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| | ==Crystal structure of Burkholderia xenovorans DmrB apo form: A Cubic Protein Cage for Redox Transfer== | | ==Crystal structure of Burkholderia xenovorans DmrB apo form: A Cubic Protein Cage for Redox Transfer== |
| - | <StructureSection load='4mwg' size='340' side='right' caption='[[4mwg]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='4mwg' size='340' side='right'caption='[[4mwg]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4mwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MWG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4mwg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MWG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MWG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wis|3wis]]</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=4mwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mwg OCA], [https://pdbe.org/4mwg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mwg RCSB], [https://www.ebi.ac.uk/pdbsum/4mwg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mwg ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Bxeno_B0583, Bxe_B2440, DmrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 BURXL])</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=4mwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mwg OCA], [http://pdbe.org/4mwg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mwg RCSB], [http://www.ebi.ac.uk/pdbsum/4mwg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mwg ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q13QT8_PARXL Q13QT8_PARXL] |
| | <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: Burxl]] | + | [[Category: Large Structures]] |
| - | [[Category: Bobik, T A]] | + | [[Category: Paraburkholderia xenovorans LB400]] |
| - | [[Category: Bustos, C]] | + | [[Category: Bobik TA]] |
| - | [[Category: Cascio, D]] | + | [[Category: Bustos C]] |
| - | [[Category: Jorda, J]] | + | [[Category: Cascio D]] |
| - | [[Category: McNamara, D E]] | + | [[Category: Jorda J]] |
| - | [[Category: Rasche, M E]] | + | [[Category: McNamara DE]] |
| - | [[Category: Wang, T C]] | + | [[Category: Rasche ME]] |
| - | [[Category: Yeates, T O]] | + | [[Category: Wang TC]] |
| - | [[Category: Dihydromethanopterin reductase]]
| + | [[Category: Yeates TO]] |
| - | [[Category: Flavin]]
| + | |
| - | [[Category: Methanopterin]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Protein cage]]
| + | |
| Structural highlights
Function
Q13QT8_PARXL
Publication Abstract from PubMed
Dihydromethanopterin reductase (Dmr) is a redox enzyme that plays a key role in generating tetrahydromethanopterin (H4MPT) for use in one-carbon metabolism by archaea and some bacteria. DmrB is a bacterial enzyme understood to reduce dihydromethanopterin (H2MPT) to H4MPT using flavins as the source of reducing equivalents, but the mechanistic details have not been elucidated previously. Here we report the crystal structure of DmrB from Burkholderia xenovorans at a resolution of 1.9 A. Unexpectedly, the biological unit is a 24-mer composed of eight homotrimers located at the corners of a cubic cage-like structure. Within a homotrimer, each monomer-monomer interface exhibits an active site with two adjacently bound flavin mononucleotide (FMN) ligands, one deeply buried and tightly bound and one more peripheral, for a total of 48 ligands in the biological unit. Computational docking suggested that the peripheral site could bind either the observed FMN (the electron donor for the overall reaction) or the pterin, H2MPT (the electron acceptor for the overall reaction), in configurations ideal for electron transfer to and from the tightly bound FMN. On this basis, we propose that DmrB uses a ping-pong mechanism to transfer reducing equivalents from FMN to the pterin substrate. Sequence comparisons suggested that the catalytic mechanism is conserved among the bacterial homologs of DmrB and partially conserved in archaeal homologs, where an alternate electron donor is likely used. In addition to the mechanistic revelations, the structure of DmrB could help guide the development of anti-obesity drugs based on modification of the ecology of the human gut.
Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer.,McNamara DE, Cascio D, Jorda J, Bustos C, Wang TC, Rasche ME, Yeates TO, Bobik TA J Biol Chem. 2014 Mar 28;289(13):8852-64. doi: 10.1074/jbc.M113.522342. Epub 2014, Feb 12. PMID:24523405[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ McNamara DE, Cascio D, Jorda J, Bustos C, Wang TC, Rasche ME, Yeates TO, Bobik TA. Structure of dihydromethanopterin reductase, a cubic protein cage for redox transfer. J Biol Chem. 2014 Mar 28;289(13):8852-64. doi: 10.1074/jbc.M113.522342. Epub 2014, Feb 12. PMID:24523405 doi:http://dx.doi.org/10.1074/jbc.M113.522342
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