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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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 |
doi_str_mv | 10.1038/nature12061 |
format | Article |
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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. ; Williams, Howard J. ; Dangott, Lawrence J. ; Chakrabarti, Mrinmoy ; Raushel, Frank M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c420t-276bc9c1700cb1b885f57687b066c1d64a8630d9b05ca4f953e7ea1a28ba5fcf3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>631/45/173</topic><topic>631/92/607</topic><topic>Aerobiosis</topic><topic>Archaea - metabolism</topic><topic>Bacteria - metabolism</topic><topic>Bacterial Proteins - chemistry</topic><topic>Bacterial Proteins - metabolism</topic><topic>Biocatalysis</topic><topic>Biosynthesis</topic><topic>Deoxyadenosines - chemistry</topic><topic>Deoxyadenosines - metabolism</topic><topic>Electron Spin Resonance Spectroscopy</topic><topic>Enzymes</topic><topic>Glycine - chemistry</topic><topic>Glycine - metabolism</topic><topic>Greenhouse gases</topic><topic>Humanities and Social Sciences</topic><topic>Hydrogen - metabolism</topic><topic>letter</topic><topic>Lyases - chemistry</topic><topic>Lyases - metabolism</topic><topic>Marine organisms</topic><topic>Mass Spectrometry</topic><topic>Methane</topic><topic>Methane - biosynthesis</topic><topic>Methane - chemistry</topic><topic>Methane - metabolism</topic><topic>Methionine - metabolism</topic><topic>multidisciplinary</topic><topic>Mutant Proteins - chemistry</topic><topic>Mutant Proteins - genetics</topic><topic>Mutant Proteins - metabolism</topic><topic>Pentosephosphates - chemistry</topic><topic>Pentosephosphates - metabolism</topic><topic>Proteins</topic><topic>Ribonucleotide reductase</topic><topic>S-Adenosylmethionine - metabolism</topic><topic>Science</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kamat, Siddhesh S.</creatorcontrib><creatorcontrib>Williams, Howard J.</creatorcontrib><creatorcontrib>Dangott, Lawrence J.</creatorcontrib><creatorcontrib>Chakrabarti, Mrinmoy</creatorcontrib><creatorcontrib>Raushel, Frank M.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>ProQuest Nursing and Allied Health Journals</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Health and Medical</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Psychology Database (Alumni)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>eLibrary</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><jtitle>Nature (London)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kamat, Siddhesh S.</au><au>Williams, Howard J.</au><au>Dangott, Lawrence J.</au><au>Chakrabarti, Mrinmoy</au><au>Raushel, Frank M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The catalytic mechanism for aerobic formation of methane by bacteria</atitle><jtitle>Nature (London)</jtitle><stitle>Nature</stitle><addtitle>Nature</addtitle><date>2013-05-02</date><risdate>2013</risdate><volume>497</volume><issue>7447</issue><spage>132</spage><epage>136</epage><pages>132-136</pages><issn>0028-0836</issn><eissn>1476-4687</eissn><coden>NATUAS</coden><abstract>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.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>23615610</pmid><doi>10.1038/nature12061</doi><tpages>5</tpages></addata></record> |
fulltext | fulltext |
identifier | ISSN: 0028-0836 |
ispartof | Nature (London), 2013-05, Vol.497 (7447), p.132-136 |
issn | 0028-0836 1476-4687 |
language | eng |
recordid | cdi_proquest_miscellaneous_1348499894 |
source | MEDLINE; Nature; SpringerLink Journals - AutoHoldings |
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 |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-07T20%3A20%3A05IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20catalytic%20mechanism%20for%20aerobic%20formation%20of%20methane%20by%20bacteria&rft.jtitle=Nature%20(London)&rft.au=Kamat,%20Siddhesh%20S.&rft.date=2013-05-02&rft.volume=497&rft.issue=7447&rft.spage=132&rft.epage=136&rft.pages=132-136&rft.issn=0028-0836&rft.eissn=1476-4687&rft.coden=NATUAS&rft_id=info:doi/10.1038/nature12061&rft_dat=%3Cproquest_cross%3E2973308911%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1352835753&rft_id=info:pmid/23615610&rfr_iscdi=true |