3b0m: Difference between revisions
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<StructureSection load='3b0m' size='340' side='right'caption='[[3b0m]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='3b0m' size='340' side='right'caption='[[3b0m]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3b0m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3b0m]] 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=3B0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B0M FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | ||
<tr id=' | <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=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=3b0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b0m OCA], [https://pdbe.org/3b0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b0m RCSB], [https://www.ebi.ac.uk/pdbsum/3b0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b0m ProSAT]</span></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=3b0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b0m OCA], [https://pdbe.org/3b0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b0m RCSB], [https://www.ebi.ac.uk/pdbsum/3b0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b0m ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q76KB0_TOBAC Q76KB0_TOBAC] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Katayanagi | [[Category: Nicotiana tabacum]] | ||
[[Category: Morikawa | [[Category: Katayanagi K]] | ||
[[Category: Nakano | [[Category: Morikawa H]] | ||
[[Category: Sakamoto | [[Category: Nakano S]] | ||
[[Category: Takahashi | [[Category: Sakamoto A]] | ||
[[Category: Takahashi M]] | |||
Latest revision as of 11:51, 11 October 2023
M175K mutant of assimilatory nitrite reductase (Nii3) from tobbaco leafM175K mutant of assimilatory nitrite reductase (Nii3) from tobbaco leaf
Structural highlights
FunctionPublication Abstract from PubMedTobacco expresses four isomers of assimilatory nitrite reductase (aNiR), leaf-type (Nii1 and Nii3), and root-type (Nii2 and Nii4). The high-resolution crystal structures of Nii3 and Nii4, determined at 1.25 and 2.3 A resolutions, respectively, revealed that both proteins had very similar structures. The Nii3 structure provided detailed geometries for the [4Fe-4S] cluster and the siroheme prosthetic groups. We have generated two types of Nii3 variants: one set focuses on residue Met175 (Nii3-M175G, Nii3-M175E, and Nii3-M175K), a residue that is located on the substrate entrance pathway; the second set targets residue Gln448 (Nii3-Q448K), a residue near the prosthetic groups. Comparison of the structures and kinetics of the Nii3 wild-type (Nii3-WT) and the Met175 variants showed that the hydrophobic side-chain of Met175 facilitated enzyme efficiency (k(cat) /K(m) ). The Nii4-WT has Lys449 at the equivalent position of Gln448 in Nii3-WT. The enzyme activity assay revealed that the turnover number (k(cat) ) and Michaelis constant (K(m) ) of Nii4-WT were lower than those of Nii3-WT. However, the k(cat) /K(m) of Nii4-WT was about 1.4 times higher than that of Nii3-WT. A comparison of the kinetics of the Nii3-Q448K and Nii4-K449Q variants revealed that the change in k(cat) /K(m) was brought about by the difference in Residue 448 (defined as Gln448 in Nii3 and Lys449 in Nii4). By combining detailed crystal structures with enzyme kinetics, we have proposed that Nii3 is the low-affinity and Nii4 is the high-affinity aNiR. Structure-function relationship of assimilatory nitrite reductases from the leaf and root of tobacco based on high-resolution structures.,Nakano S, Takahashi M, Sakamoto A, Morikawa H, Katayanagi K Protein Sci. 2012 Mar;21(3):383-95. doi: 10.1002/pro.2025. Epub 2012 Jan 31. PMID:22238192[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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