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| | <StructureSection load='6l46' size='340' side='right'caption='[[6l46]], [[Resolution|resolution]] 1.30Å' scene=''> | | <StructureSection load='6l46' size='340' side='right'caption='[[6l46]], [[Resolution|resolution]] 1.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6l46]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thermodenitrificans"_klaushofer_and_hollaus_1970 "bacillus thermodenitrificans" klaushofer and hollaus 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L46 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6l46]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L46 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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.3Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nirK, GTHT12_00198 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33940 "Bacillus thermodenitrificans" Klaushofer and Hollaus 1970])</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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=6l46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l46 OCA], [https://pdbe.org/6l46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l46 RCSB], [https://www.ebi.ac.uk/pdbsum/6l46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l46 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6l46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l46 OCA], [http://pdbe.org/6l46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l46 RCSB], [http://www.ebi.ac.uk/pdbsum/6l46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l46 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/A0A1W6VP04_GEOTD A0A1W6VP04_GEOTD] |
| - | Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide, which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from the failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 A resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of approximately 106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation states of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels.
| + | |
| - | | + | |
| - | High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase.,Fukuda Y, Hirano Y, Kusaka K, Inoue T, Tamada T Proc Natl Acad Sci U S A. 2020 Feb 10. pii: 1918125117. doi:, 10.1073/pnas.1918125117. PMID:32041886<ref>PMID:32041886</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6l46" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus thermodenitrificans klaushofer and hollaus 1970]] | + | [[Category: Geobacillus thermodenitrificans]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Fukuda, Y]] | + | [[Category: Fukuda Y]] |
| - | [[Category: Hirano, Y]] | + | [[Category: Hirano Y]] |
| - | [[Category: Inoue, T]] | + | [[Category: Inoue T]] |
| - | [[Category: Kusaka, K]] | + | [[Category: Kusaka K]] |
| - | [[Category: Tamada, T]] | + | [[Category: Tamada T]] |
| - | [[Category: Copper]]
| + | |
| - | [[Category: Neutron]]
| + | |
| - | [[Category: Nitrite reductase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
