3vm1: Difference between revisions

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-[[Image:3vm1.jpg|left|200px]]
+==assimilatory nitrite reductase (Nii3) - N226K mutant - HCO3 complex from tobacco leaf==
+<StructureSection load='3vm1' size='340' side='right' caption='[[3vm1]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3vm1]] 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=3VM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VM1 FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b0g|3b0g]], [[3vlx|3vlx]], [[3vly|3vly]], [[3vlz|3vlz]], [[3vm0|3vm0]]</td></tr>
+<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nii3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4097 Nicotiana tabacum])</td></tr>
+<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin--nitrite_reductase Ferredoxin--nitrite reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.7.1 1.7.7.1] </span></td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vm1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vm1 RCSB], [http://www.ebi.ac.uk/pdbsum/3vm1 PDBsum]</span></td></tr>
+<table>
+<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.
-{{STRUCTURE_3vm1|  PDB=3vm1  |  SCENE=  }}
+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>
-===assimilatory nitrite reductase (Nii3) - N226K mutant - HCO3 complex from tobacco leaf===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_22976986}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[3vm1]] 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=3VM1 OCA].
+</StructureSection>
 [[Category: Ferredoxin--nitrite reductase]]
 [[Category: Nicotiana tabacum]]