5t5m: Difference between revisions

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<StructureSection load='5t5m' size='340' side='right'caption='[[5t5m]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='5t5m' size='340' side='right'caption='[[5t5m]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5t5m]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_wolfeii Methanothermobacter wolfeii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T5M FirstGlance]. <br>
<table><tr><td colspan='2'>[[5t5m]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_wolfeii Methanothermobacter wolfeii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T5M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T5M FirstGlance]. <br>
</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=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=W:TUNGSTEN+ION'>W</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></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=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=W:TUNGSTEN+ION'>W</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formylmethanofuran_dehydrogenase Formylmethanofuran dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.5 1.2.99.5] </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=5t5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5m OCA], [https://pdbe.org/5t5m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t5m RCSB], [https://www.ebi.ac.uk/pdbsum/5t5m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5m ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5t5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t5m OCA], [http://pdbe.org/5t5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t5m RCSB], [http://www.ebi.ac.uk/pdbsum/5t5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t5m ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/O74030_METWO O74030_METWO]
Biological methane formation starts with a challenging adenosine triphosphate (ATP)-independent carbon dioxide (CO2) fixation process. We explored this enzymatic process by solving the x-ray crystal structure of formyl-methanofuran dehydrogenase, determined here as Fwd(ABCDFG)2 and Fwd(ABCDFG)4 complexes, from Methanothermobacter wolfeii The latter 800-kilodalton apparatus consists of four peripheral catalytic sections and an electron-supplying core with 46 electronically coupled [4Fe-4S] clusters. Catalysis is separately performed by subunits FwdBD (FwdB and FwdD), which are related to tungsten-containing formate dehydrogenase, and subunit FwdA, a binuclear metal center carrying amidohydrolase. CO2 is first reduced to formate in FwdBD, which then diffuses through a 43-angstrom-long tunnel to FwdA, where it condenses with methanofuran to formyl-methanofuran. The arrangement of [4Fe-4S] clusters functions as an electron relay but potentially also couples the four tungstopterin active sites over 206 angstroms.
 
The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.,Wagner T, Ermler U, Shima S Science. 2016 Oct 7;354(6308):114-117. PMID:27846502<ref>PMID:27846502</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5t5m" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Formylmethanofuran dehydrogenase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Methanothermobacter wolfeii]]
[[Category: Methanothermobacter wolfeii]]
[[Category: Ermler, U]]
[[Category: Ermler U]]
[[Category: Shima, S]]
[[Category: Shima S]]
[[Category: Wagner, T]]
[[Category: Wagner T]]
[[Category: Anaerobic]]
[[Category: Beta helicoidal]]
[[Category: Binuclear center]]
[[Category: Carboxylysine]]
[[Category: Channel]]
[[Category: Co2]]
[[Category: Co2 fixation]]
[[Category: Coupling]]
[[Category: Enzyme]]
[[Category: Ferredoxin]]
[[Category: Formate]]
[[Category: Formate dehydrogenase]]
[[Category: Formylmethanofuran]]
[[Category: Gate]]
[[Category: Green house gas]]
[[Category: Iron sulfur cluster]]
[[Category: Metallohydrolase]]
[[Category: Methanofuran]]
[[Category: Methanogenesis]]
[[Category: Nanomachine]]
[[Category: Oxidoreductase]]
[[Category: Tungsten]]
[[Category: Tungstopterin]]
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