3vx3

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Current revision (08:42, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3vx3' size='340' side='right'caption='[[3vx3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='3vx3' size='340' side='right'caption='[[3vx3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vx3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VX3 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vx3]] 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=3VX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VX3 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
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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]] 2.1&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK2007 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=3vx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vx3 OCA], [https://pdbe.org/3vx3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vx3 RCSB], [https://www.ebi.ac.uk/pdbsum/3vx3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vx3 ProSAT]</span></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=3vx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vx3 OCA], [https://pdbe.org/3vx3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vx3 RCSB], [https://www.ebi.ac.uk/pdbsum/3vx3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vx3 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q5JIH4_THEKO Q5JIH4_THEKO]
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HypB (metal-binding GTPase) and HypA (nickel metallochaperone) are required for nickel insertion into [NiFe] hydrogenase. However, the HypB homolog proteins are not found in some archaeal species including Thermococcales. In this article, we identify a novel archaeal Mrp/MinD family ATPase-type HypB from Thermococcus kodakarensis (Tk-mmHypB) and determine its crystal structure. The mmhypB gene is conserved among species lacking the hypB gene and is located adjacent to the hypA gene on their genome. Deletion of the mmhypB gene leads to a significant reduction in hydrogen-dependent growth of T. kodakarensis, which is restored by nickel supplementation. The monomer structure of Tk-mmHypB is similar to those of the Mrp/MinD family ATPases. The ADP molecules are tightly bound to the protein. Isothermal titration calorimetry shows that Tk-mmHypB binds ATP with a K(d) value of 84nM. ADP binds more tightly than does ATP, with a K(d) value of 15nM. The closed Tk-mmHypB dimer in the crystallographic asymmetric unit is consistent with the ATP-hydrolysis-deficient dimer of the Mrp/MinD family Soj/MinD proteins. Structural comparisons with these proteins suggest the ATP-binding dependent conformational change and rearrangement of the Tk-mmHypB dimer. These observations imply that the nickel insertion process during the [NiFe] hydrogenase maturation is performed by HypA, mmHypB, and a nucleotide exchange factor in these archaea.
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Identification and Structure of a Novel Archaeal HypB for [NiFe] Hydrogenase Maturation.,Sasaki D, Watanabe S, Matsumi R, Shoji T, Yasukochi A, Tagashira K, Fukuda W, Kanai T, Atomi H, Imanaka T, Miki K J Mol Biol. 2013 Feb 8. pii: S0022-2836(13)00073-9. doi:, 10.1016/j.jmb.2013.02.004. PMID:23399544<ref>PMID:23399544</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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<div class="pdbe-citations 3vx3" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[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]]
*[[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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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Miki, K]]
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[[Category: Thermococcus kodakarensis KOD1]]
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[[Category: Sasaki, D]]
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[[Category: Miki K]]
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[[Category: Watanabe, S]]
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[[Category: Sasaki D]]
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[[Category: Adp binding protein]]
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[[Category: Watanabe S]]
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[[Category: Mrp/mind family atpase]]
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Current revision

Crystal structure of [NiFe] hydrogenase maturation protein HypB from Thermococcus kodakarensis KOD1

PDB ID 3vx3

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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