5dcr: Difference between revisions
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==R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (short soak)== | ==R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (short soak)== | ||
<StructureSection load='5dcr' size='340' side='right' caption='[[5dcr]], [[Resolution|resolution]] 2.11Å' scene=''> | <StructureSection load='5dcr' size='340' side='right'caption='[[5dcr]], [[Resolution|resolution]] 2.11Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5dcr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCR OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[5dcr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Geoka Geoka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DCR FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MN3:MANGANESE+(III)+ION'>MN3</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4hr0|4hr0]], [[4hr4|4hr4]], [[4hr5|4hr5]], [[4xbv|4xbv]], [[4xb9|4xb9]], [[5dco|5dco]], [[4xbw|4xbw]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4hr0|4hr0]], [[4hr4|4hr4]], [[4hr5|4hr5]], [[4xbv|4xbv]], [[4xb9|4xb9]], [[5dco|5dco]], [[4xbw|4xbw]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GK2771 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=235909 GEOKA])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dcr OCA], [http://pdbe.org/5dcr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dcr RCSB], [http://www.ebi.ac.uk/pdbsum/5dcr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dcr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Geoka]] | |||
[[Category: Large Structures]] | |||
[[Category: Ribonucleoside-diphosphate reductase]] | [[Category: Ribonucleoside-diphosphate reductase]] | ||
[[Category: Griese, J J]] | [[Category: Griese, J J]] | ||
Revision as of 10:59, 8 April 2020
R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (short soak)R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (short soak)
Structural highlights
Publication Abstract from PubMedTwo recently discovered groups of prokaryotic di-metal carboxylate proteins harbor a heterodinuclear Mn/Fe cofactor. These are the class Ic ribonucleotide reductase R2 proteins and a group of oxidases that are found predominantly in pathogens and extremophiles, called R2-like ligand-binding oxidases (R2lox). We have recently shown that the Mn/Fe cofactor of R2lox self-assembles from MnII and FeII in vitro and catalyzes formation of a tyrosine-valine ether crosslink in the protein scaffold [Griese JJ et al. (2013) Proc. Natl. Acad. Sci. USA 110:17189-17194]. Here we present a detailed structural analysis of R2lox in the non-activated, reduced and oxidized resting Mn/Fe- and Fe/Fe-bound states, as well as the non-activated Mn/Mn-bound state. X-ray crystallography and X-ray absorption spectroscopy demonstrate that the active site ligand configuration of R2lox is essentially the same regardless of cofactor composition. Both the Mn/Fe and the diiron cofactor activate oxygen and catalyze formation of the ether crosslink, whereas the dimanganese cluster does not. The structures delineate likely routes for gated oxygen and substrate access to the active site that are controlled by the redox state of the cofactor. These results suggest that oxygen activation proceeds via the same mechanism at the Mn/Fe and Fe/Fe center, and that R2lox proteins might utilize either cofactor in vivo based on metal availability. Structural Basis for Oxygen Activation at a Heterodinuclear Mn/Fe Cofactor.,Griese JJ, Kositzki R, Schrapers P, Branca RM, Nordstrom A, Lehtio J, Haumann M, Hogbom M J Biol Chem. 2015 Aug 31. pii: jbc.M115.675223. PMID:26324712[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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