3dag
From Proteopedia
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| - | [[Image:3dag.png|left|200px]] | ||
| - | + | ==The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII== | |
| + | <StructureSection load='3dag' size='340' side='right'caption='[[3dag]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3dag]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. The March 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Hydrogenase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_3 10.2210/rcsb_pdb/mom_2009_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DAG FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FEG:5-O-[(S)-{[2-(CARBOXYMETHYL)-6-HYDROXY-3,5-DIMETHYLPYRIDIN-4-YL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE'>FEG</scene></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=3dag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dag OCA], [https://pdbe.org/3dag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dag RCSB], [https://www.ebi.ac.uk/pdbsum/3dag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dag ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/HMD_METJA HMD_METJA] Catalyzes the reversible reduction of methenyl-H(4)MPT(+) to methylene-H(4)MPT (By similarity). | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/3dag_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dag ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Biological formation and consumption of molecular hydrogen (H2) are catalyzed by hydrogenases, of which three phylogenetically unrelated types are known: [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]-hydrogenase. We present a crystal structure of [Fe]-hydrogenase at 1.75 angstrom resolution, showing a mononuclear iron coordinated by the sulfur of cysteine 176, two carbon monoxide (CO) molecules, and the sp2-hybridized nitrogen of a 2-pyridinol compound with back-bonding properties similar to those of cyanide. The three-dimensional arrangement of the ligands is similar to that of thiolate, CO, and cyanide ligated to the low-spin iron in binuclear [NiFe]- and [FeFe]-hydrogenases, although the enzymes have evolved independently and the CO and cyanide ligands are not found in any other metalloenzyme. The related iron ligation pattern of hydrogenases exemplifies convergent evolution and presumably plays an essential role in H2 activation. This finding may stimulate the ongoing synthesis of catalysts that could substitute for platinum in applications such as fuel cells. | ||
| - | + | The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site.,Shima S, Pilak O, Vogt S, Schick M, Stagni MS, Meyer-Klaucke W, Warkentin E, Thauer RK, Ermler U Science. 2008 Jul 25;321(5888):572-5. PMID:18653896<ref>PMID:18653896</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 3dag" style="background-color:#fffaf0;"></div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | == | + | __TOC__ |
| - | + | </StructureSection> | |
| - | + | ||
| - | == | + | |
| - | < | + | |
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[[Category: Hydrogenase]] | [[Category: Hydrogenase]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Methanocaldococcus jannaschii]] | [[Category: Methanocaldococcus jannaschii]] | ||
[[Category: RCSB PDB Molecule of the Month]] | [[Category: RCSB PDB Molecule of the Month]] | ||
| - | [[Category: Ermler | + | [[Category: Ermler U]] |
| - | [[Category: Pilak | + | [[Category: Pilak O]] |
| - | [[Category: Shima | + | [[Category: Shima S]] |
| - | [[Category: Thauer | + | [[Category: Thauer RK]] |
| - | [[Category: Warkentin | + | [[Category: Warkentin E]] |
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Current revision
The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII
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