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| | ==R2-like ligand-binding oxidase with anaerobically reconstituted metal cofactor== | | ==R2-like ligand-binding oxidase with anaerobically reconstituted metal cofactor== |
| - | <StructureSection load='4hr4' size='340' side='right' caption='[[4hr4]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='4hr4' size='340' side='right'caption='[[4hr4]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4hr4]] 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=4HR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HR4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4hr4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus_HTA426 Geobacillus kaustophilus HTA426]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HR4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]], [[4hr5|4hr5]]</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=4hr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hr4 OCA], [https://pdbe.org/4hr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hr4 RCSB], [https://www.ebi.ac.uk/pdbsum/4hr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hr4 ProSAT]</span></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='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=4hr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hr4 OCA], [http://pdbe.org/4hr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hr4 RCSB], [http://www.ebi.ac.uk/pdbsum/4hr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hr4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5KW80_GEOKA Q5KW80_GEOKA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4hr4" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4hr4" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Geoka]] | + | [[Category: Geobacillus kaustophilus HTA426]] |
| - | [[Category: Ribonucleoside-diphosphate reductase]] | + | [[Category: Large Structures]] |
| - | [[Category: Griese, J J]] | + | [[Category: Griese JJ]] |
| - | [[Category: Hogbom, M]] | + | [[Category: Hogbom M]] |
| - | [[Category: Fatty acid/long-chain hydrocarbon ligand]]
| + | |
| - | [[Category: Heterodinuclear mn/fe cofactor]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Manganese]]
| + | |
| - | [[Category: Metalloprotein]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: R2-like ligand-binding oxidase]]
| + | |
| - | [[Category: Ribonucleotide reductase r2 subunit fold]]
| + | |
| Structural highlights
Function
Q5KW80_GEOKA
Publication Abstract from PubMed
Although metallocofactors are ubiquitous in enzyme catalysis, how metal binding specificity arises remains poorly understood, especially in the case of metals with similar primary ligand preferences such as manganese and iron. The biochemical selection of manganese over iron presents a particularly intricate problem because manganese is generally present in cells at a lower concentration than iron, while also having a lower predicted complex stability according to the Irving-Williams series (Mn(II) < Fe(II) < Ni(II) < Co(II) < Cu(II) > Zn(II)). Here we show that a heterodinuclear Mn/Fe cofactor with the same primary protein ligands in both metal sites self-assembles from Mn(II) and Fe(II) in vitro, thus diverging from the Irving-Williams series without requiring auxiliary factors such as metallochaperones. Crystallographic, spectroscopic, and computational data demonstrate that one of the two metal sites preferentially binds Fe(II) over Mn(II) as expected, whereas the other site is nonspecific, binding equal amounts of both metals in the absence of oxygen. Oxygen exposure results in further accumulation of the Mn/Fe cofactor, indicating that cofactor assembly is at least a two-step process governed by both the intrinsic metal specificity of the protein scaffold and additional effects exerted during oxygen binding or activation. We further show that the mixed-metal cofactor catalyzes a two-electron oxidation of the protein scaffold, yielding a tyrosine-valine ether cross-link. Theoretical modeling of the reaction by density functional theory suggests a multistep mechanism including a valyl radical intermediate.
Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein.,Griese JJ, Roos K, Cox N, Shafaat HS, Branca RM, Lehtio J, Graslund A, Lubitz W, Siegbahn PE, Hogbom M Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17189-94. doi:, 10.1073/pnas.1304368110. Epub 2013 Oct 7. PMID:24101498[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Griese JJ, Roos K, Cox N, Shafaat HS, Branca RM, Lehtio J, Graslund A, Lubitz W, Siegbahn PE, Hogbom M. Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein. Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17189-94. doi:, 10.1073/pnas.1304368110. Epub 2013 Oct 7. PMID:24101498 doi:http://dx.doi.org/10.1073/pnas.1304368110
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