Mechanistic insights into 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase, a key enzyme of the MEP terpenoid biosynthetic pathway
The binding mode of 1‐deoxy‐d‐xylulose 5‐phosphate (DXP) to 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase (DXR) (EC 1.1.1.267) from Escherichia coli was investigated via 18O isotope exchange experiments and determination of the kinetic parameters of the reaction. The results support a C3–C4 substr...
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| creator | Li, Heng Tian, Jie Sun, Wei Qin, Wei Gao, Wen‐Yun |
| description | The binding mode of 1‐deoxy‐d‐xylulose 5‐phosphate (DXP) to 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase (DXR) (EC 1.1.1.267) from Escherichia coli was investigated via 18O isotope exchange experiments and determination of the kinetic parameters of the reaction. The results support a C3–C4 substrate binding mode in which DXP chelates a DXR‐bound divalent cation via its hydroxyl groups at C3 and C4. Based on this binding mode and the early results, a catalytic cycle for the conversion of DXP to 2‐methyl‐d‐erythritol 4‐phosphate mediated by DXR including a pseudo‐single molecule transition state of the retro‐aldol intermediates is proposed. Taking into account the binding mode of DXP and the catalytic cycle of DXR, the mechanistic insights of DXR are disclosed and the current discrepancies concerning the catalysis of this enzyme are interpreted within the accepted retro‐aldol/aldol sequence.
A C3–C4 DXP binding mode and a catalytic cycle for DXR are established. Taking into account the binding mode of DXP and the catalytic cycle of DXR, the mechanistic insights of DXR are disclosed and the current discrepancies concerning the catalysis of this enzyme are interpreted within the accepted retro‐aldol/aldol sequence. |
| doi_str_mv | 10.1111/febs.12516 |
| format | Article |
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A C3–C4 DXP binding mode and a catalytic cycle for DXR are established. Taking into account the binding mode of DXP and the catalytic cycle of DXR, the mechanistic insights of DXR are disclosed and the current discrepancies concerning the catalysis of this enzyme are interpreted within the accepted retro‐aldol/aldol sequence.</description><identifier>ISSN: 1742-464X</identifier><identifier>EISSN: 1742-4658</identifier><identifier>DOI: 10.1111/febs.12516</identifier><identifier>PMID: 24010408</identifier><language>eng</language><publisher>England: Blackwell Publishing Ltd</publisher><subject>1‐deoxy‐d‐xylulose 5‐phosphate ; 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase ; Aldose-Ketose Isomerases - chemistry ; Aldose-Ketose Isomerases - metabolism ; binding mode ; Biosynthesis ; Biosynthetic Pathways ; catalytic cycle ; E coli ; Enzymes ; Erythritol - analogs & derivatives ; Erythritol - biosynthesis ; Erythritol - chemistry ; Escherichia coli ; Escherichia coli - enzymology ; Escherichia coli Proteins - chemistry ; Escherichia coli Proteins - metabolism ; Kinetics ; Magnetic Resonance Spectroscopy ; MEP pathway ; Models, Biological ; Molecular Structure ; Pentosephosphates - chemistry ; Pentosephosphates - metabolism ; Reaction kinetics ; Spectrometry, Mass, Electrospray Ionization ; Sugar Phosphates - biosynthesis ; Sugar Phosphates - chemistry ; Terpenes - chemistry ; Terpenes - metabolism</subject><ispartof>The FEBS journal, 2013-11, Vol.280 (22), p.5896-5905</ispartof><rights>2013 FEBS</rights><rights>2013 FEBS.</rights><rights>Copyright © 2013 Federation of European Biochemical Societies</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4266-2042d609d4966531383aa6edffc897a6c94f6c323983df1b1ac93b4e61c87d743</citedby><cites>FETCH-LOGICAL-c4266-2042d609d4966531383aa6edffc897a6c94f6c323983df1b1ac93b4e61c87d743</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Ffebs.12516$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Ffebs.12516$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,1427,27901,27902,45550,45551,46384,46808</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24010408$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Heng</creatorcontrib><creatorcontrib>Tian, Jie</creatorcontrib><creatorcontrib>Sun, Wei</creatorcontrib><creatorcontrib>Qin, Wei</creatorcontrib><creatorcontrib>Gao, Wen‐Yun</creatorcontrib><title>Mechanistic insights into 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase, a key enzyme of the MEP terpenoid biosynthetic pathway</title><title>The FEBS journal</title><addtitle>FEBS J</addtitle><description>The binding mode of 1‐deoxy‐d‐xylulose 5‐phosphate (DXP) to 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase (DXR) (EC 1.1.1.267) from Escherichia coli was investigated via 18O isotope exchange experiments and determination of the kinetic parameters of the reaction. The results support a C3–C4 substrate binding mode in which DXP chelates a DXR‐bound divalent cation via its hydroxyl groups at C3 and C4. Based on this binding mode and the early results, a catalytic cycle for the conversion of DXP to 2‐methyl‐d‐erythritol 4‐phosphate mediated by DXR including a pseudo‐single molecule transition state of the retro‐aldol intermediates is proposed. Taking into account the binding mode of DXP and the catalytic cycle of DXR, the mechanistic insights of DXR are disclosed and the current discrepancies concerning the catalysis of this enzyme are interpreted within the accepted retro‐aldol/aldol sequence.
A C3–C4 DXP binding mode and a catalytic cycle for DXR are established. Taking into account the binding mode of DXP and the catalytic cycle of DXR, the mechanistic insights of DXR are disclosed and the current discrepancies concerning the catalysis of this enzyme are interpreted within the accepted retro‐aldol/aldol sequence.</description><subject>1‐deoxy‐d‐xylulose 5‐phosphate</subject><subject>1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase</subject><subject>Aldose-Ketose Isomerases - chemistry</subject><subject>Aldose-Ketose Isomerases - metabolism</subject><subject>binding mode</subject><subject>Biosynthesis</subject><subject>Biosynthetic Pathways</subject><subject>catalytic cycle</subject><subject>E coli</subject><subject>Enzymes</subject><subject>Erythritol - analogs & derivatives</subject><subject>Erythritol - biosynthesis</subject><subject>Erythritol - chemistry</subject><subject>Escherichia coli</subject><subject>Escherichia coli - enzymology</subject><subject>Escherichia coli Proteins - chemistry</subject><subject>Escherichia coli Proteins - metabolism</subject><subject>Kinetics</subject><subject>Magnetic Resonance Spectroscopy</subject><subject>MEP pathway</subject><subject>Models, Biological</subject><subject>Molecular Structure</subject><subject>Pentosephosphates - chemistry</subject><subject>Pentosephosphates - metabolism</subject><subject>Reaction kinetics</subject><subject>Spectrometry, Mass, Electrospray Ionization</subject><subject>Sugar Phosphates - biosynthesis</subject><subject>Sugar Phosphates - chemistry</subject><subject>Terpenes - chemistry</subject><subject>Terpenes - metabolism</subject><issn>1742-464X</issn><issn>1742-4658</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkUuL1jAUhoMozkU3_gAJuBHxG3Nr2ix1-EaFGRRUcFfS5NRmbJtOkjLTWbl152_0l5j6jbNwIR44nAsP7-HwIvSIkiOa40ULTTyirKDyDtqnpWAbIYvq7m0vPu-hgxjPCeGFUOo-2mOCUCJItY--n4Hp9Ohicga7MbovXYq5SR7Tn99-WPBXy1pzXi393PsIuMjD1Pk4dToBDmBnk7yLfoCgIzzHGn-FBcN4vQyAfYtTB_hs-x4nCBOM3lncOB-XMe_Xq5NO3aVeHqB7re4jPLyph-jTyfbj8ZvN6bvXb49fnm6MYFJuGBHMSqKsUFIWnPKKay3Btq2pVKmlUaKVhjOuKm5b2lBtFG8ESGqq0paCH6KnO90p-IsZYqoHFw30vR7Bz7GmQjFJSqrK_0BFSYkshczok7_Qcz-HMT-yUqKQjBVVpp7tKBN8jAHaegpu0GGpKalXL-vVy_q3lxl-fCM5NwPYW_SPeRmgO-DS9bD8Q6o-2b76sBP9BWR0rgk</recordid><startdate>201311</startdate><enddate>201311</enddate><creator>Li, Heng</creator><creator>Tian, Jie</creator><creator>Sun, Wei</creator><creator>Qin, Wei</creator><creator>Gao, Wen‐Yun</creator><general>Blackwell Publishing Ltd</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>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201311</creationdate><title>Mechanistic insights into 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase, a key enzyme of the MEP terpenoid biosynthetic pathway</title><author>Li, Heng ; Tian, Jie ; Sun, Wei ; Qin, Wei ; Gao, Wen‐Yun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4266-2042d609d4966531383aa6edffc897a6c94f6c323983df1b1ac93b4e61c87d743</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>1‐deoxy‐d‐xylulose 5‐phosphate</topic><topic>1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase</topic><topic>Aldose-Ketose Isomerases - chemistry</topic><topic>Aldose-Ketose Isomerases - metabolism</topic><topic>binding mode</topic><topic>Biosynthesis</topic><topic>Biosynthetic Pathways</topic><topic>catalytic cycle</topic><topic>E coli</topic><topic>Enzymes</topic><topic>Erythritol - analogs & derivatives</topic><topic>Erythritol - biosynthesis</topic><topic>Erythritol - chemistry</topic><topic>Escherichia coli</topic><topic>Escherichia coli - enzymology</topic><topic>Escherichia coli Proteins - chemistry</topic><topic>Escherichia coli Proteins - metabolism</topic><topic>Kinetics</topic><topic>Magnetic Resonance Spectroscopy</topic><topic>MEP pathway</topic><topic>Models, Biological</topic><topic>Molecular Structure</topic><topic>Pentosephosphates - chemistry</topic><topic>Pentosephosphates - metabolism</topic><topic>Reaction kinetics</topic><topic>Spectrometry, Mass, Electrospray Ionization</topic><topic>Sugar Phosphates - biosynthesis</topic><topic>Sugar Phosphates - chemistry</topic><topic>Terpenes - chemistry</topic><topic>Terpenes - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Heng</creatorcontrib><creatorcontrib>Tian, Jie</creatorcontrib><creatorcontrib>Sun, Wei</creatorcontrib><creatorcontrib>Qin, Wei</creatorcontrib><creatorcontrib>Gao, Wen‐Yun</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The FEBS journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Heng</au><au>Tian, Jie</au><au>Sun, Wei</au><au>Qin, Wei</au><au>Gao, Wen‐Yun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mechanistic insights into 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase, a key enzyme of the MEP terpenoid biosynthetic pathway</atitle><jtitle>The FEBS journal</jtitle><addtitle>FEBS J</addtitle><date>2013-11</date><risdate>2013</risdate><volume>280</volume><issue>22</issue><spage>5896</spage><epage>5905</epage><pages>5896-5905</pages><issn>1742-464X</issn><eissn>1742-4658</eissn><abstract>The binding mode of 1‐deoxy‐d‐xylulose 5‐phosphate (DXP) to 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase (DXR) (EC 1.1.1.267) from Escherichia coli was investigated via 18O isotope exchange experiments and determination of the kinetic parameters of the reaction. The results support a C3–C4 substrate binding mode in which DXP chelates a DXR‐bound divalent cation via its hydroxyl groups at C3 and C4. Based on this binding mode and the early results, a catalytic cycle for the conversion of DXP to 2‐methyl‐d‐erythritol 4‐phosphate mediated by DXR including a pseudo‐single molecule transition state of the retro‐aldol intermediates is proposed. Taking into account the binding mode of DXP and the catalytic cycle of DXR, the mechanistic insights of DXR are disclosed and the current discrepancies concerning the catalysis of this enzyme are interpreted within the accepted retro‐aldol/aldol sequence.
A C3–C4 DXP binding mode and a catalytic cycle for DXR are established. Taking into account the binding mode of DXP and the catalytic cycle of DXR, the mechanistic insights of DXR are disclosed and the current discrepancies concerning the catalysis of this enzyme are interpreted within the accepted retro‐aldol/aldol sequence.</abstract><cop>England</cop><pub>Blackwell Publishing Ltd</pub><pmid>24010408</pmid><doi>10.1111/febs.12516</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 1‐deoxy‐d‐xylulose 5‐phosphate 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase Aldose-Ketose Isomerases - chemistry Aldose-Ketose Isomerases - metabolism binding mode Biosynthesis Biosynthetic Pathways catalytic cycle E coli Enzymes Erythritol - analogs & derivatives Erythritol - biosynthesis Erythritol - chemistry Escherichia coli Escherichia coli - enzymology Escherichia coli Proteins - chemistry Escherichia coli Proteins - metabolism Kinetics Magnetic Resonance Spectroscopy MEP pathway Models, Biological Molecular Structure Pentosephosphates - chemistry Pentosephosphates - metabolism Reaction kinetics Spectrometry, Mass, Electrospray Ionization Sugar Phosphates - biosynthesis Sugar Phosphates - chemistry Terpenes - chemistry Terpenes - metabolism |
| title | Mechanistic insights into 1‐deoxy‐d‐xylulose 5‐phosphate reductoisomerase, a key enzyme of the MEP terpenoid biosynthetic pathway |
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