3vm0: Difference between revisions

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-[[Image:3vm0.jpg|left|200px]]
-{{STRUCTURE_3vm0|  PDB=3vm0  |  SCENE=  }}
+==Assimilatory nitrite reductase (Nii3) - N226K mutant - NO2 complex from tobacco leaf==
+<StructureSection load='3vm0' size='340' side='right'caption='[[3vm0]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3vm0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VM0 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]] 1.695&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</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=3vm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vm0 OCA], [https://pdbe.org/3vm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vm0 RCSB], [https://www.ebi.ac.uk/pdbsum/3vm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vm0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q76KB0_TOBAC Q76KB0_TOBAC]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Assimilatory nitrite reductase (aNiR) reduces nitrite ions (NO$\rm{{_{2}^{-}}}$) to ammonium ions (NH$\rm{{_{4}^{+}}}$), whereas assimilatory sulfite reductase reduces sulfite (SO$\rm{{_{3}^{2-}}}$) to hydrogen sulfide (HS(-) ). Although aNiR can also reduce SO$\rm{{_{3}^{2-}}}$, its activity is much lower than when NO$\rm{{_{2}^{-}}}$ is reduced as the substrate. To increase the SO$\rm{{_{3}^{2-}}}$-reduction activity of aNiR, we performed a N226K mutation of Nii3, a representative aNiR. The resulting Nii3-N226K variant could bind non-native targets, SO$\rm{{_{3}^{2-}}}$, and HCO$\rm{{_{3}^{-}}}$, in addition to its native target, i.e., NO$\rm{{_{2}^{-}}}$. We have determined the high-resolution structure of Nii3-N226K in its apo-state and in complex with SO$\rm{{_{3}^{2-}}}$, NO$\rm{{_{2}^{-}}}$, and HCO$\rm{{_{3}^{-}}}$. This analysis revealed conformational changes of Lys226 and the adjacent Lys224 upon binding of SO$\rm{{_{3}^{2-}}}$, but not NO$\rm{{_{2}^{-}}}$. In contrast, HCO$\rm{{_{3}^{-}}}$ binding induced a conformational change at Arg179. After replacing Asn226 with a positively charged Lys, aNiR showed affinity for several anions. A comparison of all ligand-bound structures for Nii3-N226K revealed that structural changes in the active site depend on the size of the substrate.
-===Assimilatory nitrite reductase (Nii3) - N226K mutant - NO2 complex from tobacco leaf===
+X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity.,Nakano S, Takahashi M, Sakamoto A, Morikawa H, Katayanagi K Chem Biodivers. 2012 Sep;9(9):1989-99. doi: 10.1002/cbdv.201100442. PMID:22976986<ref>PMID:22976986</ref>
-{{ABSTRACT_PUBMED_22976986}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3vm0" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3vm0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VM0 OCA].
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
-[[Category: Ferredoxin--nitrite reductase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Nicotiana tabacum]]
-[[Category: Katayanagi, K.]]
+[[Category: Katayanagi K]]
-[[Category: Morikawa, H.]]
+[[Category: Morikawa H]]
-[[Category: Nakano, S.]]
+[[Category: Nakano S]]
-[[Category: Sakamoto, A.]]
+[[Category: Sakamoto A]]
-[[Category: Takahashi, M.]]
+[[Category: Takahashi M]]
-[[Category: 3 alpha/beta domain]]
-[[Category: Nii3 n226k mutant]]
-[[Category: No2 complex]]
-[[Category: Oxidoreductase]]
-[[Category: Reductase]]