3o72

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Revision as of 10:03, 14 February 2024

Crystal structure of EfeB in complex with heme

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 <StructureSection load='3o72' size='340' side='right'caption='[[3o72]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3o72]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Eco5t Eco5t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O72 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3o72]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7_str._TW14359 Escherichia coli O157:H7 str. TW14359]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O72 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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]] 1.95&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">efeB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=544404 ECO5T])</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=3o72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o72 OCA], [https://pdbe.org/3o72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o72 RCSB], [https://www.ebi.ac.uk/pdbsum/3o72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o72 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/EFEB_ECO57 EFEB_ECO57] Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the protoporphyrin ring intact. Also displays peroxidase activity on guaiacol and catechol in vitro. The deferrochelatase activity appears to be closely related to the peroxidation activity, but the link is unclear.<ref>PMID:21324904</ref>
-EfeB/YcdB is a member of the dye-decolorizing peroxidase (DyP) protein family. Recent study has shown that this protein can extract iron from heme without breaking the tetrapyrrole ring. We report the crystal structure of EfeB from E. coli O157 bound to heme at 1.95 Aresolution. The EfeB monomer contains two domains. The heme molecule is located in a large hydrophobic pocket in the C-terminal domain. A long loop connecting the two domains extensively interacts with the heme, which is a distinctive structural feature of EfeB homologues. A large tunnel formed by this loop and the beta-sheet of C-terminal domain provides a potential cofactor/substrate binding site. Biochemical data show that the production of protoporphyrin IX (PPIX) is closely related to the peroxidation activity. The mutant D235N keeps nearly the same activity of guaiacol peroxidase as the wild type protein, while the corresponding mutation in the classic DyP protein family completely abolishes the peroxidation activity. These results suggest that EfeB is a unique member of the DyP protein family. In addition, dramatically enhanced fluorescence excitation and emission of EfeB-PPIX was observed, implying this protein may be used as a red color fluorescence marker.
-Crystal structure and biochemical features of EfeB/YcdB from Escherichia coli O157: Asp235 plays divergent roles in different enzyme-catalyzed processes.,Liu X, Du Q, Wang Z, Zhu D, Huang Y, Li N, Wei T, Xu S, Gu L J Biol Chem. 2011 Feb 15. PMID:21324904<ref>PMID:21324904</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3o72" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Eco5t]]
+[[Category: Escherichia coli O157:H7 str. TW14359]]
 [[Category: Large Structures]]
-[[Category: Du, Q]]
+[[Category: Du Q]]
-[[Category: Gu, L]]
+[[Category: Gu L]]
-[[Category: Huang, Y]]
+[[Category: Huang Y]]
-[[Category: Li, N]]
+[[Category: Li N]]
-[[Category: Liu, X]]
+[[Category: Liu X]]
-[[Category: Wang, Z]]
+[[Category: Wang Z]]
-[[Category: Xu, S]]
+[[Category: Xu S]]
-[[Category: Zhu, D]]
+[[Category: Zhu D]]
-[[Category: Efeb in complex with heme]]
-[[Category: Heme binding]]
-[[Category: Heme deferrochelatase]]
-[[Category: Heme-binding protein]]

3o72

From Proteopedia

Revision as of 10:03, 14 February 2024

Crystal structure of EfeB in complex with heme

Structural highlights

Function

References

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