View source for 6the


==Crystal structure of core domain of four-domain heme-cupredoxin-Cu nitrite reductase from Bradyrhizobium sp. ORS 375==
<StructureSection load='6the' size='340' side='right'caption='[[6the]], [[Resolution|resolution]] 2.87&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6the]] 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=6THE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6THE 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]] 2.87&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9JE:pentane-1,5-diol'>9JE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=ER3:ERBIUM+(III)+ION'>ER3</scene>, <scene name='pdbligand=TB:TERBIUM(III)+ION'>TB</scene>, <scene name='pdbligand=YB:YTTERBIUM+(III)+ION'>YB</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</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=6the FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6the OCA], [https://pdbe.org/6the PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6the RCSB], [https://www.ebi.ac.uk/pdbsum/6the PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6the ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/H0SHH5_BRAS3 H0SHH5_BRAS3] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cu-containing nitrite reductases that convert NO2 (-) to NO are critical enzymes in nitrogen-based energy metabolism. Among organisms in the order Rhizobiales, we have identified two copies of nirK, one encoding a new class of 4-domain CuNiR that has both cytochrome and cupredoxin domains fused at the N-terminus and the other, a classical 2-domain CuNiR (Br(2D) NiR). We report the first enzymatic studies of a novel 4-domain CuNiR from Bradyrhizobium sp. ORS 375 (BrNiR), its genetically engineered 3- and 2-domain variants, and Br(2D) NiR revealing up to ~500-fold difference in catalytic efficiency in comparison with classical 2-domain CuNiRs. Contrary to the expectation that tethering would enhance electron delivery by restricting the conformational search by having a self-contained donor-acceptor system, we demonstrate that 4-domain BrNiR utilises N-terminal tethering for down-regulating enzymatic activity instead. Both Br(2D) NiR, as well as engineered 2-domain variant of BrNiR (Delta(Cytc-Cup) BrNiR), have 3 to 5 % NiR activity compared to the well-characterized 2-domain CuNiRs from Alcaligenes xylosoxidans (AxNiR) and Achromobacter cycloclastes (AcNiR). Structural comparison of Delta(Cytc-Cup) BrNiR and Br(2D) NiR with classical 2-domain AxNiR and AcNiR reveals structural differences of the proton transfer pathway that could be responsible for the lowering of activity. Our study provides insights into unique structural and functional characteristics of naturally-occurring 4-domain CuNiR and its engineered 3- and 2-domain variants.The reverse protein engineering approach utilized here provides has shed light onto the broader question of the evolution of transient encounter complexes and tethered electron transfer complexes.

Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction.,Sasaki D, Watanabe TF, Eady RR, Garratt RC, Antonyuk SV, Hasnain SS FEBS J. 2020 Apr 7. doi: 10.1111/febs.15324. PMID:32255260<ref>PMID:32255260</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6the" style="background-color:#fffaf0;"></div>

==See Also==
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bradyrhizobium sp. ORS 375]]
[[Category: Large Structures]]
[[Category: Antonyuk SV]]
[[Category: Eady RR]]
[[Category: Garratt RC]]
[[Category: Hasnain SS]]
[[Category: Sasaki D]]
[[Category: Watanabe TF]]