3vkq: Difference between revisions
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==Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with middle X-ray dose== | ==Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with middle X-ray dose== | ||
<StructureSection load='3vkq' size='340' side='right' caption='[[3vkq]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='3vkq' size='340' side='right'caption='[[3vkq]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vkq]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3vkq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/American_tobacco American tobacco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VKQ FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b0g|3b0g]], [[3vkp|3vkp]], [[3vkr|3vkr]], [[3vks|3vks]], [[3vkt|3vkt]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3b0g|3b0g]], [[3vkp|3vkp]], [[3vkr|3vkr]], [[3vks|3vks]], [[3vkt|3vkt]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nii3 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nii3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4097 American tobacco])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ferredoxin--nitrite_reductase Ferredoxin--nitrite reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.7.1 1.7.7.1] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vkq OCA], [https://pdbe.org/3vkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vkq RCSB], [https://www.ebi.ac.uk/pdbsum/3vkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vkq ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</div> | </div> | ||
<div class="pdbe-citations 3vkq" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3vkq" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: American tobacco]] | [[Category: American tobacco]] | ||
[[Category: Ferredoxin--nitrite reductase]] | [[Category: Ferredoxin--nitrite reductase]] | ||
[[Category: Large Structures]] | |||
[[Category: Katayanagi, K]] | [[Category: Katayanagi, K]] | ||
[[Category: Morikawa, H]] | [[Category: Morikawa, H]] | ||
Revision as of 21:50, 27 July 2022
Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with middle X-ray doseAssimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with middle X-ray dose
Structural highlights
Publication Abstract from PubMedAssimilatory nitrite reductase (aNiR) reduces nitrite to an ammonium ion and has siroheme and a [Fe(4)S(4)] cluster as prosthetic groups. A reaction mechanism for Nii3, an aNiR from tobacco, is proposed based on high resolution X-ray structures and UV-Vis (ultraviolet-visible) microspectroscopy of Nii3-ligand complexes. Analysis of UV-Vis spectral changes in Nii3 crystals with increasing X-ray exposure showed prosthetic group reductions. In Nii3-NO2(-) structures, X-ray irradiation enhanced the progress of the reduction reaction, and cleavage of the N-O bond was observed when X-ray doses were increased. Crystal structures of Nii3 with other bound ligands, such as Nii3-NO and Nii3-NH(2)OH, were also determined. Further, by combining information from these Nii3 ligand-bound structures, including that of Nii3-NO2(-), with UV-Vis microspectral data obtained using different X-ray doses, a reaction mechanism for aNiR was suggested. Cleavage of the two N-O bonds of nitrite was envisaged as a two-step process: first, the N-O bond close to Lys224 was cleaved, followed by cleavage of the N-O bond close to Arg109. X-ray structures also indicated that aNiR-catalyzed nitrite reduction proceeded without the need for conformation changes in active site residues. Geometrical changes in the ligand molecules and the placement of neighboring water molecules appeared to be important to the stability of the active site residue interactions (Arg109, Arg179, and Lys224) and the ligand molecule. These interactions may contribute to the efficiency of aNiR reduction reactions. The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-visible microspectroscopy.,Nakano S, Takahashi M, Sakamoto A, Morikawa H, Katayanagi K Proteins. 2012 Aug;80(8):2035-45. doi: 10.1002/prot.24094. Epub 2012 May 17. PMID:22499059[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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