3iqf
From Proteopedia
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| - | + | ==Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin== | |
| - | + | <StructureSection load='3iqf' size='340' side='right' caption='[[3iqf]], [[Resolution|resolution]] 2.10Å' scene=''> | |
| - | {{ | + | == Structural highlights == |
| + | <table><tr><td colspan='2'>[[3iqf]] is a 12 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=3IQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IQF FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3iqe|3iqe]], [[3iqz|3iqz]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mtd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2320 Methanopyrus kandleri])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | ||
| + | <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=3iqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iqf RCSB], [http://www.ebi.ac.uk/pdbsum/3iqf PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | == 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/3iqf_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/chain_selection.php?pdb_ID=2ata 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> | |
| - | + | == References == | |
| - | == | + | <references/> |
| - | + | __TOC__ | |
| + | </StructureSection> | ||
[[Category: Methanopyrus kandleri]] | [[Category: Methanopyrus kandleri]] | ||
[[Category: Methylenetetrahydromethanopterin dehydrogenase]] | [[Category: Methylenetetrahydromethanopterin dehydrogenase]] | ||
| - | [[Category: Ceh, K E | + | [[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, R K | + | [[Category: Thauer, R K]] |
| - | [[Category: Warkentin, E | + | [[Category: Warkentin, E]] |
[[Category: Binary complex of protein and substrate]] | [[Category: Binary complex of protein and substrate]] | ||
[[Category: Methanogenesis]] | [[Category: Methanogenesis]] | ||
[[Category: One-carbon metabolism]] | [[Category: One-carbon metabolism]] | ||
[[Category: Oxidoreductase]] | [[Category: Oxidoreductase]] | ||
Revision as of 16:54, 18 December 2014
Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin
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