2z1d

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[[Image:2z1d.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis==
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|PDB= 2z1d |SIZE=350|CAPTION= <scene name='initialview01'>2z1d</scene>, resolution 2.07&Aring;
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<StructureSection load='2z1d' size='340' side='right'caption='[[2z1d]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SF4:IRON/SULFUR CLUSTER'>SF4</scene>
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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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|ACTIVITY=
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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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|GENE= hypD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311400 Thermococcus kodakarensis])
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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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}}
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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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'''Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus kodakaraensis'''
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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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==Overview==
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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 ==
[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.
[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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==About this Structure==
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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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2Z1D is a [[Single protein]] structure of 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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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17612488 17612488]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 2z1d" style="background-color:#fffaf0;"></div>
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[[Category: Thermococcus kodakarensis]]
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[[Category: Arai, T.]]
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[[Category: Atomi, H.]]
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[[Category: Imanaka, T.]]
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[[Category: Matsumi, R.]]
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[[Category: Miki, K.]]
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[[Category: Watanabe, S.]]
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[[Category: SF4]]
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[[Category: [4fe-4s] cluster]]
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[[Category: [nife] hydrogenase maturation]]
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[[Category: thiol redox]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:51:04 2008''
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==See Also==
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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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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Thermococcus kodakarensis KOD1]]
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[[Category: Arai T]]
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[[Category: Atomi H]]
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[[Category: Imanaka T]]
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[[Category: Matsumi R]]
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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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