1j0o: Difference between revisions

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-[[Image:1j0o.jpg|left|200px]]
- {{Structure
+==High Resolution Crystal Structure of the wild type Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F==
-|PDB= 1j0o |SIZE=350|CAPTION= <scene name='initialview01'>1j0o</scene>, resolution 1.15&Aring;
+<StructureSection load='1j0o' size='340' side='right'caption='[[1j0o]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>
+<table><tr><td colspan='2'>[[1j0o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J0O FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.15&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0o OCA], [https://pdbe.org/1j0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j0o RCSB], [https://www.ebi.ac.uk/pdbsum/1j0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j0o ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1j0p|1J0P]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0o OCA], [http://www.ebi.ac.uk/pdbsum/1j0o PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1j0o RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/CYC3_NITV9 CYC3_NITV9] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
+== 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/j0/1j0o_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=1j0o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tyrosine 43 is positioned parallel to the fifth heme axial ligand, His34, of heme 1 in the tetraheme cytochrome c(3). The replacement of tyrosine with leucine increased the redox potential of heme 1 by 44 and 35 mV at the first and last reduction steps, respectively; its effects on the other hemes are small. In contrast, the Y43F mutation hardly changed the potentials. It shows that the aromatic ring at this position contributes to lowering the redox potential of heme 1 locally, although this cannot be the major contribution to the extremely low redox potentials of cytochrome c(3). Furthermore, temperature-dependent line-width broadening in partially reduced samples established that the aromatic ring at position 43 participates in the control of the kinetics of intramolecular electron transfer. The rate of reduction of Y43L cytochrome c(3) by 5-deazariboflavin semiquinone under partially reduced conditions was significantly different from that of the wild type in the last stage of the reduction, supporting the involvement of Tyr43 in regulation of reduction kinetics. The mutation of Y43L, however, did not induce a significant change in the crystal structure.
-'''High Resolution Crystal Structure of the wild type Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F'''
+Role of the aromatic ring of Tyr43 in tetraheme cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F.,Ozawa K, Takayama Y, Yasukawa F, Ohmura T, Cusanovich MA, Tomimoto Y, Ogata H, Higuchi Y, Akutsu H Biophys J. 2003 Nov;85(5):3367-74. PMID:14581238<ref>PMID:14581238</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1j0o" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Tyrosine 43 is positioned parallel to the fifth heme axial ligand, His34, of heme 1 in the tetraheme cytochrome c(3). The replacement of tyrosine with leucine increased the redox potential of heme 1 by 44 and 35 mV at the first and last reduction steps, respectively; its effects on the other hemes are small. In contrast, the Y43F mutation hardly changed the potentials. It shows that the aromatic ring at this position contributes to lowering the redox potential of heme 1 locally, although this cannot be the major contribution to the extremely low redox potentials of cytochrome c(3). Furthermore, temperature-dependent line-width broadening in partially reduced samples established that the aromatic ring at position 43 participates in the control of the kinetics of intramolecular electron transfer. The rate of reduction of Y43L cytochrome c(3) by 5-deazariboflavin semiquinone under partially reduced conditions was significantly different from that of the wild type in the last stage of the reduction, supporting the involvement of Tyr43 in regulation of reduction kinetics. The mutation of Y43L, however, did not induce a significant change in the crystal structure.
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-J0O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0O OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Role of the aromatic ring of Tyr43 in tetraheme cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F., Ozawa K, Takayama Y, Yasukawa F, Ohmura T, Cusanovich MA, Tomimoto Y, Ogata H, Higuchi Y, Akutsu H, Biophys J. 2003 Nov;85(5):3367-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14581238 14581238]
 [[Category: Desulfovibrio vulgaris]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Akutsu, H.]]
+[[Category: Akutsu H]]
-[[Category: Cusanvich, M A.]]
+[[Category: Cusanvich MA]]
-[[Category: Higuchi, Y.]]
+[[Category: Higuchi Y]]
-[[Category: Kumagai, J.]]
+[[Category: Kumagai J]]
-[[Category: Ogata, H.]]
+[[Category: Ogata H]]
-[[Category: Ohmura, T.]]
+[[Category: Ohmura T]]
-[[Category: Ozawa, K.]]
+[[Category: Ozawa K]]
-[[Category: Tomimoto, Y.]]
+[[Category: Tomimoto Y]]
-[[Category: Yasukawa, F.]]
+[[Category: Yasukawa F]]
-[[Category: high resolution x-ray structure]]
-[[Category: tetraheme cytochrome c3]]
-[[Category: wild type]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:27:17 2008''