|
|
| Line 3: |
Line 3: |
| | <StructureSection load='5i6m' size='340' side='right'caption='[[5i6m]], [[Resolution|resolution]] 1.09Å' scene=''> | | <StructureSection load='5i6m' size='340' side='right'caption='[[5i6m]], [[Resolution|resolution]] 1.09Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5i6m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_cycloclastes"_(gray_and_thornton)_bergey_et_al. "achromobacter cycloclastes" (gray and thornton) bergey et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I6M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I6M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5i6m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I6M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.09Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=223 "Achromobacter cycloclastes" (Gray and Thornton) Bergey et al.])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</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=5i6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i6m OCA], [https://pdbe.org/5i6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i6m RCSB], [https://www.ebi.ac.uk/pdbsum/5i6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i6m ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5i6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i6m OCA], [http://pdbe.org/5i6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i6m RCSB], [http://www.ebi.ac.uk/pdbsum/5i6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i6m ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/NIR_ACHCY NIR_ACHCY] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 25: |
Line 26: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Achromobacter cycloclastes]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Horrell, S]] | + | [[Category: Horrell S]] |
| - | [[Category: Hough, M A]] | + | [[Category: Hough MA]] |
| - | [[Category: Strange, R W]] | + | [[Category: Strange RW]] |
| - | [[Category: Copper nitrite reductase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Reaction mechanism]]
| + | |
| - | [[Category: Serial crystallography]]
| + | |
| Structural highlights
5i6m is a 1 chain structure with sequence from Achromobacter cycloclastes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.09Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
NIR_ACHCY
Publication Abstract from PubMed
Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07-1.62 A resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a 'catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.
Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.,Horrell S, Antonyuk SV, Eady RR, Hasnain SS, Hough MA, Strange RW IUCrJ. 2016 Jun 15;3(Pt 4):271-81. doi: 10.1107/S205225251600823X. eCollection, 2016 Jul 1. PMID:27437114[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Horrell S, Antonyuk SV, Eady RR, Hasnain SS, Hough MA, Strange RW. Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal. IUCrJ. 2016 Jun 15;3(Pt 4):271-81. doi: 10.1107/S205225251600823X. eCollection, 2016 Jul 1. PMID:27437114 doi:http://dx.doi.org/10.1107/S205225251600823X
|
