Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297
The metal-independent lipase from Streptomyces albidoflavus NA297 (SaPLA1) is a phospholipase A1 as it preferentially hydrolyzes the sn-1 acyl ester in glycerophospholipids, yielding a fatty acid and 2-acyl-lysophospholipid. The molecular mechanism underlying the substrate binding by SaPLA1 is curre...
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| Veröffentlicht in: | Journal of structural biology 2013-05, Vol.182 (2), p.192-196 |
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| creator | Murayama, Kazutaka Kano, Kota Matsumoto, Yusaku Sugimori, Daisuke |
| description | The metal-independent lipase from Streptomyces albidoflavus NA297 (SaPLA1) is a phospholipase A1 as it preferentially hydrolyzes the sn-1 acyl ester in glycerophospholipids, yielding a fatty acid and 2-acyl-lysophospholipid. The molecular mechanism underlying the substrate binding by SaPLA1 is currently unknown. In this study, the crystal structure of SaPLA1 was determined at 1.75Å resolutions by molecular replacement. A structural similarity search indicated the highest structural similarity to an esterase from Streptomyces scabies, followed by GDSL family enzymes. The SaPLA1 active site is composed of a Ser-His dyad (Ser11 and His218), whereby stabilization of the imidazole is provided by the main-chain carbonyl oxygen of Ser216, a common variation of the catalytic triad in many serine hydrolases, where this carbonyl maintains the orientation of the active site histidine residue. The hydrophobic pocket and cleft for lipid binding are adjacent to the active site, and are approximately 13–15Å deep and 14–16Å long. A partial polyethylene glycol structure was found in this hydrophobic pocket. |
| doi_str_mv | 10.1016/j.jsb.2013.02.003 |
| format | Article |
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The molecular mechanism underlying the substrate binding by SaPLA1 is currently unknown. In this study, the crystal structure of SaPLA1 was determined at 1.75Å resolutions by molecular replacement. A structural similarity search indicated the highest structural similarity to an esterase from Streptomyces scabies, followed by GDSL family enzymes. The SaPLA1 active site is composed of a Ser-His dyad (Ser11 and His218), whereby stabilization of the imidazole is provided by the main-chain carbonyl oxygen of Ser216, a common variation of the catalytic triad in many serine hydrolases, where this carbonyl maintains the orientation of the active site histidine residue. The hydrophobic pocket and cleft for lipid binding are adjacent to the active site, and are approximately 13–15Å deep and 14–16Å long. A partial polyethylene glycol structure was found in this hydrophobic pocket.</description><identifier>ISSN: 1047-8477</identifier><identifier>EISSN: 1095-8657</identifier><identifier>DOI: 10.1016/j.jsb.2013.02.003</identifier><identifier>PMID: 23416196</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Amino Acid Sequence ; Catalytic Domain - genetics ; Catalytic dyad ; Crystallization ; Hydrophobic pocket ; Metal-independent lipase ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Phospholipase A1 ; Phospholipases A1 - chemistry ; Polyethylene Glycols - chemistry ; Protein Conformation ; Species Specificity ; Streptomyces - enzymology</subject><ispartof>Journal of structural biology, 2013-05, Vol.182 (2), p.192-196</ispartof><rights>2013 Elsevier Inc.</rights><rights>Copyright © 2013 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c334t-136b7d852c53d34e91bdabf4c4ebd7c8e90afb3d2ea0642228e45e1e8a60f2443</citedby><cites>FETCH-LOGICAL-c334t-136b7d852c53d34e91bdabf4c4ebd7c8e90afb3d2ea0642228e45e1e8a60f2443</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jsb.2013.02.003$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23416196$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Murayama, Kazutaka</creatorcontrib><creatorcontrib>Kano, Kota</creatorcontrib><creatorcontrib>Matsumoto, Yusaku</creatorcontrib><creatorcontrib>Sugimori, Daisuke</creatorcontrib><title>Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297</title><title>Journal of structural biology</title><addtitle>J Struct Biol</addtitle><description>The metal-independent lipase from Streptomyces albidoflavus NA297 (SaPLA1) is a phospholipase A1 as it preferentially hydrolyzes the sn-1 acyl ester in glycerophospholipids, yielding a fatty acid and 2-acyl-lysophospholipid. The molecular mechanism underlying the substrate binding by SaPLA1 is currently unknown. In this study, the crystal structure of SaPLA1 was determined at 1.75Å resolutions by molecular replacement. A structural similarity search indicated the highest structural similarity to an esterase from Streptomyces scabies, followed by GDSL family enzymes. The SaPLA1 active site is composed of a Ser-His dyad (Ser11 and His218), whereby stabilization of the imidazole is provided by the main-chain carbonyl oxygen of Ser216, a common variation of the catalytic triad in many serine hydrolases, where this carbonyl maintains the orientation of the active site histidine residue. The hydrophobic pocket and cleft for lipid binding are adjacent to the active site, and are approximately 13–15Å deep and 14–16Å long. A partial polyethylene glycol structure was found in this hydrophobic pocket.</description><subject>Amino Acid Sequence</subject><subject>Catalytic Domain - genetics</subject><subject>Catalytic dyad</subject><subject>Crystallization</subject><subject>Hydrophobic pocket</subject><subject>Metal-independent lipase</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Molecular Structure</subject><subject>Phospholipase A1</subject><subject>Phospholipases A1 - chemistry</subject><subject>Polyethylene Glycols - chemistry</subject><subject>Protein Conformation</subject><subject>Species Specificity</subject><subject>Streptomyces - enzymology</subject><issn>1047-8477</issn><issn>1095-8657</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kD1PwzAQhi0EolD4ASwoI0uCz3a-xFRVfKqCAZgtx76IREkdbKdS_z2pWhgZTnfD877SPYRcAU2AQnbbJq2vEkaBJ5QllPIjcga0TOMiS_Pj3S3yuBB5PiPn3reUUgEMTsmMcQEZlNkZeVm6rQ-qi3xwow6jw8jW0fBl_TRdMyiP0QKi2tk-eg8Oh2D7rUYfqa5qjK07tRl99LpgZX5BTmrVebw87Dn5fLj_WD7Fq7fH5-ViFWvORYiBZ1VuipTplBsusITKqKoWWmBlcl1gSVVdccNQ0UwwxgoUKQIWKqM1E4LPyc2-d3D2e0QfZN94jV2n1mhHL4HzgpcZg3JCYY9qZ713WMvBNb1yWwlU7hTKVk4K5U6hpExOCqfM9aF-rHo0f4lfZxNwtwdwenLToJNeN7jWaBqHOkhjm3_qfwBgJoFh</recordid><startdate>201305</startdate><enddate>201305</enddate><creator>Murayama, Kazutaka</creator><creator>Kano, Kota</creator><creator>Matsumoto, Yusaku</creator><creator>Sugimori, Daisuke</creator><general>Elsevier Inc</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></search><sort><creationdate>201305</creationdate><title>Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297</title><author>Murayama, Kazutaka ; Kano, Kota ; Matsumoto, Yusaku ; Sugimori, Daisuke</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c334t-136b7d852c53d34e91bdabf4c4ebd7c8e90afb3d2ea0642228e45e1e8a60f2443</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Amino Acid Sequence</topic><topic>Catalytic Domain - genetics</topic><topic>Catalytic dyad</topic><topic>Crystallization</topic><topic>Hydrophobic pocket</topic><topic>Metal-independent lipase</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Molecular Structure</topic><topic>Phospholipase A1</topic><topic>Phospholipases A1 - chemistry</topic><topic>Polyethylene Glycols - chemistry</topic><topic>Protein Conformation</topic><topic>Species Specificity</topic><topic>Streptomyces - enzymology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Murayama, Kazutaka</creatorcontrib><creatorcontrib>Kano, Kota</creatorcontrib><creatorcontrib>Matsumoto, Yusaku</creatorcontrib><creatorcontrib>Sugimori, Daisuke</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><jtitle>Journal of structural biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Murayama, Kazutaka</au><au>Kano, Kota</au><au>Matsumoto, Yusaku</au><au>Sugimori, Daisuke</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297</atitle><jtitle>Journal of structural biology</jtitle><addtitle>J Struct Biol</addtitle><date>2013-05</date><risdate>2013</risdate><volume>182</volume><issue>2</issue><spage>192</spage><epage>196</epage><pages>192-196</pages><issn>1047-8477</issn><eissn>1095-8657</eissn><abstract>The metal-independent lipase from Streptomyces albidoflavus NA297 (SaPLA1) is a phospholipase A1 as it preferentially hydrolyzes the sn-1 acyl ester in glycerophospholipids, yielding a fatty acid and 2-acyl-lysophospholipid. The molecular mechanism underlying the substrate binding by SaPLA1 is currently unknown. In this study, the crystal structure of SaPLA1 was determined at 1.75Å resolutions by molecular replacement. A structural similarity search indicated the highest structural similarity to an esterase from Streptomyces scabies, followed by GDSL family enzymes. The SaPLA1 active site is composed of a Ser-His dyad (Ser11 and His218), whereby stabilization of the imidazole is provided by the main-chain carbonyl oxygen of Ser216, a common variation of the catalytic triad in many serine hydrolases, where this carbonyl maintains the orientation of the active site histidine residue. The hydrophobic pocket and cleft for lipid binding are adjacent to the active site, and are approximately 13–15Å deep and 14–16Å long. A partial polyethylene glycol structure was found in this hydrophobic pocket.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>23416196</pmid><doi>10.1016/j.jsb.2013.02.003</doi><tpages>5</tpages></addata></record> |
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| ispartof | Journal of structural biology, 2013-05, Vol.182 (2), p.192-196 |
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| subjects | Amino Acid Sequence Catalytic Domain - genetics Catalytic dyad Crystallization Hydrophobic pocket Metal-independent lipase Models, Molecular Molecular Sequence Data Molecular Structure Phospholipase A1 Phospholipases A1 - chemistry Polyethylene Glycols - chemistry Protein Conformation Species Specificity Streptomyces - enzymology |
| title | Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297 |
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