7dlk
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 7dlk is ON HOLD Authors: Dhankhar, P., Dalal, V., Kumar, P. Description: Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase fr...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis== | |
| + | <StructureSection load='7dlk' size='340' side='right'caption='[[7dlk]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[7dlk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DLK FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=VOH:Veratryl+alcohol'>VOH</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=7dlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dlk OCA], [https://pdbe.org/7dlk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dlk RCSB], [https://www.ebi.ac.uk/pdbsum/7dlk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dlk ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/EFEN_BACSU EFEN_BACSU] Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the protoporphyrin ring intact (By similarity).<ref>PMID:16672620</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP- veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065s(-1), followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (kcat) of 0.07s(-1) and 0.07s(-1), respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates. | ||
| - | + | Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol.,Dhankhar P, Dalal V, Singh V, Sharma AK, Kumar P Int J Biol Macromol. 2021 Oct 20. pii: S0141-8130(21)02258-3. doi:, 10.1016/j.ijbiomac.2021.10.100. PMID:34687768<ref>PMID:34687768</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: Dalal | + | <div class="pdbe-citations 7dlk" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Bacillus subtilis]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Dalal V]] | ||
| + | [[Category: Dhankhar P]] | ||
| + | [[Category: Kumar P]] | ||
Current revision
Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis
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