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| | <StructureSection load='6kmm' size='340' side='right'caption='[[6kmm]], [[Resolution|resolution]] 1.93Å' scene=''> | | <StructureSection load='6kmm' size='340' side='right'caption='[[6kmm]], [[Resolution|resolution]] 1.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6kmm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KMM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KMM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6kmm]] 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=6KMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KMM 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.93Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">efeB, FC605_19685 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kmm OCA], [http://pdbe.org/6kmm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kmm RCSB], [http://www.ebi.ac.uk/pdbsum/6kmm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kmm ProSAT]</span></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=6kmm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kmm OCA], [https://pdbe.org/6kmm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kmm RCSB], [https://www.ebi.ac.uk/pdbsum/6kmm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kmm ProSAT]</span></td></tr> |
| | </table> | | </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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Dalal, V]] | + | [[Category: Dalal V]] |
| - | [[Category: Dhankhar, P]] | + | [[Category: Dhankhar P]] |
| - | [[Category: Kumar, P]] | + | [[Category: Kumar P]] |
| - | [[Category: Mahto, J K]] | + | [[Category: Mahto JK]] |
| - | [[Category: Dye-decolorizing peroxidase]]
| + | |
| - | [[Category: Ferredoxin like fold]]
| + | |
| - | [[Category: Hepe]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
6kmm 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 1.93Å |
| Ligands: | , , , , , , , |
| 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
The dye-decolorizing peroxidases (DyPs) belong to a unique heme peroxidase family for their biotechnological potential to detoxify synthetic dyes. In this work, we have biochemically and structurally characterized the dye-decolorizing peroxidase from Bacillus subtilis (BsDyP). The biochemical studies of BsDyP demonstrate that pH 4.0 is optimum for the oxidation of malachite green (MG) and methyl violet (MV). However, it oxidizes the MG with higher catalytic efficiency (kcat/Km = 6.3 x 10(2) M(-1)s(-1)), than MV (kcat/Km = 5.0 x 10(2) M(-1)s(-1)). While reactive black 5 (RB5) is oxidized at pH 3.0 with the catalytic efficiency of kcat/Km = 3.6 x 10(2) M(-1)s(-1). The calculated thermodynamic parameters by isothermal titration calorimetry (ITC) reveal the feasibility and spontaneity of dyes binding with BsDyP. Further, the crystal structures of a HEPES bound and unbound of BsDyP provide insight into the probable binding sites of the substrates. In BsDyP-HEPES bound structure, the HEPES-1 molecule is found in the heme cavity at the gamma-edge, and another HEPES-2 molecule is bound ~16 A away from the heme that is fenced by Ile231, Arg234, Ser235, Asp239, Glu334, and surface-exposed Tyr335 residues. Furthermore, the molecular docking, simulation, and MMPBSA studies support the binding of dyes at both the sites of BsDyP and produce lower-energy stable BsDyP-dyes complexes. Here, the BsDyP study allows the identification of its two potential binding sites and shows the oxidation of a variety of dyes. Structural and functional insight of BsDyP will facilitate its engineering for the improved decolorization of dyes.
Characterization of dye-decolorizing peroxidase from Bacillus subtilis.,Dhankhar P, Dalal V, Mahto JK, Gurjar BR, Tomar S, Sharma AK, Kumar P Arch Biochem Biophys. 2020 Oct 30;693:108590. doi: 10.1016/j.abb.2020.108590., Epub 2020 Sep 21. PMID:32971035[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:http://dx.doi.org/188/10/3664
- ↑ Dhankhar P, Dalal V, Mahto JK, Gurjar BR, Tomar S, Sharma AK, Kumar P. Characterization of dye-decolorizing peroxidase from Bacillus subtilis. Arch Biochem Biophys. 2020 Oct 30;693:108590. doi: 10.1016/j.abb.2020.108590., Epub 2020 Sep 21. PMID:32971035 doi:http://dx.doi.org/10.1016/j.abb.2020.108590
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