0 Å. As a member of the short‐chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two‐step reaction mechanism is proposed for cis‐dihydrodiol dehydrogenases.</description><subject>Asparagine</subject><subject>Binding Sites</subject><subject>Crystallization</subject><subject>Crystallography, X-Ray</subject><subject>Hydrogen Bonding</subject><subject>Macromolecular Substances</subject><subject>Models, Molecular</subject><subject>NAD - metabolism</subject><subject>NAD‐dependent oxidoreductase</subject><subject>Oxidoreductases - chemistry</subject><subject>Oxidoreductases - metabolism</subject><subject>PCB degradation</subject><subject>Polychlorinated Biphenyls - metabolism</subject><subject>Protein Folding</subject><subject>short‐chain alcohol dehydrogenase</subject><subject>substrate docking</subject><subject>Substrate Specificity</subject><subject>X‐ray crystallography</subject><issn>0961-8368</issn><issn>1469-896X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1998</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc1u1DAUhS1EVYbClh2SV6zI9Po3yQYJRvxUqtQKgcTOcuLrGaNMPNhJUXZs2PNOvAlPQuiMyrBi42vfc-7nKx1CnjBYMgB-vktxqZQGKEGDuEcWTOq6qGr96T5ZQK1ZUQldPSAPc_4MAJJxcUpOa62UEGxBblZpyoPtaB7S2A5jQho9bUP-9e1HE3Yb7KduvvLnYj5d2EwuRRfiUQ9ve2vsbUbqU9xSS69Xr6jDdbIOE7UD5UugP7_ThDl24xBi_4iceNtlfHyoZ-Tjm9cfVu-Ky6u3F6uXl0UrmRYFZ01bloJ7JXUplGeaIauE9FahUzVTTlUcbKNAVxVH27SgvefQOOE4b4Q4Iy_23N3YbNG12A_JdmaXwtamyUQbzL9KHzZmHW8MZ1KCgBnw7ABI8cuIeTDbkFvsOttjHLMp67qSpeSzcbk3tinmnNDffcLA_ElqfkfzN6l54Onxanf2QzSzXu_1r6HD6T80c_3-6oj9Gz7Tpjo</recordid><startdate>199806</startdate><enddate>199806</enddate><creator>Hülsmeyer, Martin</creator><creator>Hecht, Hans‐Jürgen</creator><creator>Niefind, Karsten</creator><creator>Schomburg, Dietmar</creator><creator>Hofer, Bernd</creator><creator>Timmis, Kenneth N.</creator><creator>Eltis, Lindsay D.</creator><general>Cold Spring Harbor Laboratory Press</general><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>7X8</scope><scope>5PM</scope></search><sort><creationdate>199806</creationdate><title>Crystal structure of cis‐biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase from a PCB degrader at 2.0 Å resolution</title><author>Hülsmeyer, Martin ; Hecht, Hans‐Jürgen ; Niefind, Karsten ; Schomburg, Dietmar ; Hofer, Bernd ; Timmis, Kenneth N. ; Eltis, Lindsay D.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4163-21bc7732f546735f161e1834fa5ed5915d5820ab506882eabc06ff20bd3d22b33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1998</creationdate><topic>Asparagine</topic><topic>Binding Sites</topic><topic>Crystallization</topic><topic>Crystallography, X-Ray</topic><topic>Hydrogen Bonding</topic><topic>Macromolecular Substances</topic><topic>Models, Molecular</topic><topic>NAD - metabolism</topic><topic>NAD‐dependent oxidoreductase</topic><topic>Oxidoreductases - chemistry</topic><topic>Oxidoreductases - metabolism</topic><topic>PCB degradation</topic><topic>Polychlorinated Biphenyls - metabolism</topic><topic>Protein Folding</topic><topic>short‐chain alcohol dehydrogenase</topic><topic>substrate docking</topic><topic>Substrate Specificity</topic><topic>X‐ray crystallography</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hülsmeyer, Martin</creatorcontrib><creatorcontrib>Hecht, Hans‐Jürgen</creatorcontrib><creatorcontrib>Niefind, Karsten</creatorcontrib><creatorcontrib>Schomburg, Dietmar</creatorcontrib><creatorcontrib>Hofer, Bernd</creatorcontrib><creatorcontrib>Timmis, Kenneth N.</creatorcontrib><creatorcontrib>Eltis, Lindsay D.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Protein science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hülsmeyer, Martin</au><au>Hecht, Hans‐Jürgen</au><au>Niefind, Karsten</au><au>Schomburg, Dietmar</au><au>Hofer, Bernd</au><au>Timmis, Kenneth N.</au><au>Eltis, Lindsay D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Crystal structure of cis‐biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase from a PCB degrader at 2.0 Å resolution</atitle><jtitle>Protein science</jtitle><addtitle>Protein Sci</addtitle><date>1998-06</date><risdate>1998</risdate><volume>7</volume><issue>6</issue><spage>1286</spage><epage>1293</epage><pages>1286-1293</pages><issn>0961-8368</issn><eissn>1469-896X</eissn><abstract>cis‐Biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+‐enzyme complex was determined by molecular replacement and refined to an R‐value of 17.9% at 2.0 Å. As a member of the short‐chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two‐step reaction mechanism is proposed for cis‐dihydrodiol dehydrogenases.</abstract><cop>Bristol</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>9655331</pmid><doi>10.1002/pro.5560070603</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| source | Wiley Online Library - AutoHoldings Journals; MEDLINE; EZB-FREE-00999 freely available EZB journals; Wiley Online Library (Open Access Collection); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Asparagine Binding Sites Crystallization Crystallography, X-Ray Hydrogen Bonding Macromolecular Substances Models, Molecular NAD - metabolism NAD‐dependent oxidoreductase Oxidoreductases - chemistry Oxidoreductases - metabolism PCB degradation Polychlorinated Biphenyls - metabolism Protein Folding short‐chain alcohol dehydrogenase substrate docking Substrate Specificity X‐ray crystallography |
| title | Crystal structure of cis‐biphenyl‐2,3‐dihydrodiol‐2,3‐dehydrogenase from a PCB degrader at 2.0 Å resolution |
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