2z1d

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[[Image:2z1d.png|left|200px]]
 
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{{STRUCTURE_2z1d| PDB=2z1d | SCENE= }}
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==Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis==
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<StructureSection load='2z1d' size='340' side='right'caption='[[2z1d]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2z1d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z1D 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]] 2.07&#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=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
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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=2z1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1d OCA], [https://pdbe.org/2z1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z1d RCSB], [https://www.ebi.ac.uk/pdbsum/2z1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z1d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q5JII1_THEKO Q5JII1_THEKO]
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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/z1/2z1d_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2z1d 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] hydrogenase maturation proteins HypC, HypD, and HypE catalyze the insertion and cyanation of the iron center of [NiFe] hydrogenases by an unknown mechanism. We have determined the crystal structures of HypC, HypD, and HypE from Thermococcus kodakaraensis KOD1 at 1.8 A, 2.07 A, and 1.55 A resolution, respectively. The structure of HypD reveals its probable iron binding and active sites for cyanation. An extended conformation of each conserved motif of HypC and HypE allows the essential cysteine residues of both proteins to interact with the active site of HypD. Furthermore, the C-terminal tail of HypE is shown to exist in an ATP-dependent dynamic equilibrium between outward and inward conformations. Unexpectedly, the [4Fe-4S] cluster environment of HypD is quite similar to that of ferredoxin:thioredoxin reductase (FTR), indicating the existence of a redox cascade similar to the FTR system. These results suggest a cyanation reaction mechanism via unique thiol redox signaling in the HypCDE complex.
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===Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis===
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Crystal structures of [NiFe] hydrogenase maturation proteins HypC, HypD, and HypE: insights into cyanation reaction by thiol redox signaling.,Watanabe S, Matsumi R, Arai T, Atomi H, Imanaka T, Miki K Mol Cell. 2007 Jul 6;27(1):29-40. PMID:17612488<ref>PMID:17612488</ref>
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{{ABSTRACT_PUBMED_17612488}}
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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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<div class="pdbe-citations 2z1d" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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[[2z1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1D OCA].
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*[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]]
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*[[HypA-HypB-HypC-HypD-HypE-HypF|HypA-HypB-HypC-HypD-HypE-HypF]]
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==Reference==
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== References ==
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<ref group="xtra">PMID:017612488</ref><references group="xtra"/>
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<references/>
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[[Category: Thermococcus kodakarensis]]
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__TOC__
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[[Category: Arai, T.]]
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</StructureSection>
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[[Category: Atomi, H.]]
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[[Category: Large Structures]]
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[[Category: Imanaka, T.]]
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[[Category: Thermococcus kodakarensis KOD1]]
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[[Category: Matsumi, R.]]
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[[Category: Arai T]]
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[[Category: Miki, K.]]
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[[Category: Atomi H]]
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[[Category: Watanabe, S.]]
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[[Category: Imanaka T]]
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[[Category: Metal binding protein]]
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[[Category: Matsumi R]]
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[[Category: Thiol redox]]
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[[Category: Miki K]]
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[[Category: Watanabe S]]

Current revision

Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis

PDB ID 2z1d

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