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| <StructureSection load='6i93' size='340' side='right'caption='[[6i93]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='6i93' size='340' side='right'caption='[[6i93]], [[Resolution|resolution]] 2.10Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[6i93]] 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=6I93 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I93 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6i93]] 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=6I93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I93 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=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</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]] 2.101Å</td></tr> |
- | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4hr0|4hr0]], [[4hr4|4hr4]], [[4hr5|4hr5]], [[4xb9|4xb9]], [[4xbv|4xbv]], [[4xbw|4xbw]], [[5dco|5dco]], [[5dcr|5dcr]], [[5dcs|5dcs]], [[5ekb|5ekb]], [[5omk|5omk]], [[5omj|5omj]], [[6f65|6f65]], [[6f6b|6f6b]], [[6f6c|6f6c]], [[6f6e|6f6e]], [[6f6f|6f6f]], [[6f6g|6f6g]], [[6f6h|6f6h]], [[6f6k|6f6k]], [[6f6l|6f6l]], [[6f6m|6f6m]], [[6i92|6i92]], [[6i94|6i94]], [[6i95|6i95]], [[6i90|6i90]]</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=OCA:OCTANOIC+ACID+(CAPRYLIC+ACID)'>OCA</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6i93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i93 OCA], [https://pdbe.org/6i93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i93 RCSB], [https://www.ebi.ac.uk/pdbsum/6i93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i93 ProSAT]</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6i93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i93 OCA], [http://pdbe.org/6i93 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i93 RCSB], [http://www.ebi.ac.uk/pdbsum/6i93 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i93 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 6i93" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6i93" 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: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Ribonucleoside-diphosphate reductase]]
| + | [[Category: Griese JJ]] |
- | [[Category: Griese, J J]] | + | [[Category: Hogbom M]] |
- | [[Category: Hogbom, M]] | + | |
- | [[Category: Metalloprotein oxidoreductase]]
| + | |
- | [[Category: Mn/fe cofactor]]
| + | |
- | [[Category: Oxidoreductase]]
| + | |
- | [[Category: R2-like ligand-binding oxidase]]
| + | |
- | [[Category: Ribonucleotide reductase r2 subunit fold]]
| + | |
| Structural highlights
Function
Q5KW80_GEOKA
Publication Abstract from PubMed
A heterobimetallic Mn/Fe cofactor is present in the R2 subunit of class Ic ribonucleotide reductases (R2c) and in R2-like ligand-binding oxidases (R2lox). Although the protein-derived metal ligands are the same in both groups of proteins, the connectivity of the two metal ions and the chemistry each cofactor performs are different: in R2c, a one-electron oxidant, the Mn/Fe dimer is linked by two oxygen bridges (mu-oxo/mu-hydroxo), whereas in R2lox, a two-electron oxidant, it is linked by a single oxygen bridge (mu-hydroxo) and a fatty acid ligand. Here, we identified a second coordination sphere residue that directs the divergent reactivity of the protein scaffold. We found that the residue that directly precedes the N-terminal carboxylate metal ligand is conserved as a glycine within the R2lox group, but not in R2c. Substitution of the glycine with leucine converted the resting-state R2lox cofactor to an R2c-like cofactor, a micro-oxo/micro-hydroxo-bridged MnIII/FeIII dimer. This species has recently been observed as an intermediate of the oxygen activation reaction in wild-type R2lox, indicating that it is physiologically relevant. Cofactor maturation in R2c and R2lox therefore follows the same pathway, with structural and functional divergence of the two cofactor forms following oxygen activation. We also show that the leucine-substituted variant no longer functions as a two-electron oxidant. Our results reveal that the residue preceding the N-terminal metal ligand directs the cofactor's reactivity toward one- or two-electron redox chemistry, presumably by setting the protonation state of the bridging oxygens and thereby perturbing the redox potential of the Mn ion.
Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins.,Kutin Y, Kositzki R, Branca RMM, Srinivas V, Lundin D, Haumann M, Hogbom M, Cox N, Griese JJ J Biol Chem. 2019 Oct 7. pii: RA119.010570. doi: 10.1074/jbc.RA119.010570. PMID:31591267[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kutin Y, Kositzki R, Branca RMM, Srinivas V, Lundin D, Haumann M, Hogbom M, Cox N, Griese JJ. Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins. J Biol Chem. 2019 Oct 7. pii: RA119.010570. doi: 10.1074/jbc.RA119.010570. PMID:31591267 doi:http://dx.doi.org/10.1074/jbc.RA119.010570
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