1d4c: Difference between revisions

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-[[Image:1d4c.jpg|left|200px]]<br /><applet load="1d4c" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1d4c, resolution 2.9&Aring;" />
-'''CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1==
-Fumarate respiration is one of the most widespread types of anaerobic, respiration. The soluble fumarate reductase of Shewanella putrefaciens, MR-1 is a periplasmic tetraheme flavocytochrome c. The crystal structures, of the enzyme were solved to 2.9 A for the uncomplexed form and to 2.8 A, and 2.5 A for the fumarate and the succinate-bound protein, respectively., The structures reveal a flexible capping domain linked to the FAD-binding, domain. A catalytic mechanism for fumarate reduction based on the, structure of the complexed protein is proposed. The mechanism for the, reverse reaction is a model for the homologous succinate dehydrogenase, (complex II) of the respiratory chain. In flavocytochrome c fumarate, reductase, all redox centers are in van der Waals contact with one, another, thus providing an efficient conduit of electrons from the hemes, via the FAD to fumarate.
+<StructureSection load='1d4c' size='340' side='right'caption='[[1d4c]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1d4c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D4C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D4C 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1d4c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d4c OCA], [https://pdbe.org/1d4c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d4c RCSB], [https://www.ebi.ac.uk/pdbsum/1d4c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d4c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FCCA_SHEON FCCA_SHEON] Flavocytochrome that catalyzes the reduction of fumarate to succinate (PubMed:12196158, PubMed:12899636, PubMed:22458729). Is essential for fumarate respiration during anaerobic growth, acting as the terminal reductase (By similarity). Receives electrons from the membrane-bound tetraheme c-type cytochrome CymA (PubMed:12196158, PubMed:12899636, PubMed:19837833, PubMed:22458729). Under ferric iron-reducing conditions, can be part of an electron transport chain to ferric iron, by accepting electrons from CymA and transfering them to the c-type cytochrome MtrA (PubMed:19837833). Also plays an important role in the reduction of selenite to elemental selenium (PubMed:24435070). May act as a transient electron storage protein (PubMed:19837833).[UniProtKB:Q07WU7]<ref>PMID:12196158</ref> <ref>PMID:12899636</ref> <ref>PMID:19837833</ref> <ref>PMID:22458729</ref> <ref>PMID:24435070</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/d4/1d4c_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1d4c ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Fumarate respiration is one of the most widespread types of anaerobic respiration. The soluble fumarate reductase of Shewanella putrefaciens MR-1 is a periplasmic tetraheme flavocytochrome c. The crystal structures of the enzyme were solved to 2.9 A for the uncomplexed form and to 2.8 A and 2.5 A for the fumarate and the succinate-bound protein, respectively. The structures reveal a flexible capping domain linked to the FAD-binding domain. A catalytic mechanism for fumarate reduction based on the structure of the complexed protein is proposed. The mechanism for the reverse reaction is a model for the homologous succinate dehydrogenase (complex II) of the respiratory chain. In flavocytochrome c fumarate reductase, all redox centers are in van der Waals contact with one another, thus providing an efficient conduit of electrons from the hemes via the FAD to fumarate.
-==About this Structure==
+Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1.,Leys D, Tsapin AS, Nealson KH, Meyer TE, Cusanovich MA, Van Beeumen JJ Nat Struct Biol. 1999 Dec;6(12):1113-7. PMID:10581551<ref>PMID:10581551</ref>
-D4C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Shewanella_putrefaciens Shewanella putrefaciens] with SO4, HEM and FAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Succinate_dehydrogenase Succinate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.1 1.3.99.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D4C OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1., Leys D, Tsapin AS, Nealson KH, Meyer TE, Cusanovich MA, Van Beeumen JJ, Nat Struct Biol. 1999 Dec;6(12):1113-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10581551 10581551]
+</div>
-[[Category: Shewanella putrefaciens]]
+<div class="pdbe-citations 1d4c" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
-[[Category: Succinate dehydrogenase]]
+<references/>
-[[Category: Beeumen, J.J.Van.]]
+__TOC__
-[[Category: Cusanovich, M.A.]]
+</StructureSection>
-[[Category: Leys, D.]]
+[[Category: Large Structures]]
-[[Category: Meyer, T.E.]]
+[[Category: Shewanella oneidensis]]
-[[Category: Tsapin, A.S.]]
+[[Category: Cusanovich MA]]
-[[Category: FAD]]
+[[Category: Leys D]]
-[[Category: HEM]]
+[[Category: Meyer TE]]
-[[Category: SO4]]
+[[Category: Tsapin AS]]
-[[Category: tetraheme flavocytochrome c]]
+[[Category: Van Beeumen JJ]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:59:55 2007''