3iqz
From Proteopedia
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| - | {{STRUCTURE_3iqz| PDB=3iqz | SCENE= }} | ||
| - | ===Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin=== | ||
| - | {{ABSTRACT_PUBMED_19761261}} | ||
| - | == | + | ==Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin== |
| - | [[http://www.uniprot.org/uniprot/MTD_METKA MTD_METKA | + | <StructureSection load='3iqz' size='340' side='right'caption='[[3iqz]], [[Resolution|resolution]] 2.10Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3iqz]] 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=3IQZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IQZ 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]] 2.1Å</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=GOL:GLYCEROL'>GOL</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=3iqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iqz OCA], [https://pdbe.org/3iqz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iqz RCSB], [https://www.ebi.ac.uk/pdbsum/3iqz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iqz 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/3iqz_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=3iqz 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. | ||
| - | + | 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> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | < | + | </div> |
| + | <div class="pdbe-citations 3iqz" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Methanopyrus kandleri]] | [[Category: Methanopyrus kandleri]] | ||
| - | + | [[Category: Ceh KE]] | |
| - | [[Category: Ceh | + | [[Category: Demmer U]] |
| - | [[Category: Demmer | + | [[Category: Ermler U]] |
| - | [[Category: Ermler | + | [[Category: Moll J]] |
| - | [[Category: Moll | + | [[Category: Shima S]] |
| - | [[Category: Shima | + | [[Category: Thauer RK]] |
| - | [[Category: Thauer | + | [[Category: Warkentin E]] |
| - | [[Category: Warkentin | + | |
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| - | + | ||
| - | + | ||
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Current revision
Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin
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Categories: Large Structures | Methanopyrus kandleri | Ceh KE | Demmer U | Ermler U | Moll J | Shima S | Thauer RK | Warkentin E
