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| | <StructureSection load='6huy' size='340' side='right'caption='[[6huy]], [[Resolution|resolution]] 2.25Å' scene=''> | | <StructureSection load='6huy' size='340' side='right'caption='[[6huy]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6huy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Destd Destd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HUY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6huy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurobacterium_thermolithotrophum_DSM_11699 Desulfurobacterium thermolithotrophum DSM 11699]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HUY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HUY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FE9:IRON-GUANYLYL+PYRIDINOL+COFACTOR'>FE9</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUE:5,10-Methenyltetrahydrofolate'>GUE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 2.25Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUE:(2~{S})-2-[[4-[(6~{a}~{R})-3-azanyl-1-oxidanylidene-5,6,6~{a},7-tetrahydro-4~{H}-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl]carbonylamino]pentanedioic+acid'>GUE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dester_1504 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=868864 DESTD])</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=6huy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6huy OCA], [https://pdbe.org/6huy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6huy RCSB], [https://www.ebi.ac.uk/pdbsum/6huy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6huy 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/5,10-methenyltetrahydromethanopterin_hydrogenase 5,10-methenyltetrahydromethanopterin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.98.2 1.12.98.2] </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=6huy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6huy OCA], [http://pdbe.org/6huy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6huy RCSB], [http://www.ebi.ac.uk/pdbsum/6huy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6huy ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/F0S2B6_DESTD F0S2B6_DESTD] |
| | <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: 5,10-methenyltetrahydromethanopterin hydrogenase]] | + | [[Category: Desulfurobacterium thermolithotrophum DSM 11699]] |
| - | [[Category: Destd]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ataka, K]] | + | [[Category: Ataka K]] |
| - | [[Category: Ermler, U]] | + | [[Category: Ermler U]] |
| - | [[Category: Huang, G]] | + | [[Category: Huang G]] |
| - | [[Category: Kahnt, J]] | + | [[Category: Kahnt J]] |
| - | [[Category: Shima, S]] | + | [[Category: Shima S]] |
| - | [[Category: Wagner, T]] | + | [[Category: Wagner T]] |
| - | [[Category: Watanabe, T]] | + | [[Category: Watanabe T]] |
| - | [[Category: Cofactor biosynthesis]]
| + | |
| - | [[Category: H2-activation]]
| + | |
| - | [[Category: Hydrogenase]]
| + | |
| - | [[Category: Lateral gene-transfer]]
| + | |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Paralog]]
| + | |
| - | [[Category: Sulfur-reducing bacteria]]
| + | |
| - | [[Category: Tetrahydrofolate]]
| + | |
| - | [[Category: Tetrahydromethanopterin]]
| + | |
| Structural highlights
6huy is a 4 chain structure with sequence from Desulfurobacterium thermolithotrophum DSM 11699. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.25Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
F0S2B6_DESTD
Publication Abstract from PubMed
[Fe]-hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyl-tetrahydromethanopterin (methenyl-H4MPT+) with H2. H4MPT is a C1-carrier of methanogenic archaea. One bacterial genus, Desulfurobacterium, contains putative genes for the Hmd paralog (HmdII) and the HcgA-G proteins. The latter are involved in biosynthesis of the prosthetic group of Hmd, the iron-guanylylpyridinol (FeGP) cofactor. This finding is intriguing because Hmd and HmdII strictly use H4MPT derivatives that are absent in most bacteria. We identified the presence of the FeGP cofactor in D. thermolithotrophum. The bacterial HmdII reconstituted with the FeGP cofactor catalyzed the enzyme reactions using the tetrahydrofolate derivatives, which are the bacterial C1 carrier, albeit with low enzymatic activities. Crystal structure provided the basis for how the enzyme was adapted to the bacterial C1-carrier. This finding has impact on future biotechnology by developing the Hmd variants functioning in Bacteria.
The bacterial [Fe]-hydrogenase paralog uses tetrahydrofolate derivatives as substrates.,Watanabe T, Wagner T, Huang G, Kahnt J, Ataka K, Ermler U, Shima S Angew Chem Int Ed Engl. 2019 Jan 2. doi: 10.1002/anie.201813465. PMID:30600878[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Watanabe T, Wagner T, Huang G, Kahnt J, Ataka K, Ermler U, Shima S. The bacterial [Fe]-hydrogenase paralog uses tetrahydrofolate derivatives as substrates. Angew Chem Int Ed Engl. 2019 Jan 2. doi: 10.1002/anie.201813465. PMID:30600878 doi:http://dx.doi.org/10.1002/anie.201813465
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