1fj0: Difference between revisions

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-{{Seed}}
-[[Image:1fj0.png|left|200px]]
-<!--
+==STRUCTURE DETERMINATION OF THE FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS==
-The line below this paragraph, containing "STRUCTURE_1fj0", creates the "Structure Box" on the page.
+<StructureSection load='1fj0' size='340' side='right'caption='[[1fj0]], [[Resolution|resolution]] 1.70&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'>[[1fj0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FJ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FJ0 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1fj0|  PDB=1fj0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fj0 OCA], [https://pdbe.org/1fj0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fj0 RCSB], [https://www.ebi.ac.uk/pdbsum/1fj0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fj0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CYC22_RHOPA CYC22_RHOPA] Cytochrome c2 is found mainly in purple, non-sulfur, photosynthetic bacteria where it functions as the electron donor to the oxidized bacteriochlorophyll in the photophosphorylation pathway. However, it may also have a role in the respiratory chain and is found in some non-photosynthetic bacteria.
+== 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/fj/1fj0_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=1fj0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structures of the native cytochrome c(2) from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 A and in the reduced state at 1.95 A resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c(2) with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 3(10)-helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c(2) with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles phi and psi of approximately -140 and -130 degrees, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 A resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c(2) of the rare six-residue insertion in the helix 3(10) conformation that increases Met loop flexibility.
-===STRUCTURE DETERMINATION OF THE FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS PALUSTRIS===
+Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.,Geremia S, Garau G, Vaccari L, Sgarra R, Viezzoli MS, Calligaris M, Randaccio L Protein Sci. 2002 Jan;11(1):6-17. PMID:11742117<ref>PMID:11742117</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1fj0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11742117}}, 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 11742117 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11742117}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-FJ0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FJ0 OCA].
-==Reference==
-Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex., Geremia S, Garau G, Vaccari L, Sgarra R, Viezzoli MS, Calligaris M, Randaccio L, Protein Sci. 2002 Jan;11(1):6-17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11742117 11742117]
 [[Category: Rhodopseudomonas palustris]]
-[[Category: Single protein]]
+[[Category: Geremia S]]
-[[Category: Geremia, S.]]
-[[Category: Electron carrier]]
-[[Category: Heme protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 03:20:29 2008''