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1qv9

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[[Image:1qv9.jpg|left|200px]]
 
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{{Structure
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==Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: A methanogenic enzyme with an unusual quarternary structure==
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|PDB= 1qv9 |SIZE=350|CAPTION= <scene name='initialview01'>1qv9</scene>, resolution 1.54&Aring;
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<StructureSection load='1qv9' size='340' side='right'caption='[[1qv9]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
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<table><tr><td colspan='2'>[[1qv9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QV9 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylenetetrahydromethanopterin_dehydrogenase Methylenetetrahydromethanopterin dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.9 1.5.99.9] </span>
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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]] 1.54&#8491;</td></tr>
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|GENE= MTD OR MK0011 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 Methanopyrus kandleri])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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|DOMAIN=
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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=1qv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qv9 OCA], [https://pdbe.org/1qv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qv9 RCSB], [https://www.ebi.ac.uk/pdbsum/1qv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qv9 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qv9 OCA], [http://www.ebi.ac.uk/pdbsum/1qv9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qv9 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/MTD_METKA MTD_METKA] Catalyzes the reversible reduction of methenyl-H(4)MPT(+) to methylene-H(4)MPT.<ref>PMID:9151968</ref>
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== Evolutionary Conservation ==
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'''Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: A methanogenic enzyme with an unusual quarternary structure'''
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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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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qv/1qv9_consurf.spt"</scriptWhenChecked>
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The fourth reaction step of CO(2)-reduction to methane in methanogenic archaea is catalyzed by coenzyme F(420)-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd). We have structurally characterized this enzyme in the selenomethionine-labelled form from the hyperthermophilic methanogenic archaeon Methanopyrus kandleri at 1.54A resolution using the single wavelength anomalous dispersion method for phase determination. Mtd was found to be a homohexameric protein complex that is organized as a trimer of dimers. The fold of the individual subunits is composed of two domains: a larger alpha,beta domain and a smaller helix bundle domain with a short C-terminal beta-sheet segment. In the homohexamer the alpha,beta domains are positioned at the outside of the enzyme, whereas, the helix bundle domains assemble towards the inside to form an unusual quarternary structure with a 12-helix bundle around a 3-fold axis. No structural similarities are detectable to other enzymes with F(420) and/or substituted tetrahydropterins as substrates. The substrate binding sites of F(420) and methylenetetrahydromethanopterin are most likely embedded into a crevice between the domains of one subunit, their isoalloxazine and tetrahydropterin rings being placed inside a pocket formed by this crevice and a loop segment of the adjacent monomer of the dimer. Mtd revealed the highest stability at low salt concentrations of all structurally characterized enzymes from M.kandleri. This finding might be due to the compact quaternary structure that buries 36% of the monomer surface and to the large number of ion pairs.
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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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==About this Structure==
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</jmolCheckbox>
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1QV9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QV9 OCA].
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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=1qv9 ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure., Hagemeier CH, Shima S, Thauer RK, Bourenkov G, Bartunik HD, Ermler U, J Mol Biol. 2003 Oct 3;332(5):1047-57. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14499608 14499608]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Methanopyrus kandleri]]
[[Category: Methanopyrus kandleri]]
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[[Category: Methylenetetrahydromethanopterin dehydrogenase]]
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[[Category: Bartunik HD]]
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[[Category: Single protein]]
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[[Category: Bourenkov G]]
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[[Category: Bartunik, H D.]]
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[[Category: Ermler U]]
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[[Category: Bourenkov, G.]]
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[[Category: Hagemeier CH]]
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[[Category: Ermler, U.]]
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[[Category: Shima S]]
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[[Category: Hagemeier, C H.]]
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[[Category: Thauer RK]]
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[[Category: Shima, S.]]
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[[Category: Thauer, R K.]]
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[[Category: helix bundle]]
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[[Category: monomer: alpha/beta domain]]
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[[Category: trimer of dimer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:19:29 2008''
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Current revision

Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: A methanogenic enzyme with an unusual quarternary structure

PDB ID 1qv9

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