7e5q: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7e5q]] is a 2 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=7E5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E5Q FirstGlance]. <br>
<table><tr><td colspan='2'>[[7e5q]] is a 2 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=7E5Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E5Q FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7e5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e5q OCA], [https://pdbe.org/7e5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e5q RCSB], [https://www.ebi.ac.uk/pdbsum/7e5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e5q 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=7e5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e5q OCA], [https://pdbe.org/7e5q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e5q RCSB], [https://www.ebi.ac.uk/pdbsum/7e5q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e5q ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/EFEB_BACSU EFEB_BACSU] Involved in the recovery of exogenous heme iron (By similarity). Extracts iron from heme while preserving the protoporphyrin ring intact (By similarity). Part of the iron transporter system efeUOB/M involved in iron import (PubMed:16672620, PubMed:23764491). Catalyzes the peroxide-mediated oxidation of Fe(2+) into Fe(3+); EfeM binds Fe(3+) and delivers it to the cell membrane permease EfeU (PubMed:23764491).[UniProtKB:P31545]<ref>PMID:16672620</ref> <ref>PMID:23764491</ref>  
Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the crystal structures of class A-type DyP from Bacillus subtilis at pH 7.0 (BsDyP7), exposing the location of three binding sites for small substrates and high redox-potential substrates. The biochemical studies revealed the optimum acidic pH for enzyme activity. In the present study, the crystal structure of BsDyP at acidic pH (BsDyP4) reveals two-monomer units stabilized by intermolecular salt bridges and a hydrogen bond network in a homo-dimeric unit. Based on the monomeric structural comparison of BsDyP4 and BsDyP7, minor differences were observed in the loop regions, that is, LI (Ala64-Gln71), LII (Glu96-Lys108), LIII (Pro117-Leu124), and LIV (Leu295-Asp303). Despite these differences, BsDyP4 adopts similar heme architecture as well as three substrate-binding sites to BsDyP7. In BsDyP4, a shift in Asp187, heme pocket residue discloses the plausible reason for optimal acidic pH for BsDyP activity. This study provides insight into the structural changes in BsDyP at acidic pH, where BsDyP is biologically active.
 
Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis.,Dhankhar P, Dalal V, Sharma AK, Kumar P Proteins. 2022 Nov 8. doi: 10.1002/prot.26444. PMID:36345957<ref>PMID:36345957</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7e5q" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 14:11, 13 August 2026

Crystal Structure of Dye Decolorizing peroxidase from Bacillus subtilis at acidic pH

7e5q, resolution 1.90Å

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