4zk8: Difference between revisions

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 ==Copper-containing nitrite reductase from thermophilic bacterium Geobacillus thermodenitrificans (Re-refined)==
-<StructureSection load='4zk8' size='340' side='right' caption='[[4zk8]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
+<StructureSection load='4zk8' size='340' side='right'caption='[[4zk8]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4zk8]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wko 3wko]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZK8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4zk8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wko 3wko]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZK8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
+</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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4zk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zk8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4zk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4zk8 PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4zk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zk8 OCA], [https://pdbe.org/4zk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zk8 RCSB], [https://www.ebi.ac.uk/pdbsum/4zk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zk8 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/A4IL26_GEOTN A4IL26_GEOTN]
-Copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO(-)2) to nitric oxide (NO) during denitrification. We determined the crystal structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus thermodenitrificans (GtNIR) in chloride- and formate-bound forms of wild type at 1.15 A resolution and the nitrite-bound form of the C135A mutant at 1.90 A resolution. The structure of C135A with nitrite displays a unique eta(1)-O coordination mode of nitrite at the catalytic copper site (T2Cu), which has never been observed at the T2Cu site in known wild-type CuNIRs, because the mobility of two residues essential to catalytic activity, Asp98 and His244, are sterically restricted in GtNIR by Phe109 on a characteristic loop structure that is found above Asp98 and by an unusually short CH-O hydrogen bond observed between His244 and water, respectively. A detailed comparison of the WT structure with the nitrite-bound C135A structure implies the replacement of hydrogen-bond networks around His244 and predicts the flow path of protons consumed by nitrite reduction. On the basis of these observations, the reaction mechanism of GtNIR through the eta(1)-O coordination manner is proposed.
-Structural insights into the function of a thermostable copper-containing nitrite reductase.,Fukuda Y, Tse KM, Lintuluoto M, Fukunishi Y, Mizohata E, Matsumura H, Takami H, Nojiri M, Inoue T J Biochem. 2014 Feb;155(2):123-35. doi: 10.1093/jb/mvt107. Epub 2013 Nov 30. PMID:24293549<ref>PMID:24293549</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Fukuda, Y]]
+[[Category: Geobacillus thermodenitrificans NG80-2]]
-[[Category: Inoue, T]]
+[[Category: Large Structures]]
-[[Category: Copper]]
+[[Category: Fukuda Y]]
-[[Category: Denitrification]]
+[[Category: Inoue T]]
-[[Category: Electron transfer]]
-[[Category: Nitrite]]
-[[Category: Oxidoreductase]]