1fdi: Difference between revisions

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OCA

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-[[Image:1fdi.gif|left|200px]]<br />
-<applet load="1fdi" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1fdi, resolution 2.9&Aring;" />
-'''OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI COMPLEXED WITH THE INHIBITOR NITRITE'''<br />
-==Overview==
+==OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI COMPLEXED WITH THE INHIBITOR NITRITE==
-Formate dehydrogenase H from Escherichia coli contains selenocysteine, (SeCys), molybdenum, two molybdopterin guanine dinucleotide (MGD), cofactors, and an Fe4S4 cluster at the active site and catalyzes the, two-electron oxidation of formate to carbon dioxide. The crystal, structures of the oxidized [Mo(VI), Fe4S4(ox)] form of formate, dehydrogenase H (with and without bound inhibitor) and the reduced, [Mo(IV), Fe4S4(red)] form have been determined, revealing a four-domain, alphabeta structure with the molybdenum directly coordinated to selenium, and both MGD cofactors. These structures suggest a reaction mechanism that, directly involves SeCys140 and His141 in proton abstraction and the, molybdenum, molybdopterin, Lys44, and the Fe4S4 cluster in electron, transfer.
+<StructureSection load='1fdi' size='340' side='right'caption='[[1fdi]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1fdi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FDI 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]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MO:MOLYBDENUM(VI)+ION'>6MO</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1fdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fdi OCA], [https://pdbe.org/1fdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fdi RCSB], [https://www.ebi.ac.uk/pdbsum/1fdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fdi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FDHF_ECOLI FDHF_ECOLI] Decomposes formic acid to hydrogen and carbon dioxide under anaerobic conditions in the absence of exogenous electron acceptors.
+== 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/fd/1fdi_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=1fdi ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-FDI is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]] with NO2, SF4, MGD and 6MO as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/ ]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2]]. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FDI OCA]].
+*[[Formate dehydrogenase 3D structures|Formate dehydrogenase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster., Boyington JC, Gladyshev VN, Khangulov SV, Stadtman TC, Sun PD, Science. 1997 Feb 28;275(5304):1305-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9036855 9036855]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Boyington, J.C.]]
+[[Category: Boyington JC]]
-[[Category: Sun, P.D.]]
+[[Category: Sun PD]]
-[[Category: 6MO]]
-[[Category: MGD]]
-[[Category: NO2]]
-[[Category: SF4]]
-[[Category: anaerobic]]
-[[Category: dehydrogenase]]
-[[Category: fe4s4]]
-[[Category: formate]]
-[[Category: iron sulfur cluster]]
-[[Category: mgd]]
-[[Category: molybdenum]]
-[[Category: molybdopterin]]
-[[Category: molybdopterin guanine dinucleotide]]
-[[Category: mpt]]
-[[Category: oxidoreductase]]
-[[Category: secys]]
-[[Category: selenium]]
-[[Category: selenocysteine]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Oct 29 20:12:02 2007''