6hbe: Difference between revisions

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-'''Unreleased structure'''
-The entry 6hbe is ON HOLD
+==Cu-containing nitrite reductase (NirK) from Thermus scotoductus SA-01==
+<StructureSection load='6hbe' size='340' side='right'caption='[[6hbe]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6hbe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thess Thess]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HBE FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TSC_c17620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=743525 THESS])</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=6hbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hbe OCA], [http://pdbe.org/6hbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hbe RCSB], [http://www.ebi.ac.uk/pdbsum/6hbe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hbe ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dissimilatory nitrite reductases are key enzymes in the denitrification pathway, reducing nitrite and leading to the production of gaseous products (NO, N2O and N2). The reaction is catalysed either by a Cu-containing nitrite reductase (NirK) or by a cytochrome cd 1 nitrite reductase (NirS), as the simultaneous presence of the two enzymes has never been detected in the same microorganism. The thermophilic bacterium Thermus scotoductus SA-01 is an exception to this rule, harbouring both genes within a denitrification cluster, which encodes for an atypical NirK. The crystal structure of TsNirK has been determined at 1.63 A resolution. TsNirK is a homotrimer with subunits of 451 residues that contain three copper atoms each. The N-terminal region possesses a type 2 Cu (T2Cu) and a type 1 Cu (T1CuN) while the C-terminus contains an extra type 1 Cu (T1CuC) bound within a cupredoxin motif. T1CuN shows an unusual Cu atom coordination (His2-Cys-Gln) compared with T1Cu observed in NirKs reported so far (His2-Cys-Met). T1CuC is buried at approximately 5 A from the molecular surface and located approximately 14.1 A away from T1CuN; T1CuN and T2Cu are approximately 12.6 A apart. All these distances are compatible with an electron-transfer process T1CuC --&gt; T1CuN --&gt; T2Cu. T1CuN and T2Cu are connected by a typical Cys-His bridge and an unexpected sensing loop which harbours a SerCAT residue close to T2Cu, suggesting an alternative nitrite-reduction mechanism in these enzymes. Biophysicochemical and functional features of TsNirK are discussed on the basis of X-ray crystallography, electron paramagnetic resonance, resonance Raman and kinetic experiments.
-Authors: Opperman, D.J., Ferroni, F.M.
+A three-domain copper-nitrite reductase with a unique sensing loop.,Opperman DJ, Murgida DH, Dalosto SD, Brondino CD, Ferroni FM IUCrJ. 2019 Feb 9;6(Pt 2):248-258. doi: 10.1107/S2052252519000241. eCollection, 2019 Mar 1. PMID:30867922<ref>PMID:30867922</ref>
-Description: Cu-containing nitrite reductase (NirK) from Thermus scotoductus SA-01
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Ferroni, F.M]]
+<div class="pdbe-citations 6hbe" style="background-color:#fffaf0;"></div>
-[[Category: Opperman, D.J]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thess]]
+[[Category: Ferroni, F M]]
+[[Category: Opperman, D J]]
+[[Category: Denitrification]]
+[[Category: Nitrite reductase]]
+[[Category: Oxidoreductase]]
+[[Category: Three-domain nirk]]