5onx: Difference between revisions
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==Resting state copper nitrite reductase determined by serial femtosecond rotation crystallography== | ==Resting state copper nitrite reductase determined by serial femtosecond rotation crystallography== | ||
<StructureSection load='5onx' size='340' side='right' caption='[[5onx]], [[Resolution|resolution]] 1.60Å' scene=''> | <StructureSection load='5onx' size='340' side='right'caption='[[5onx]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5onx]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5onx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ONX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ONX FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5onx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5onx OCA], [https://pdbe.org/5onx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5onx RCSB], [https://www.ebi.ac.uk/pdbsum/5onx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5onx ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/O68601_ALCXX O68601_ALCXX] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Nitrite reductase|Nitrite reductase]] | *[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Achromobacter xylosoxidans | [[Category: Achromobacter xylosoxidans]] | ||
[[Category: Ago | [[Category: Large Structures]] | ||
[[Category: Antonyuk | [[Category: Ago H]] | ||
[[Category: Eady | [[Category: Antonyuk SV]] | ||
[[Category: Halsted | [[Category: Eady RR]] | ||
[[Category: Hasnain | [[Category: Halsted TP]] | ||
[[Category: Hirata | [[Category: Hasnain SS]] | ||
[[Category: Tosha | [[Category: Hirata K]] | ||
[[Category: Ueno | [[Category: Tosha T]] | ||
[[Category: Yamamoto | [[Category: Ueno G]] | ||
[[Category: Yamashita | [[Category: Yamamoto M]] | ||
[[Category: Yamashita K]] | |||
Latest revision as of 19:56, 13 December 2023
Resting state copper nitrite reductase determined by serial femtosecond rotation crystallographyResting state copper nitrite reductase determined by serial femtosecond rotation crystallography
Structural highlights
FunctionPublication Abstract from PubMedSynchrotron-based X-ray structural studies of ligand-bound enzymes are powerful tools to further our understanding of reaction mechanisms. For redox enzymes, it is necessary to study both the oxidized and reduced active sites to fully elucidate the reaction, an objective that is complicated by potential X-ray photoreduction. In the presence of the substrate, this can be exploited to construct a structural movie of the events associated with catalysis. Using the newly developed approach of serial femtosecond rotation crystallography (SF-ROX), an X-ray damage-free structure of the as-isolated copper nitrite reductase (CuNiR) was visualized. The sub-10 fs X-ray pulse length from the SACLA X-ray free-electron laser allowed diffraction data to be collected to 1.6 A resolution in a 'time-frozen' state. The extremely short duration of the X-ray pulses ensures the capture of data prior to the onset of radiation-induced changes, including radiolysis. Unexpectedly, an O2 ligand was identified bound to the T2Cu in a brand-new binding mode for a diatomic ligand in CuNiRs. The observation of O2 in a time-frozen structure of the as-isolated oxidized enzyme provides long-awaited clear-cut evidence for the mode of O2 binding in CuNiRs. This provides an insight into how CuNiR from Alcaligenes xylosoxidans can function as an oxidase, reducing O2 to H2O2, or as a superoxide dismutase (SOD) since it was shown to have approximately 56% of the dismutase activity of the bovine SOD enzyme some two decades ago. An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase.,Halsted TP, Yamashita K, Hirata K, Ago H, Ueno G, Tosha T, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS IUCrJ. 2018 Jan 1;5(Pt 1):22-31. doi: 10.1107/S2052252517016128. eCollection 2018, Jan 1. PMID:29354268[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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