1yq9

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[[Image:1yq9.png|left|200px]]
 
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==Structure of the unready oxidized form of [NiFe] hydrogenase==
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The line below this paragraph, containing "STRUCTURE_1yq9", creates the "Structure Box" on the page.
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<StructureSection load='1yq9' size='340' side='right'caption='[[1yq9]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1yq9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YQ9 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=FCO:CARBONMONOXIDE-(DICYANO)+IRON'>FCO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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{{STRUCTURE_1yq9| PDB=1yq9 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yq9 OCA], [https://pdbe.org/1yq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yq9 RCSB], [https://www.ebi.ac.uk/pdbsum/1yq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yq9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PHNS_MEGGA PHNS_MEGGA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yq/1yq9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1yq9 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide.
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===Structure of the unready oxidized form of [NiFe] hydrogenase===
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Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.,Volbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SP, Garcin E, Rousset M, Fontecilla-Camps JC J Biol Inorg Chem. 2005 May;10(3):239-49. Epub 2005 Apr 1. PMID:15803334<ref>PMID:15803334</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_15803334}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1yq9" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 15803334 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15803334}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[1yq9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQ9 OCA].
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[[Category: Megalodesulfovibrio gigas]]
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[[Category: Albracht SP]]
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==Reference==
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[[Category: Cavazza C]]
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<ref group="xtra">PMID:15803334</ref><ref group="xtra">PMID:7854413</ref><references group="xtra"/>
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[[Category: Faber BW]]
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[[Category: Cytochrome-c3 hydrogenase]]
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[[Category: Fontecilla-Camps JC]]
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[[Category: Desulfovibrio gigas]]
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[[Category: Garcin E]]
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[[Category: Albracht, S P.]]
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[[Category: Martin L]]
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[[Category: Cavazza, C.]]
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[[Category: Matho M]]
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[[Category: Faber, B W.]]
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[[Category: Roseboom W]]
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[[Category: Fontecilla-Camps, J C.]]
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[[Category: Rousset M]]
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[[Category: Garcin, E.]]
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[[Category: Volbeda A]]
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[[Category: Martin, L.]]
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[[Category: Matho, M.]]
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[[Category: Roseboom, W.]]
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[[Category: Rousset, M.]]
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[[Category: Volbeda, A.]]
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[[Category: Oxidoreductase]]
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Current revision

Structure of the unready oxidized form of [NiFe] hydrogenase

PDB ID 1yq9

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