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| | <StructureSection load='5g0r' size='340' side='right'caption='[[5g0r]], [[Resolution|resolution]] 1.25Å' scene=''> | | <StructureSection load='5g0r' size='340' side='right'caption='[[5g0r]], [[Resolution|resolution]] 1.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5g0r]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_marburgensis Methanothermobacter marburgensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G0R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G0R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5g0r]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_marburgensis Methanothermobacter marburgensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G0R FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F43:FACTOR+430'>F43</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.25Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGM:5-METHYL-ARGININE'>AGM</scene>, <scene name='pdbligand=DYA:DIDEHYDROASPARTATE'>DYA</scene>, <scene name='pdbligand=GL3:THIOGLYCIN'>GL3</scene>, <scene name='pdbligand=MGN:2-METHYL-GLUTAMINE'>MGN</scene>, <scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGM:5-METHYL-ARGININE'>AGM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DYA:DIDEHYDROASPARTATE'>DYA</scene>, <scene name='pdbligand=F43:FACTOR+430'>F43</scene>, <scene name='pdbligand=GL3:THIOGLYCIN'>GL3</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MGN:2-METHYL-GLUTAMINE'>MGN</scene>, <scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coenzyme-B_sulfoethylthiotransferase Coenzyme-B sulfoethylthiotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.4.1 2.8.4.1] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5g0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g0r OCA], [https://pdbe.org/5g0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g0r RCSB], [https://www.ebi.ac.uk/pdbsum/5g0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g0r ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5g0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g0r OCA], [http://pdbe.org/5g0r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g0r RCSB], [http://www.ebi.ac.uk/pdbsum/5g0r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g0r ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/MCRA_METTM MCRA_METTM]] Reduction of methyl-coenzyme M (2-(methylthio) ethanesulfonic acid) with 7-mercaptoheptanoylthreonine phosphate to methane and a heterodisulfide. [[http://www.uniprot.org/uniprot/MCRG_METTM MCRG_METTM]] Reduction of methyl-coenzyme M (2-(methylthio) ethanesulfonic acid) with 7-mercaptoheptanoylthreonine phosphate to methane and a heterodisulfide. [[http://www.uniprot.org/uniprot/MCRB_METTM MCRB_METTM]] Reduction of methyl-coenzyme M (2-(methylthio) ethanesulfonic acid) with 7-mercaptoheptanoylthreonine phosphate to methane and a heterodisulfide. | + | [https://www.uniprot.org/uniprot/MCRA_METTM MCRA_METTM] Reduction of methyl-coenzyme M (2-(methylthio) ethanesulfonic acid) with 7-mercaptoheptanoylthreonine phosphate to methane and a heterodisulfide. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Coenzyme-B sulfoethylthiotransferase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Methanothermobacter marburgensis]] | | [[Category: Methanothermobacter marburgensis]] |
| - | [[Category: Wagner, T]] | + | [[Category: Wagner T]] |
| - | [[Category: 3- nitrooxypropanol]]
| + | |
| - | [[Category: Binding site]]
| + | |
| - | [[Category: Catalysis]]
| + | |
| - | [[Category: Coenzyme]]
| + | |
| - | [[Category: Disulfide]]
| + | |
| - | [[Category: Greenhouse gas]]
| + | |
| - | [[Category: Hydrogen]]
| + | |
| - | [[Category: Inhibitor]]
| + | |
| - | [[Category: Ligand]]
| + | |
| - | [[Category: Mesna]]
| + | |
| - | [[Category: Metalloporphyrin]]
| + | |
| - | [[Category: Methane]]
| + | |
| - | [[Category: Methanobacterium]]
| + | |
| - | [[Category: Methyl-coenzymem]]
| + | |
| - | [[Category: Methyl-coenzymem reductase exposed to 3-nitrooxypropanol]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Oxdoreductase]]
| + | |
| - | [[Category: Oxidation-reduction]]
| + | |
| - | [[Category: Phosphothreonine]]
| + | |
| - | [[Category: Posttranslational modification]]
| + | |
| - | [[Category: Thioglycine]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
5g0r is a 6 chain structure with sequence from Methanothermobacter marburgensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.25Å |
| Ligands: | , , , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
MCRA_METTM Reduction of methyl-coenzyme M (2-(methylthio) ethanesulfonic acid) with 7-mercaptoheptanoylthreonine phosphate to methane and a heterodisulfide.
Publication Abstract from PubMed
Ruminants, such as cows, sheep, and goats, predominantly ferment in their rumen plant material to acetate, propionate, butyrate, CO2, and methane. Whereas the short fatty acids are absorbed and metabolized by the animals, the greenhouse gas methane escapes via eructation and breathing of the animals into the atmosphere. Along with the methane, up to 12% of the gross energy content of the feedstock is lost. Therefore, our recent report has raised interest in 3-nitrooxypropanol (3-NOP), which when added to the feed of ruminants in milligram amounts persistently reduces enteric methane emissions from livestock without apparent negative side effects [Hristov AN, et al. (2015) Proc Natl Acad Sci USA 112(34):10663-10668]. We now show with the aid of in silico, in vitro, and in vivo experiments that 3-NOP specifically targets methyl-coenzyme M reductase (MCR). The nickel enzyme, which is only active when its Ni ion is in the +1 oxidation state, catalyzes the methane-forming step in the rumen fermentation. Molecular docking suggested that 3-NOP preferably binds into the active site of MCR in a pose that places its reducible nitrate group in electron transfer distance to Ni(I). With purified MCR, we found that 3-NOP indeed inactivates MCR at micromolar concentrations by oxidation of its active site Ni(I). Concomitantly, the nitrate ester is reduced to nitrite, which also inactivates MCR at micromolar concentrations by oxidation of Ni(I). Using pure cultures, 3-NOP is demonstrated to inhibit growth of methanogenic archaea at concentrations that do not affect the growth of nonmethanogenic bacteria in the rumen.
Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol.,Duin EC, Wagner T, Shima S, Prakash D, Cronin B, Yanez-Ruiz DR, Duval S, Rumbeli R, Stemmler RT, Thauer RK, Kindermann M Proc Natl Acad Sci U S A. 2016 May 2. pii: 201600298. PMID:27140643[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Duin EC, Wagner T, Shima S, Prakash D, Cronin B, Yanez-Ruiz DR, Duval S, Rumbeli R, Stemmler RT, Thauer RK, Kindermann M. Mode of action uncovered for the specific reduction of methane emissions from ruminants by the small molecule 3-nitrooxypropanol. Proc Natl Acad Sci U S A. 2016 May 2. pii: 201600298. PMID:27140643 doi:http://dx.doi.org/10.1073/pnas.1600298113
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