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| | ==DMSP-dependent demethylase from P. ubique - apo== | | ==DMSP-dependent demethylase from P. ubique - apo== |
| - | <StructureSection load='3tfh' size='340' side='right' caption='[[3tfh]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3tfh' size='340' side='right'caption='[[3tfh]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3tfh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_pelagibacter_ubique Candidatus pelagibacter ubique]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TFH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TFH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3tfh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Pelagibacter_ubique_HTCC1062 Candidatus Pelagibacter ubique HTCC1062]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TFH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3tfi|3tfi]], [[3tfj|3tfj]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dmdA, SAR11_0246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198252 Candidatus Pelagibacter ubique])</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=3tfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tfh OCA], [https://pdbe.org/3tfh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tfh RCSB], [https://www.ebi.ac.uk/pdbsum/3tfh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tfh ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminomethyltransferase Aminomethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.10 2.1.2.10] </span></td></tr>
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| - | <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=3tfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tfh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tfh RCSB], [http://www.ebi.ac.uk/pdbsum/3tfh PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/DMDA_PELUB DMDA_PELUB] Major contributor to the demethylation of dimethlysulfonioproprionate (DMSP). Demethylates DMSP to methyl-mercaptopropionate (MMPA).<ref>PMID:17068264</ref> |
| - | Dimethylsulfoniopropionate (DMSP) is a ubiquitous algal metabolite and common carbon and sulfur source for marine bacteria. DMSP is a precursor for the climatically active gas dimethylsulfide that is readily oxidized to sulfate, sulfur dioxide, methanesulfonic acid, and other products that act as cloud condensation nuclei. Although the environmental importance of DMSP metabolism has been known for some time, the enzyme responsible for DMSP demethylation by marine bacterioplankton, dimethylsufoniopropionate-dependent demethylase A (DmdA, EC 2.1.1.B5), has only recently been identified and biochemically characterized. In this work, we report the structure for the apoenzyme DmdA from Pelagibacter ubique (2.1 A), as well as for DmdA co-crystals soaked with substrate DMSP (1.6 A) or the cofactor tetrahydrofolate (THF) (1.6 A). Surprisingly, the overall fold of the DmdA is not similar to other enzymes that typically utilize the reduced form of THF and in fact is a triple domain structure similar to what has been observed for the glycine cleavage T protein or sarcosine oxidase. Specifically, while the THF binding fold appears conserved, previous biochemical studies have shown that all enzymes with a similar fold produce 5, 10-methylene-THF, while DmdA catalyzes a redox-neutral methyl transfer reaction to produce 5-methyl-THF. Based on the findings presented herein and the available biochemical data, we outline a mechanism for a redox-neutral methyl transfer reaction that is novel to this conserved THF binding domain.
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| - | Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism pelagabacter ubique.,Schuller DJ, Reisch CR, Moran MA, Whitman WB, Lanzilotta WN Protein Sci. 2011 Dec 7. doi: 10.1002/pro.2015. PMID:22162093<ref>PMID:22162093</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| | ==See Also== | | ==See Also== |
| - | *[[Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)|Dimethylsulfoniopropionate-Dependent Demethylase (DmdA)]] | + | *[[Aminomethyltransferase|Aminomethyltransferase]] |
| | + | *[[Aminomethyltransferase 3D structures|Aminomethyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aminomethyltransferase]] | + | [[Category: Candidatus Pelagibacter ubique HTCC1062]] |
| - | [[Category: Candidatus pelagibacter ubique]] | + | [[Category: Large Structures]] |
| - | [[Category: Lanzilotta, W N]] | + | [[Category: Lanzilotta WN]] |
| - | [[Category: Moran, M A]] | + | [[Category: Moran MA]] |
| - | [[Category: Reisch, C R]] | + | [[Category: Reisch CR]] |
| - | [[Category: Schuller, D J]] | + | [[Category: Schuller DJ]] |
| - | [[Category: Whitman, W B]] | + | [[Category: Whitman WB]] |
| - | [[Category: Demethylase]]
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| - | [[Category: Thf]]
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| - | [[Category: Transferase]]
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