7dlk: Difference between revisions

Revision as of 16:35, 29 November 2023

Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis

Structural highlights

7dlk is a 6 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	CL, EPE, GOL, HEM, MPD, OXY, PO4, VOH
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EFEN_BACSU Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the protoporphyrin ring intact (By similarity).^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ollinger J, Song KB, Antelmann H, Hecker M, Helmann JD. Role of the Fur regulon in iron transport in Bacillus subtilis. J Bacteriol. 2006 May;188(10):3664-73. PMID:16672620 doi:https://dx.doi.org/188/10/3664
↑ Dhankhar P, Dalal V, Singh V, Sharma AK, Kumar P. Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol. Int J Biol Macromol. 2021 Oct 20. pii: S0141-8130(21)02258-3. doi:, 10.1016/j.ijbiomac.2021.10.100. PMID:34687768 doi:https://dx.doi.org/10.1016/j.ijbiomac.2021.10.100

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Ollinger J, Song KB, Antelmann H, Hecker M, Helmann JD. Role of the Fur regulon in iron transport in Bacillus subtilis. J Bacteriol. 2006 May;188(10):3664-73. PMID:16672620 doi:https://dx.doi.org/188/10/3664

[2] Dhankhar P, Dalal V, Singh V, Sharma AK, Kumar P. Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol. Int J Biol Macromol. 2021 Oct 20. pii: S0141-8130(21)02258-3. doi:, 10.1016/j.ijbiomac.2021.10.100. PMID:34687768 doi:https://dx.doi.org/10.1016/j.ijbiomac.2021.10.100

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='7dlk' size='340' side='right'caption='[[7dlk]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7dlk]] is a 6 chain structure. 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>
+<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='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>
+</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>
+<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/A0A6G2J275_BACIU A0A6G2J275_BACIU]] Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the tetrapyrrol ring intact.[RuleBase:RU365017]
+[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 ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: Dalal, V]]
+[[Category: Dalal V]]
-[[Category: Dhankhar, P]]
+[[Category: Dhankhar P]]
-[[Category: Kumar, P]]
+[[Category: Kumar P]]
-[[Category: Dye-decolorizing peroxidase]]
-[[Category: Ferredoxin like fold]]
-[[Category: Oxidoreductase]]
-[[Category: Veratryl alcohol]]

7dlk: Difference between revisions

Revision as of 16:35, 29 November 2023

Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools