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| | ==Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis== | | ==Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis== |
| - | <StructureSection load='3pot' size='340' side='right' caption='[[3pot]], [[Resolution|resolution]] 1.20Å' scene=''> | + | <StructureSection load='3pot' size='340' side='right'caption='[[3pot]], [[Resolution|resolution]] 1.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3pot]] 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=3POT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3POT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3pot]] 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=3POT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3POT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=06C:IODOMETHANE'>06C</scene>, <scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=TP7:COENZYME+B'>TP7</scene>, <scene name='pdbligand=TXZ:O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)-L-THREONINE'>TXZ</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]] 1.2Å</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=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=06C:IODOMETHANE'>06C</scene>, <scene name='pdbligand=AGM:5-METHYL-ARGININE'>AGM</scene>, <scene name='pdbligand=COM:1-THIOETHANESULFONIC+ACID'>COM</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=SMC:S-METHYLCYSTEINE'>SMC</scene>, <scene name='pdbligand=TP7:COENZYME+B'>TP7</scene>, <scene name='pdbligand=TXZ:O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)-L-THREONINE'>TXZ</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=3pot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pot OCA], [https://pdbe.org/3pot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pot RCSB], [https://www.ebi.ac.uk/pdbsum/3pot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pot 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=3pot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pot OCA], [http://pdbe.org/3pot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pot RCSB], [http://www.ebi.ac.uk/pdbsum/3pot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pot 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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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Cytochrome P450|Cytochrome P450]] | + | *[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Coenzyme-B sulfoethylthiotransferase]] | + | [[Category: Large Structures]] |
| | [[Category: Methanothermobacter marburgensis]] | | [[Category: Methanothermobacter marburgensis]] |
| - | [[Category: Cedervall, P E]] | + | [[Category: Cedervall PE]] |
| - | [[Category: Wilmot, C M]] | + | [[Category: Wilmot CM]] |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Methanogenesis]]
| + | |
| - | [[Category: Methyl-coenzyme m reductase]]
| + | |
| - | [[Category: Methylation]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
3pot 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 1.2Å |
| 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
We present the 1.2 A resolution X-ray crystal structure of a Ni-methyl species that is a proposed catalytic intermediate in methyl-coenzyme M reductase (MCR), the enzyme that catalyzes the biological formation of methane. The methyl group is situated 2.1 A proximal of the Ni atom of the MCR coenzyme F(430). A rearrangement of the substrate channel has been posited to bring together substrate species, but Ni(III)-methyl formation alone does not lead to any observable structural changes in the channel.
Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis.,Cedervall PE, Dey M, Li X, Sarangi R, Hedman B, Ragsdale SW, Wilmot CM J Am Chem Soc. 2011 Mar 25. PMID:21438550[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Cedervall PE, Dey M, Li X, Sarangi R, Hedman B, Ragsdale SW, Wilmot CM. Structural Analysis of a Ni-Methyl Species in Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis. J Am Chem Soc. 2011 Mar 25. PMID:21438550 doi:10.1021/ja110492p
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