5gt2: Difference between revisions

Revision as of 11:41, 2 August 2023

Crystal Structure and Biochemical Features of dye-decolorizing peroxidase YfeX from Escherichia coli O157

Structural highlights

5gt2 is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.093Å
Ligands:	HEM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YFEX_ECOLI Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the tetrapyrrol ring intact.^[1]

Publication Abstract from PubMed

YfeX from Escherichia coli O157 is a bacterial dye-decolorizing peroxidase that represents both dye-decoloring activity and typical peroxidase activity. We reported the crystal structure of YfeX bound to heme at 2.09 A resolution. The YfeX monomer resembles a ferredoxin-like fold and contains two domains. The three conserved residues surrounding the heme group are His215, Asp143 and Arg232. His215 functions as the proximal axial ligand of the heme iron atom. Biochemical data show that the catalytic significance of the conserved Asp143 and Arg232 depends on the substrate types and that YfeX may adopt various catalytic mechanisms toward divergent substrates. In addition, it is observed that an access tunnel spans from the protein molecular surface to the heme distal region, it serves as the passageway for the entrance and binding of the H2O2.

Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp143 and Arg232 play divergent roles toward different substrates.,Liu X, Yuan Z, Wang J, Cui Y, Liu S, Ma Y, Gu L, Xu S Biochem Biophys Res Commun. 2017 Feb 26;484(1):40-44. doi:, 10.1016/j.bbrc.2017.01.081. Epub 2017 Jan 19. PMID:28109884^[2]

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

References

↑ Letoffe S, Heuck G, Delepelaire P, Lange N, Wandersman C. Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11719-24. doi:, 10.1073/pnas.0903842106. Epub 2009 Jun 29. PMID:19564607 doi:https://dx.doi.org/10.1073/pnas.0903842106
↑ Liu X, Yuan Z, Wang J, Cui Y, Liu S, Ma Y, Gu L, Xu S. Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp143 and Arg232 play divergent roles toward different substrates. Biochem Biophys Res Commun. 2017 Feb 26;484(1):40-44. doi:, 10.1016/j.bbrc.2017.01.081. Epub 2017 Jan 19. PMID:28109884 doi:https://dx.doi.org/10.1016/j.bbrc.2017.01.081

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Letoffe S, Heuck G, Delepelaire P, Lange N, Wandersman C. Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11719-24. doi:, 10.1073/pnas.0903842106. Epub 2009 Jun 29. PMID:19564607 doi:https://dx.doi.org/10.1073/pnas.0903842106

[2] Liu X, Yuan Z, Wang J, Cui Y, Liu S, Ma Y, Gu L, Xu S. Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp143 and Arg232 play divergent roles toward different substrates. Biochem Biophys Res Commun. 2017 Feb 26;484(1):40-44. doi:, 10.1016/j.bbrc.2017.01.081. Epub 2017 Jan 19. PMID:28109884 doi:https://dx.doi.org/10.1016/j.bbrc.2017.01.081

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='5gt2' size='340' side='right'caption='[[5gt2]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gt2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GT2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GT2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gt2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GT2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GT2 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></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]] 2.093&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yfeX, b2431, JW2424 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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></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=5gt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gt2 OCA], [http://pdbe.org/5gt2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gt2 RCSB], [http://www.ebi.ac.uk/pdbsum/5gt2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gt2 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=5gt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gt2 OCA], [https://pdbe.org/5gt2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gt2 RCSB], [https://www.ebi.ac.uk/pdbsum/5gt2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gt2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YFEX_ECOLI YFEX_ECOLI]] Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the tetrapyrrol ring intact.<ref>PMID:19564607</ref>
+[https://www.uniprot.org/uniprot/YFEX_ECOLI YFEX_ECOLI] Involved in the recovery of exogenous heme iron. Extracts iron from heme while preserving the tetrapyrrol ring intact.<ref>PMID:19564607</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Gu, L C]]
+[[Category: Gu LC]]
-[[Category: Liu, S]]
+[[Category: Liu S]]
-[[Category: Liu, X H]]
+[[Category: Liu XH]]
-[[Category: Ma, Y L]]
+[[Category: Ma YL]]
-[[Category: Wang, J X]]
+[[Category: Wang JX]]
-[[Category: Yuan, Z G]]
+[[Category: Yuan ZG]]
-[[Category: Dye-decolorizing peroxidase]]
-[[Category: Heme]]
-[[Category: Oxidoreductase]]
-[[Category: Yfex]]

5gt2: Difference between revisions

Revision as of 11:41, 2 August 2023

Crystal Structure and Biochemical Features of dye-decolorizing peroxidase YfeX from Escherichia coli O157

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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