3iqf

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{{Seed}}
 
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[[Image:3iqf.jpg|left|200px]]
 
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==Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin==
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The line below this paragraph, containing "STRUCTURE_3iqf", creates the "Structure Box" on the page.
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<StructureSection load='3iqf' size='340' side='right'caption='[[3iqf]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3iqf]] is a 12 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=3IQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IQF FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=E4M:1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol'>E4M</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_3iqf| PDB=3iqf | SCENE= }}
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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=3iqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iqf OCA], [https://pdbe.org/3iqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iqf RCSB], [https://www.ebi.ac.uk/pdbsum/3iqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iqf ProSAT]</span></td></tr>
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</table>
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== Function ==
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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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[[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/iq/3iqf_consurf.spt"</scriptWhenChecked>
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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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</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=3iqf 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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F(420)-dependent methylenetetrahydromethanopterin (methylene-H(4)MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H(4)MPT(+) and methylene-H(4)MPT using coenzyme F(420) as hydride carrier. We determined the structures of the Mtd-methylene-H(4)MPT, Mtd-methenyl-H(4)MPT(+), and the Mtd-methenyl-H(4)MPT(+)-F(420)H(2) complexes at 2.1, 2.0, and 1.8 A resolution, respectively. The pterin-imidazolidine-phenyl ring system is present in a new extended but not planar conformation which is virtually identical in methenyl-H(4)MPT(+) and methylene-H(4)MPT at the current resolution. Both substrates methenyl-H(4)MPT(+) and F(420)H(2) bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms, respectively. The polypeptide scaffold does not reveal any significant conformational change upon binding of the bulky substrates but in turn changes the conformations of the substrate rings either to avoid clashes between certain ring atoms or to adjust the rings involved in hydride transfer for providing an optimal catalytic efficiency.
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===Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin===
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Structural Basis of the Hydride Transfer Mechanism in F(420)-Dependent Methylenetetrahydromethanopterin Dehydrogenase.,Ceh K, Demmer U, Warkentin E, Moll J, Thauer RK, Shima S, Ermler U Biochemistry. 2009 Sep 29. PMID:19761261<ref>PMID:19761261</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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The line below this paragraph, {{ABSTRACT_PUBMED_19761261}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3iqf" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19761261 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19761261}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3IQF is a 12 chains structure of sequences 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=3IQF OCA].
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==Reference==
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<ref group="xtra">PMID:19761261</ref><references group="xtra"/>
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[[Category: Methanopyrus kandleri]]
[[Category: Methanopyrus kandleri]]
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[[Category: Methylenetetrahydromethanopterin dehydrogenase]]
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[[Category: Ceh KE]]
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[[Category: Ceh, K E.]]
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[[Category: Demmer U]]
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[[Category: Demmer, U.]]
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[[Category: Ermler U]]
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[[Category: Ermler, U.]]
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[[Category: Moll J]]
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[[Category: Moll, J.]]
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[[Category: Shima S]]
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[[Category: Shima, S.]]
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[[Category: Thauer RK]]
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[[Category: Thauer, R K.]]
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[[Category: Warkentin E]]
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[[Category: Warkentin, E.]]
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[[Category: Binary complex of protein and substrate]]
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[[Category: Methanogenesis]]
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[[Category: One-carbon metabolism]]
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[[Category: Oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 7 14:02:01 2009''
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Current revision

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

PDB ID 3iqf

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