The catalytic mechanism for aerobic formation of methane by bacteria

A mechanism is proposed for the formation of methane by bacteria, through the cleavage of a highly unreactive carbon–phosphorus bond in methyl phosphonate by PhnJ in the bacterial C–P lyase complex. Novel bacterial biosynthesis of methane Aerobic marine organisms produce significant quantities of th...

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Veröffentlicht in:Nature (London) 2013-05, Vol.497 (7447), p.132-136
Hauptverfasser: Kamat, Siddhesh S., Williams, Howard J., Dangott, Lawrence J., Chakrabarti, Mrinmoy, Raushel, Frank M.
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container_issue 7447
container_start_page 132
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Williams, Howard J.
Dangott, Lawrence J.
Chakrabarti, Mrinmoy
Raushel, Frank M.
description A mechanism is proposed for the formation of methane by bacteria, through the cleavage of a highly unreactive carbon–phosphorus bond in methyl phosphonate by PhnJ in the bacterial C–P lyase complex. Novel bacterial biosynthesis of methane Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S -adenosyl- L -methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate. Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms 1 . These bacteria apparently catalyse the formation of methane through the cleavage of the highly unreactive carbon–phosphorus bond in methyl phosphonate (MPn), but the biological or terrestrial source of this compound is unclear 2 . However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate 3 and the bacterial C–P lyase complex is known to convert MPn to methane 4 , 5 , 6 , 7 . In addition to MPn, the bacterial C–P lyase complex catalyses C–P bond cleavage of many alkyl phosphonates when the environmental concentration of phosphate is low 4 , 5 , 6 , 7 . PhnJ from the C–P lyase complex catalyses an unprecedented C–P bond cleavage reaction of ribose-1-phosphonate-5-phosphate to methane and ribose-1,2-cyclic-phosphate-5-phosphate. This reaction requires a redox-active [4Fe–4S]-cluster and S -adenosyl- l -methionine, which is reductively cleaved to l -methionine and 5′-deoxyadenosine 8 . Here we show that PhnJ is a novel radical S -adenosyl- l -methionine enzyme that catalyses C–P bond cleavage through the initial formation of a 5′-deoxyadenosyl radical and two protein-based radicals localized at Gly 32 and Cys 272. During this transformation, the pro-R hydrogen from Gly 32 is transferred to the 5′-deoxyadenosyl radical to form 5′-deoxyadenosine and the pro-S hydrogen is transferred to the radical intermediate that ultimately generates methane. A comprehensive reaction mecha
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Novel bacterial biosynthesis of methane Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S -adenosyl- L -methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate. Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms 1 . These bacteria apparently catalyse the formation of methane through the cleavage of the highly unreactive carbon–phosphorus bond in methyl phosphonate (MPn), but the biological or terrestrial source of this compound is unclear 2 . However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate 3 and the bacterial C–P lyase complex is known to convert MPn to methane 4 , 5 , 6 , 7 . In addition to MPn, the bacterial C–P lyase complex catalyses C–P bond cleavage of many alkyl phosphonates when the environmental concentration of phosphate is low 4 , 5 , 6 , 7 . PhnJ from the C–P lyase complex catalyses an unprecedented C–P bond cleavage reaction of ribose-1-phosphonate-5-phosphate to methane and ribose-1,2-cyclic-phosphate-5-phosphate. This reaction requires a redox-active [4Fe–4S]-cluster and S -adenosyl- l -methionine, which is reductively cleaved to l -methionine and 5′-deoxyadenosine 8 . Here we show that PhnJ is a novel radical S -adenosyl- l -methionine enzyme that catalyses C–P bond cleavage through the initial formation of a 5′-deoxyadenosyl radical and two protein-based radicals localized at Gly 32 and Cys 272. During this transformation, the pro-R hydrogen from Gly 32 is transferred to the 5′-deoxyadenosyl radical to form 5′-deoxyadenosine and the pro-S hydrogen is transferred to the radical intermediate that ultimately generates methane. A comprehensive reaction mechanism is proposed for cleavage of the C–P bond by the C–P lyase complex that uses a covalent thiophosphate intermediate for methane and phosphate formation.</description><identifier>ISSN: 0028-0836</identifier><identifier>EISSN: 1476-4687</identifier><identifier>DOI: 10.1038/nature12061</identifier><identifier>PMID: 23615610</identifier><identifier>CODEN: NATUAS</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/45/173 ; 631/92/607 ; Aerobiosis ; Archaea - metabolism ; Bacteria - metabolism ; Bacterial Proteins - chemistry ; Bacterial Proteins - metabolism ; Biocatalysis ; Biosynthesis ; Deoxyadenosines - chemistry ; Deoxyadenosines - metabolism ; Electron Spin Resonance Spectroscopy ; Enzymes ; Glycine - chemistry ; Glycine - metabolism ; Greenhouse gases ; Humanities and Social Sciences ; Hydrogen - metabolism ; letter ; Lyases - chemistry ; Lyases - metabolism ; Marine organisms ; Mass Spectrometry ; Methane ; Methane - biosynthesis ; Methane - chemistry ; Methane - metabolism ; Methionine - metabolism ; multidisciplinary ; Mutant Proteins - chemistry ; Mutant Proteins - genetics ; Mutant Proteins - metabolism ; Pentosephosphates - chemistry ; Pentosephosphates - metabolism ; Proteins ; Ribonucleotide reductase ; S-Adenosylmethionine - metabolism ; Science</subject><ispartof>Nature (London), 2013-05, Vol.497 (7447), p.132-136</ispartof><rights>Springer Nature Limited 2013</rights><rights>Copyright Nature Publishing Group May 2, 2013</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c420t-276bc9c1700cb1b885f57687b066c1d64a8630d9b05ca4f953e7ea1a28ba5fcf3</citedby><cites>FETCH-LOGICAL-c420t-276bc9c1700cb1b885f57687b066c1d64a8630d9b05ca4f953e7ea1a28ba5fcf3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nature12061$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nature12061$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23615610$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kamat, Siddhesh S.</creatorcontrib><creatorcontrib>Williams, Howard J.</creatorcontrib><creatorcontrib>Dangott, Lawrence J.</creatorcontrib><creatorcontrib>Chakrabarti, Mrinmoy</creatorcontrib><creatorcontrib>Raushel, Frank M.</creatorcontrib><title>The catalytic mechanism for aerobic formation of methane by bacteria</title><title>Nature (London)</title><addtitle>Nature</addtitle><addtitle>Nature</addtitle><description>A mechanism is proposed for the formation of methane by bacteria, through the cleavage of a highly unreactive carbon–phosphorus bond in methyl phosphonate by PhnJ in the bacterial C–P lyase complex. Novel bacterial biosynthesis of methane Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S -adenosyl- L -methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate. Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms 1 . These bacteria apparently catalyse the formation of methane through the cleavage of the highly unreactive carbon–phosphorus bond in methyl phosphonate (MPn), but the biological or terrestrial source of this compound is unclear 2 . However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate 3 and the bacterial C–P lyase complex is known to convert MPn to methane 4 , 5 , 6 , 7 . In addition to MPn, the bacterial C–P lyase complex catalyses C–P bond cleavage of many alkyl phosphonates when the environmental concentration of phosphate is low 4 , 5 , 6 , 7 . PhnJ from the C–P lyase complex catalyses an unprecedented C–P bond cleavage reaction of ribose-1-phosphonate-5-phosphate to methane and ribose-1,2-cyclic-phosphate-5-phosphate. This reaction requires a redox-active [4Fe–4S]-cluster and S -adenosyl- l -methionine, which is reductively cleaved to l -methionine and 5′-deoxyadenosine 8 . Here we show that PhnJ is a novel radical S -adenosyl- l -methionine enzyme that catalyses C–P bond cleavage through the initial formation of a 5′-deoxyadenosyl radical and two protein-based radicals localized at Gly 32 and Cys 272. During this transformation, the pro-R hydrogen from Gly 32 is transferred to the 5′-deoxyadenosyl radical to form 5′-deoxyadenosine and the pro-S hydrogen is transferred to the radical intermediate that ultimately generates methane. A comprehensive reaction mechanism is proposed for cleavage of the C–P bond by the C–P lyase complex that uses a covalent thiophosphate intermediate for methane and phosphate formation.</description><subject>631/45/173</subject><subject>631/92/607</subject><subject>Aerobiosis</subject><subject>Archaea - metabolism</subject><subject>Bacteria - metabolism</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biocatalysis</subject><subject>Biosynthesis</subject><subject>Deoxyadenosines - chemistry</subject><subject>Deoxyadenosines - metabolism</subject><subject>Electron Spin Resonance Spectroscopy</subject><subject>Enzymes</subject><subject>Glycine - chemistry</subject><subject>Glycine - metabolism</subject><subject>Greenhouse gases</subject><subject>Humanities and Social Sciences</subject><subject>Hydrogen - metabolism</subject><subject>letter</subject><subject>Lyases - chemistry</subject><subject>Lyases - metabolism</subject><subject>Marine organisms</subject><subject>Mass Spectrometry</subject><subject>Methane</subject><subject>Methane - biosynthesis</subject><subject>Methane - chemistry</subject><subject>Methane - metabolism</subject><subject>Methionine - metabolism</subject><subject>multidisciplinary</subject><subject>Mutant Proteins - chemistry</subject><subject>Mutant Proteins - genetics</subject><subject>Mutant Proteins - metabolism</subject><subject>Pentosephosphates - chemistry</subject><subject>Pentosephosphates - metabolism</subject><subject>Proteins</subject><subject>Ribonucleotide reductase</subject><subject>S-Adenosylmethionine - metabolism</subject><subject>Science</subject><issn>0028-0836</issn><issn>1476-4687</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNpt0EtLAzEUBeAgiq3VlXsZcCPo6M3kOUupTyi4qeshSRM7ZR41ySz67420ShFXCbkfN4eD0DmGWwxE3nUqDt7iAjg-QGNMBc8pl-IQjQEKmYMkfIROQlgBAMOCHqNRQThmHMMYPcyXNjMqqmYTa5O11ixVV4c2c73PlPW9Tq_p3qpY913Wu0RiIjbTm0wrE62v1Sk6cqoJ9mx3TtD70-N8-pLP3p5fp_ez3NACYl4Irk1psAAwGmspmWMiJdXAucELTpXkBBalBmYUdSUjVliFVSG1Ys44MkFX271r338ONsSqrYOxTZPy9EOoMKGSlqUsaaKXf-iqH3yX0iXFCkmYYCSp660yvg_BW1etfd0qv6kwVN_lVnvlJn2x2zno1i5-7U-bCdxsQUij7sP6vU__2fcF9sGDzQ</recordid><startdate>20130502</startdate><enddate>20130502</enddate><creator>Kamat, Siddhesh S.</creator><creator>Williams, Howard J.</creator><creator>Dangott, Lawrence J.</creator><creator>Chakrabarti, Mrinmoy</creator><creator>Raushel, Frank M.</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</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>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7T5</scope><scope>7TG</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88G</scope><scope>88I</scope><scope>8AF</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BEC</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2M</scope><scope>M2O</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>MBDVC</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PSYQQ</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>R05</scope><scope>RC3</scope><scope>S0X</scope><scope>SOI</scope><scope>7X8</scope></search><sort><creationdate>20130502</creationdate><title>The catalytic mechanism for aerobic formation of methane by bacteria</title><author>Kamat, Siddhesh S. ; 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Novel bacterial biosynthesis of methane Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S -adenosyl- L -methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate. Methane is a potent greenhouse gas that is produced in significant quantities by aerobic marine organisms 1 . These bacteria apparently catalyse the formation of methane through the cleavage of the highly unreactive carbon–phosphorus bond in methyl phosphonate (MPn), but the biological or terrestrial source of this compound is unclear 2 . However, the ocean-dwelling bacterium Nitrosopumilus maritimus catalyses the biosynthesis of MPn from 2-hydroxyethyl phosphonate 3 and the bacterial C–P lyase complex is known to convert MPn to methane 4 , 5 , 6 , 7 . In addition to MPn, the bacterial C–P lyase complex catalyses C–P bond cleavage of many alkyl phosphonates when the environmental concentration of phosphate is low 4 , 5 , 6 , 7 . PhnJ from the C–P lyase complex catalyses an unprecedented C–P bond cleavage reaction of ribose-1-phosphonate-5-phosphate to methane and ribose-1,2-cyclic-phosphate-5-phosphate. This reaction requires a redox-active [4Fe–4S]-cluster and S -adenosyl- l -methionine, which is reductively cleaved to l -methionine and 5′-deoxyadenosine 8 . Here we show that PhnJ is a novel radical S -adenosyl- l -methionine enzyme that catalyses C–P bond cleavage through the initial formation of a 5′-deoxyadenosyl radical and two protein-based radicals localized at Gly 32 and Cys 272. During this transformation, the pro-R hydrogen from Gly 32 is transferred to the 5′-deoxyadenosyl radical to form 5′-deoxyadenosine and the pro-S hydrogen is transferred to the radical intermediate that ultimately generates methane. A comprehensive reaction mechanism is proposed for cleavage of the C–P bond by the C–P lyase complex that uses a covalent thiophosphate intermediate for methane and phosphate formation.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>23615610</pmid><doi>10.1038/nature12061</doi><tpages>5</tpages></addata></record>
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subjects 631/45/173
631/92/607
Aerobiosis
Archaea - metabolism
Bacteria - metabolism
Bacterial Proteins - chemistry
Bacterial Proteins - metabolism
Biocatalysis
Biosynthesis
Deoxyadenosines - chemistry
Deoxyadenosines - metabolism
Electron Spin Resonance Spectroscopy
Enzymes
Glycine - chemistry
Glycine - metabolism
Greenhouse gases
Humanities and Social Sciences
Hydrogen - metabolism
letter
Lyases - chemistry
Lyases - metabolism
Marine organisms
Mass Spectrometry
Methane
Methane - biosynthesis
Methane - chemistry
Methane - metabolism
Methionine - metabolism
multidisciplinary
Mutant Proteins - chemistry
Mutant Proteins - genetics
Mutant Proteins - metabolism
Pentosephosphates - chemistry
Pentosephosphates - metabolism
Proteins
Ribonucleotide reductase
S-Adenosylmethionine - metabolism
Science
title The catalytic mechanism for aerobic formation of methane by bacteria
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