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6i3l

From Proteopedia

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Current revision (07:35, 1 May 2024) (edit) (undo)
 
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<StructureSection load='6i3l' size='340' side='right'caption='[[6i3l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='6i3l' size='340' side='right'caption='[[6i3l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6i3l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I3L FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6i3l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Albifimbria_verrucaria Albifimbria verrucaria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I3L FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6i3j|6i3j]], [[6i3k|6i3k]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Bilirubin_oxidase Bilirubin oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.5 1.3.3.5] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6i3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3l OCA], [https://pdbe.org/6i3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i3l RCSB], [https://www.ebi.ac.uk/pdbsum/6i3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3l ProSAT]</span></td></tr>
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<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=6i3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3l OCA], [http://pdbe.org/6i3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i3l RCSB], [http://www.ebi.ac.uk/pdbsum/6i3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3l ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/BLRO_ALBVE BLRO_ALBVE]
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Unlike any protein studied so far, the active site of bilirubin oxidase from Myrothecium verrucaria contains a unique type of covalent link between tryptophan and histidine side chains. The role of this post-translational modification in substrate binding and oxidation is not sufficiently understood. Our structural and mutational studies provide evidence that this Trp396-His398 adduct modifies T1 copper coordination and is an important part of the substrate binding and oxidation site. The presence of the adduct is crucial for oxidation of substituted phenols and it substantially influences the rate of oxidation of bilirubin. Additionally, we bring the first structure of bilirubin oxidase in complex with one of its products, ferricyanide ion, interacting with the modified tryptophan side chain, Arg356 and the active site-forming loop 393-398. The results imply that structurally and chemically distinct types of substrates, including bilirubin, utilize the Trp-His adduct mainly for binding and to a smaller extent for electron transfer.
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Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.,Koval T, Svecova L, Ostergaard LH, Skalova T, Duskova J, Hasek J, Kolenko P, Fejfarova K, Stransky J, Trundova M, Dohnalek J Sci Rep. 2019 Sep 23;9(1):13700. doi: 10.1038/s41598-019-50105-3. PMID:31548583<ref>PMID:31548583</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6i3l" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bilirubin oxidase]]
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[[Category: Albifimbria verrucaria]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Dohnalek, J]]
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[[Category: Dohnalek J]]
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[[Category: Duskova, J]]
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[[Category: Duskova J]]
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[[Category: Kolenko, P]]
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[[Category: Kolenko P]]
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[[Category: Koval, T]]
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[[Category: Koval T]]
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[[Category: Ostergaard, L H]]
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[[Category: Ostergaard LH]]
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[[Category: Skalova, T]]
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[[Category: Skalova T]]
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[[Category: Svecova, L]]
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[[Category: Svecova L]]
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[[Category: Enzymatic activity]]
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[[Category: Mutant]]
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[[Category: Oxidoreductase]]
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Current revision

Bilirubin oxidase from Myrothecium verrucaria, mutant W396F

PDB ID 6i3l

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