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4yt2

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==Hmd II from Methanocaldococcus jannaschii==
==Hmd II from Methanocaldococcus jannaschii==
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<StructureSection load='4yt2' size='340' side='right' caption='[[4yt2]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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<StructureSection load='4yt2' size='340' side='right'caption='[[4yt2]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4yt2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YT2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YT2 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4yt2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YT2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YT2 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.65&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4tye|4tye]], [[4yt4|4yt4]], [[4yt8|4yt8]], [[4yt5|4yt5]]</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yt2 RCSB], [http://www.ebi.ac.uk/pdbsum/4yt2 PDBsum]</span></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=4yt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yt2 OCA], [https://pdbe.org/4yt2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yt2 RCSB], [https://www.ebi.ac.uk/pdbsum/4yt2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yt2 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/HMDY_METJA HMDY_METJA]
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[Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H2 cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H4 MPT+ ). Most hydrogenotrophic methanogens contain the hmd related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for an in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H4 MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme-methylene-H4 MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H4 MPT+ compared to Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turn-over process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared to in Hmd that impairs the catalytically necessary open-to-close transition and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H2 sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H4 MPT concentration. This article is protected by copyright. All rights reserved.
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Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs.,Fujishiro T, Ataka K, Ermler U, Shima S FEBS J. 2015 Jun 20. doi: 10.1111/febs.13351. PMID:26094576<ref>PMID:26094576</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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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Ermler, U]]
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[[Category: Large Structures]]
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[[Category: Fujishiro, T]]
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[[Category: Methanocaldococcus jannaschii]]
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[[Category: Shima, S]]
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[[Category: Ermler U]]
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[[Category: Metal binding protein]]
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[[Category: Fujishiro T]]
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[[Category: Oxidoreductase]]
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[[Category: Shima S]]
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[[Category: Rossmann-fold]]
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Current revision

Hmd II from Methanocaldococcus jannaschii

PDB ID 4yt2

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