2a3t: Difference between revisions

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-[[Image:2a3t.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2a3t", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2a3t|  PDB=2a3t  |  SCENE=  }}
-'''Cu-containing nitrite reductase'''
+==Cu-containing nitrite reductase==
+<StructureSection load='2a3t' size='340' side='right'caption='[[2a3t]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2a3t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A3T 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]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2a3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a3t OCA], [https://pdbe.org/2a3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a3t RCSB], [https://www.ebi.ac.uk/pdbsum/2a3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a3t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NIR_CERS5 NIR_CERS5]
+== 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/a3/2a3t_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=2a3t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nitrite reductase is an enzyme operating in the denitrification pathway which catalyses the conversion of nitrite (NO2(-)) to gaseous nitric oxide (NO). Here, crystal structures of the oxidized and reduced forms of the copper-containing nitrite reductase from Rhodobacter sphaeroides 2.4.3 are presented at 1.74 and 1.85 A resolution, respectively. Whereas the structure of the enzyme is very similar to those of other copper-containing nitrite reductases, folding as a trimer and containing two copper sites per monomer, the structures reported here enable conformational differences between the oxidized and reduced forms of the enzyme to be identified. In the type 1 copper site, a rotational perturbation of the side chain of the copper ligand Met182 occurs upon reduction. At the type 2 copper site, a dual conformation of the catalytic residue His287 is observed in the oxidized structure but is lacking in the reduced structure, such that the interactions of the oxidized type 2 copper ion can be regarded as adopting octahedral geometry. These findings shed light on the structural mechanism of the reduction of a copper-bound nitrite to nitric oxide and water.
-==Overview==
+Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper.,Jacobson F, Guo H, Olesen K, Okvist M, Neutze R, Sjolin L Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1190-8. Epub 2005, Aug 16. PMID:16131751<ref>PMID:16131751</ref>
-Nitrite reductase is an enzyme operating in the denitrification pathway which catalyses the conversion of nitrite (NO2(-)) to gaseous nitric oxide (NO). Here, crystal structures of the oxidized and reduced forms of the copper-containing nitrite reductase from Rhodobacter sphaeroides 2.4.3 are presented at 1.74 and 1.85 A resolution, respectively. Whereas the structure of the enzyme is very similar to those of other copper-containing nitrite reductases, folding as a trimer and containing two copper sites per monomer, the structures reported here enable conformational differences between the oxidized and reduced forms of the enzyme to be identified. In the type 1 copper site, a rotational perturbation of the side chain of the copper ligand Met182 occurs upon reduction. At the type 2 copper site, a dual conformation of the catalytic residue His287 is observed in the oxidized structure but is lacking in the reduced structure, such that the interactions of the oxidized type 2 copper ion can be regarded as adopting octahedral geometry. These findings shed light on the structural mechanism of the reduction of a copper-bound nitrite to nitric oxide and water.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-A3T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A3T OCA].
+</div>
+<div class="pdbe-citations 2a3t" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper., Jacobson F, Guo H, Olesen K, Okvist M, Neutze R, Sjolin L, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1190-8. Epub 2005, Aug 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16131751 16131751]
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-[[Category: Rhodobacter sphaeroides]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Guo, H.]]
+__TOC__
-[[Category: Jacobson, F.]]
+</StructureSection>
-[[Category: Neutze, R.]]
+[[Category: Cereibacter sphaeroides]]
-[[Category: Okvist, M.]]
+[[Category: Large Structures]]
-[[Category: Olesen, K.]]
+[[Category: Guo H]]
-[[Category: Sjolin, L.]]
+[[Category: Jacobson F]]
-[[Category: Copper protein]]
+[[Category: Neutze R]]
-[[Category: Denitrification]]
+[[Category: Okvist M]]
-[[Category: Nitrite reduction]]
+[[Category: Olesen K]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 18:33:59 2008''
+[[Category: Sjolin L]]