1gm4: Difference between revisions

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-[[Image:1gm4.png|left|200px]]
-<!--
+==OXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 at pH 7.6==
-The line below this paragraph, containing "STRUCTURE_1gm4", creates the "Structure Box" on the page.
+<StructureSection load='1gm4' size='340' side='right'caption='[[1gm4]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1gm4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GM4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1gm4|  PDB=1gm4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gm4 OCA], [https://pdbe.org/1gm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gm4 RCSB], [https://www.ebi.ac.uk/pdbsum/1gm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gm4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9L915_DESDE Q9L915_DESDE]
+== 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/gm/1gm4_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=1gm4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g. electron and proton transfer in proton-pumps. There is great interest in determining at the molecular level the structural details that control these energy transduction events, particularly those involving multiple electrons and protons, because tight control is required to avoid the production of dangerous reactive intermediates. Tetraheme cytochrome c(3) is a small soluble and monomeric protein that performs a central step in the bioenergetic metabolism of sulfate reducing bacteria, termed "proton-thrusting," linking the oxidation of molecular hydrogen with the reduction of sulfate. The mechano-chemical coupling involved in the transfer of multiple electrons and protons in cytochrome c(3) from Desulfovibrio desulfuricans ATCC 27774 is described using results derived from the microscopic thermodynamic characterization of the redox and acid-base centers involved, crystallographic studies in the oxidized and reduced states of the cytochrome, and theoretical studies of the redox and acid-base transitions. This proton-assisted two-electron step involves very small, localized structural changes that are sufficient to generate the complex network of functional cooperativities leading to energy transduction, while using molecular mechanisms distinct from those established for other Desulfovibrio sp. cytochromes from the same structural family.
-===OXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6===
+Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome.,Louro RO, Bento I, Matias PM, Catarino T, Baptista AM, Soares CM, Carrondo MA, Turner DL, Xavier AV J Biol Chem. 2001 Nov 23;276(47):44044-51. Epub 2001 Sep 10. PMID:11551953<ref>PMID:11551953</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1gm4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11551953}}, adds the Publication Abstract to the page
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11551953 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11551953}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[1gm4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_desulfuricans Desulfovibrio desulfuricans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GM4 OCA].
-==Reference==
-<ref group="xtra">PMID:11551953</ref><ref group="xtra">PMID:7548038</ref><references group="xtra"/>
 [[Category: Desulfovibrio desulfuricans]]
-[[Category: Baptista, A M.]]
+[[Category: Large Structures]]
-[[Category: Bento, I.]]
+[[Category: Baptista AM]]
-[[Category: Carrondo, M A.]]
+[[Category: Bento I]]
-[[Category: Catarino, T.]]
+[[Category: Carrondo MA]]
-[[Category: Louro, R.]]
+[[Category: Catarino T]]
-[[Category: Matias, P M.]]
+[[Category: Louro R]]
-[[Category: Soares, C M.]]
+[[Category: Matias PM]]
-[[Category: Turner, D L.]]
+[[Category: Soares CM]]
-[[Category: Xavier, A V.]]
+[[Category: Turner DL]]
-[[Category: Cytochrome]]
+[[Category: Xavier AV]]
-[[Category: Electron transport]]