1hcm: Difference between revisions

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-[[Image:1hcm.gif|left|200px]]<br /><applet load="1hcm" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1hcm, resolution 2.5&Aring;" />
-'''CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FROM FROM TETRAGONAL CRYSTALS'''<br />
-==Overview==
+==Cytochrome cd1 Nitrite Reductase, oxidised from from tetragonal crystals==
-Cytochrome cd(1) nitrite reductase is a bifunctional enzyme, which can, catalyze the 1-electron reduction of nitrite to nitric oxide and the, 4-electron reduction of dioxygen to water. Here we describe the structure, of reduced nitrite reductase, crystallized under anaerobic conditions. The, structure reveals substantial domain rearrangements with the c domain, rotated by 60 degrees and shifted by approximately 20 A compared with, previously known structures from crystals grown under oxidizing, conditions. This alternative conformation gives rise to different electron, transfer routes between the c and d(1) domains and points to the, involvement of elements of very large structural changes in the function, in this enzyme. In the present structure, the c heme has a His-69/Met-106, ligation, and this ligation does not change upon oxidation in the crystal., The d(1) heme is penta-coordinated, and the d(1) iron is displaced from, the heme plane by 0.5 A toward the proximal ligand, His-200. After, oxidation, the iron moves into the d(1) heme plane. A surprising finding, is that although reduced nitrite reductase can be readily oxidized by, dioxygen in the new crystal, it cannot turnover with its other substrate, nitrite. The results suggest that the rearrangement of the domains affects, catalysis and substrate selectivity.
+<StructureSection load='1hcm' size='340' side='right'caption='[[1hcm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1hcm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_pantotrophus Paracoccus pantotrophus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HCM 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHE:HEME+D'>DHE</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=1hcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hcm OCA], [https://pdbe.org/1hcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hcm RCSB], [https://www.ebi.ac.uk/pdbsum/1hcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hcm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NIRS_PARPN NIRS_PARPN]
+== 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/hc/1hcm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1hcm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cytochrome cd(1) nitrite reductase is a bifunctional enzyme, which can catalyze the 1-electron reduction of nitrite to nitric oxide and the 4-electron reduction of dioxygen to water. Here we describe the structure of reduced nitrite reductase, crystallized under anaerobic conditions. The structure reveals substantial domain rearrangements with the c domain rotated by 60 degrees and shifted by approximately 20 A compared with previously known structures from crystals grown under oxidizing conditions. This alternative conformation gives rise to different electron transfer routes between the c and d(1) domains and points to the involvement of elements of very large structural changes in the function in this enzyme. In the present structure, the c heme has a His-69/Met-106 ligation, and this ligation does not change upon oxidation in the crystal. The d(1) heme is penta-coordinated, and the d(1) iron is displaced from the heme plane by 0.5 A toward the proximal ligand, His-200. After oxidation, the iron moves into the d(1) heme plane. A surprising finding is that although reduced nitrite reductase can be readily oxidized by dioxygen in the new crystal, it cannot turnover with its other substrate, nitrite. The results suggest that the rearrangement of the domains affects catalysis and substrate selectivity.
-==About this Structure==
+The Structure of an alternative form of Paracoccus pantotrophus cytochrome cd(1) nitrite reductase.,Sjogren T, Hajdu J J Biol Chem. 2001 Aug 3;276(31):29450-5. Epub 2001 May 23. PMID:11373294<ref>PMID:11373294</ref>
-HCM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Paracoccus_pantotrophus Paracoccus pantotrophus] with SO4, HEC and DHE as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=C1A:The C Hem Is The Point Of Electron Entry'>C1A</scene>, <scene name='pdbsite=C1B:The C Hem Is The Point Of Electron Entry'>C1B</scene>, <scene name='pdbsite=D1A:The D Hem Is The Site Of Catalytic Activity'>D1A</scene> and <scene name='pdbsite=D1B:The D Hem Is The Site Of Catalytic Activity'>D1B</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1HCM OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The Structure of an alternative form of Paracoccus pantotrophus cytochrome cd(1) nitrite reductase., Sjogren T, Hajdu J, J Biol Chem. 2001 Aug 3;276(31):29450-5. Epub 2001 May 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11373294 11373294]
+</div>
+<div class="pdbe-citations 1hcm" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
+*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Paracoccus pantotrophus]]
-[[Category: Single protein]]
+[[Category: Hajdu J]]
-[[Category: Hajdu, J.]]
+[[Category: Sjogren T]]
-[[Category: Sjogren, T.]]
-[[Category: DHE]]
-[[Category: HEC]]
-[[Category: SO4]]
-[[Category: enzyme]]
-[[Category: nitrite reductase]]
-[[Category: oxidoreductase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 16:16:11 2007''