1oah: Difference between revisions

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-{{Seed}}
-[[Image:1oah.png|left|200px]]
-<!--
+==Cytochrome c Nitrite Reductase from Desulfovibrio desulfuricans ATCC 27774: The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).==
-The line below this paragraph, containing "STRUCTURE_1oah", creates the "Structure Box" on the page.
+<StructureSection load='1oah' size='340' side='right'caption='[[1oah]], [[Resolution|resolution]] 2.30&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'>[[1oah]] is a 2 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=1OAH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OAH 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1oah|  PDB=1oah  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oah OCA], [https://pdbe.org/1oah PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oah RCSB], [https://www.ebi.ac.uk/pdbsum/1oah PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oah ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8VNU2_DESDE Q8VNU2_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/oa/1oah_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=1oah ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The gene encoding cytochrome c nitrite reductase (NrfA) from Desulfovibrio desulfuricans ATCC 27774 was sequenced and the crystal structure of the enzyme was determined to 2.3-A resolution. In comparison with homologous structures, it presents structural differences mainly located at the regions surrounding the putative substrate inlet and product outlet, and includes a well defined second calcium site with octahedral geometry, coordinated to propionates of hemes 3 and 4, and caged by a loop non-existent in the previous structures. The highly negative electrostatic potential in the environment around hemes 3 and 4 suggests that the main role of this calcium ion may not be electrostatic but structural, namely in the stabilization of the conformation of the additional loop that cages it and influences the solvent accessibility of heme 4. The NrfA active site is similar to that of peroxidases with a nearby calcium site at the heme distal side nearly in the same location as occurs in the class II and class III peroxidases. This fact suggests that the calcium ion at the distal side of the active site in the NrfA enzymes may have a similar physiological role to that reported for the peroxidases.
-===CYTOCHROME C NITRITE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774: THE RELEVANCE OF THE TWO CALCIUM SITES IN THE STRUCTURE OF THE CATALYTIC SUBUNIT (NRFA).===
+Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).,Cunha CA, Macieira S, Dias JM, Almeida G, Goncalves LL, Costa C, Lampreia J, Huber R, Moura JJ, Moura I, Romao MJ J Biol Chem. 2003 May 9;278(19):17455-65. Epub 2003 Mar 4. PMID:12618432<ref>PMID:12618432</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1oah" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12618432}}, 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 12618432 is the PubMed ID number.
+*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
--->
+== References ==
-{{ABSTRACT_PUBMED_12618432}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-OAH is a 2 chains structure of sequences 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=1OAH OCA].
-==Reference==
-<ref group="xtra">PMID:12618432</ref><references group="xtra"/>
 [[Category: Desulfovibrio desulfuricans]]
-[[Category: Almeida, G.]]
+[[Category: Large Structures]]
-[[Category: Costa, C.]]
+[[Category: Almeida G]]
-[[Category: Cunha, C A.]]
+[[Category: Costa C]]
-[[Category: Dias, J M.]]
+[[Category: Cunha CA]]
-[[Category: Goncalves, L L.]]
+[[Category: Dias JM]]
-[[Category: Huber, R.]]
+[[Category: Goncalves LL]]
-[[Category: Lampreia, J.]]
+[[Category: Huber R]]
-[[Category: Macieira, S.]]
+[[Category: Lampreia J]]
-[[Category: Moura, I.]]
+[[Category: Macieira S]]
-[[Category: Moura, J J.G.]]
+[[Category: Moura I]]
-[[Category: Romao, M J.]]
+[[Category: Moura JJG]]
-[[Category: Cytochrome c]]
+[[Category: Romao MJ]]
-[[Category: Nitrite reductase]]
-[[Category: Nitrogen cycle]]
-[[Category: Respiratory nitrite ammonification]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:28:02 2009''