7s5o
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | ==Crystal | + | ==Crystal structure of Cytochrome c' beta from Nitrosomonas europaea ATCC 19718== |
| - | <StructureSection load='7s5o' size='340' side='right'caption='[[7s5o]]' scene=''> | + | <StructureSection load='7s5o' size='340' side='right'caption='[[7s5o]], [[Resolution|resolution]] 1.80Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S5O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7s5o]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S5O FirstGlance]. <br> |
| - | </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=7s5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s5o OCA], [https://pdbe.org/7s5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s5o RCSB], [https://www.ebi.ac.uk/pdbsum/7s5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s5o ProSAT]</span></td></tr> | + | </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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7s5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s5o OCA], [https://pdbe.org/7s5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s5o RCSB], [https://www.ebi.ac.uk/pdbsum/7s5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s5o ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH2OH) is converted to nitric oxide (NO) and nitrous oxide (N2O) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt c'beta-Met, the cross-link is absent, and the cytochrome instead binds H2O2 forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 A crystal structure of cyt c'beta-Met horizontal line a well-expressed protein in N. europaea with a lysine to a methionine replacement at the cross-linking position. The structure of cyt c'beta-Met is characterized by a large beta-sheet typical of P460 members; however, several localized structural differences render cyt c'beta-Met distinct. This includes a large lasso-like loop at the "top" of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt c'beta from the methane-oxidizing Methylococcus capsulatus Bath, which also lacks the cross-link. The phenylalanine "cap" which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NH2OH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NH2OH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt c'beta-Met to oxidize NH2OH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain's spatial position in the structure does not eliminate the possibility that it could form under certain conditions. | ||
| + | |||
| + | Structural Characterization of Cytochrome c'beta-Met from an Ammonia-Oxidizing Bacterium.,Abendroth J, Buchko GW, Liew FN, Nguyen JN, Kim HJ Biochemistry. 2022 Mar 22. doi: 10.1021/acs.biochem.1c00640. PMID:35315646<ref>PMID:35315646</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7s5o" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Structural genomic]] | ||
| + | [[Category: Cytochrome_p460 domain-containing protein]] | ||
| + | [[Category: Metal binding protein]] | ||
| + | [[Category: Ne0824]] | ||
| + | [[Category: Nitrosomonas europaea]] | ||
| + | [[Category: Ssgcid]] | ||
Revision as of 10:22, 13 April 2022
Crystal structure of Cytochrome c' beta from Nitrosomonas europaea ATCC 19718
| |||||||||||
