1e3d

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{{Seed}}
 
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[[Image:1e3d.png|left|200px]]
 
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==[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774==
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The line below this paragraph, containing "STRUCTURE_1e3d", creates the "Structure Box" on the page.
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<StructureSection load='1e3d' size='340' side='right'caption='[[1e3d]], [[Resolution|resolution]] 1.80&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'>[[1e3d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E3D FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.8&#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=FNE:(MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)'>FNE</scene>, <scene name='pdbligand=FSX:BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON]+(AQUA)(GLU-O)IRON(II)'>FSX</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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{{STRUCTURE_1e3d| PDB=1e3d | 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=1e3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e3d OCA], [https://pdbe.org/1e3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e3d RCSB], [https://www.ebi.ac.uk/pdbsum/1e3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e3d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9L869_DESDE Q9L869_DESDE]
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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/e3/1e3d_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=1e3d 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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The primary and three-dimensional structures of a [NiFe] hydrogenase isolated from D. desulfitricans ATCC 27774 were determined, by nucleotide analysis and single-crystal X-ray crystallography. The three-dimensional structural model was refined to R=0.167 and Rfree=0.223 using data to 1.8 A resolution. Two unique structural features are observed: the [4Fe-4S] cluster nearest the [NiFe] centre has been modified [4Fe-3S-3O] by loss of one sulfur atom and inclusion of three oxygen atoms; a three-fold disorder was observed for Cys536 which binds to the nickel atom in the [NiFe] centre. Also, the bridging sulfur atom that caps the active site was found to have partial occupancy, thus corresponding to a partly activated enzyme. These structural features may have biological relevance. In particular, the two less-populated rotamers of Cys536 may be involved in the activation process of the enzyme, as well as in the catalytic cycle. Molecular modelling studies were carried out on the interaction between this [NiFe] hydrogenase and its physiological partner, the tetrahaem cytochrome c3 from the same organism. The lowest energy docking solutions were found to correspond to an interaction between the haem IV region in tetrahaem cytochrome c3 with the distal [4Fe-4S] cluster in [NiFe] hydrogenase. This interaction should correspond to efficient electron transfer and be physiologically relevant, given the proximity of the two redox centres and the fact that electron transfer decay coupling calculations show high coupling values and a short electron transfer pathway. On the other hand, other docking solutions have been found that, despite showing low electron transfer efficiency, may give clues on possible proton transfer mechanisms between the two molecules.
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===[NIFE] HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774===
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[NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 A and modelling studies of its interaction with the tetrahaem cytochrome c3.,Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA J Biol Inorg Chem. 2001 Jan;6(1):63-81. PMID:11191224<ref>PMID:11191224</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_11191224}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1e3d" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 11191224 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_11191224}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1E3D is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E3D OCA].
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==Reference==
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<ref group="xtra">PMID:11191224</ref><references group="xtra"/>
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[[Category: Desulfovibrio desulfuricans]]
[[Category: Desulfovibrio desulfuricans]]
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[[Category: Carrondo, M A.]]
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[[Category: Large Structures]]
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[[Category: Coelho, R.]]
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[[Category: Carrondo MA]]
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[[Category: Legall, J.]]
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[[Category: Coelho R]]
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[[Category: Matias, P M.]]
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[[Category: Le Gall J]]
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[[Category: Morais, J.]]
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[[Category: Matias PM]]
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[[Category: Saraiva, L M.]]
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[[Category: Morais J]]
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[[Category: Soares, C M.]]
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[[Category: Saraiva LM]]
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[[Category: Crystal structure]]
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[[Category: Soares CM]]
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[[Category: Electron transfer]]
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[[Category: Hydrogenase]]
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[[Category: Molecular modelling]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:27:56 2009''
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Current revision

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

PDB ID 1e3d

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