3iqe: Difference between revisions

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-{{STRUCTURE_3iqe|  PDB=3iqe  |  SCENE=  }}
-===Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420===
-{{ABSTRACT_PUBMED_19761261}}
-==Function==
+==Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420==
-[[http://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>
+<StructureSection load='3iqe' size='340' side='right'caption='[[3iqe]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3iqe]] is a 6 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=3IQE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IQE FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<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=F42:COENZYME+F420'>F42</scene>, <scene name='pdbligand=H4M:5,10-DIMETHYLENE+TETRAHYDROMETHANOPTERIN'>H4M</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=3iqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iqe OCA], [https://pdbe.org/3iqe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iqe RCSB], [https://www.ebi.ac.uk/pdbsum/3iqe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iqe ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iq/3iqe_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3iqe ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-==About this Structure==
+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>
-[[3iqe]] is a 6 chain structure with 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=3IQE OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:019761261</ref><references group="xtra"/><references/>
+</div>
+<div class="pdbe-citations 3iqe" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Methanopyrus kandleri]]
-[[Category: Methylenetetrahydromethanopterin dehydrogenase]]
+[[Category: Ceh KE]]
-[[Category: Ceh, K E.]]
+[[Category: Demmer U]]
-[[Category: Demmer, U.]]
+[[Category: Ermler U]]
-[[Category: Ermler, U.]]
+[[Category: Moll J]]
-[[Category: Moll, J.]]
+[[Category: Shima S]]
-[[Category: Shima, S.]]
+[[Category: Thauer RK]]
-[[Category: Thauer, R K.]]
+[[Category: Warkentin E]]
-[[Category: Warkentin, E.]]
-[[Category: Methanogenesis]]
-[[Category: One-carbon metabolism]]
-[[Category: Oxidoreductase]]
-[[Category: Substrate and co-substrate]]
-[[Category: Ternary complex of protein]]