6zar
From Proteopedia
(Difference between revisions)
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==As-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.1 A resolution (unrestrained, full matrix refinement by SHELX)== | ==As-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.1 A resolution (unrestrained, full matrix refinement by SHELX)== | ||
- | <StructureSection load='6zar' size='340' side='right'caption='[[6zar]]' scene=''> | + | <StructureSection load='6zar' size='340' side='right'caption='[[6zar]], [[Resolution|resolution]] 1.10Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
- | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZAR OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[6zar]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_sp._ORS_375 Bradyrhizobium sp. ORS 375]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZAR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZAR FirstGlance]. <br> |
- | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1Å</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6zar FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zar OCA], [https://pdbe.org/6zar PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zar RCSB], [https://www.ebi.ac.uk/pdbsum/6zar PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zar ProSAT]</span></td></tr> | ||
</table> | </table> | ||
+ | == Function == | ||
+ | [https://www.uniprot.org/uniprot/H0SLX7_BRAS3 H0SLX7_BRAS3] | ||
+ | <div style="background-color:#fffaf0;"> | ||
+ | == Publication Abstract from PubMed == | ||
+ | Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK Recently, we have identified two copies of nirK genes in several alpha-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br (2D)NiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br (2D)NiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated. | ||
+ | |||
+ | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.,Rose SL, Antonyuk SV, Sasaki D, Yamashita K, Hirata K, Ueno G, Ago H, Eady RR, Tosha T, Yamamoto M, Hasnain SS Sci Adv. 2021 Jan 1;7(1):eabd8523. doi: 10.1126/sciadv.abd8523. Print 2021 Jan. PMID:33523860<ref>PMID:33523860</ref> | ||
+ | |||
+ | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
+ | </div> | ||
+ | <div class="pdbe-citations 6zar" style="background-color:#fffaf0;"></div> | ||
+ | |||
+ | ==See Also== | ||
+ | *[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] | ||
+ | == References == | ||
+ | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
+ | [[Category: Bradyrhizobium sp. ORS 375]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Ago H]] | [[Category: Ago H]] |
Current revision
As-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.1 A resolution (unrestrained, full matrix refinement by SHELX)
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Categories: Bradyrhizobium sp. ORS 375 | Large Structures | Ago H | Antonyuk SV | Eady RR | Hasnain SS | Hirata K | Rose SL | Sasaki D | Tosha T | Ueno G | Yamamoto M | Yamashita K