7z5p - Revision history

OCA at 13:29, 1 February 2024

OCA — Thu, 01 Feb 2024 13:29:12 GMT

←Older revision		Revision as of 13:29, 1 February 2024
Line 1:		Line 1:

	==Bilirubin oxidase from Bacillus pumilus==		==Bilirubin oxidase from Bacillus pumilus==
-	<StructureSection load='7z5p' size='340' side='right'caption='[[7z5p]]' scene=''>	+	<StructureSection load='7z5p' size='340' side='right'caption='[[7z5p]], [[Resolution\|resolution]] 2.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7z5p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_pumilus_SAFR-032 Bacillus pumilus SAFR-032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z5P FirstGlance]. <br>
-	</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=7z5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z5p OCA], [https://pdbe.org/7z5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z5p RCSB], [https://www.ebi.ac.uk/pdbsum/7z5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z5p ProSAT]</span></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]] 2.991Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=7z5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z5p OCA], [https://pdbe.org/7z5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z5p RCSB], [https://www.ebi.ac.uk/pdbsum/7z5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z5p ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A8FAG9_BACP2 A8FAG9_BACP2]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Efficient oxygen-reducing biocatalysts are essential for the development of biofuel cells or photo-bioelectrochemical applications. Bilirubin oxidase (BOD) is a promising biocatalyst for oxygen reduction processes at neutral pH and low overpotentials. BOD has been extensively investigated over the last few decades. While the enzyme's internal electron transfer process and methods to establish electrical communication with electrodes have been elucidated, a crystal structure of BOD from bacterial origin has never been determined. Here we present the first crystal structure of BOD from Bacillus pumilus (BpBOD) at 3.5 A resolution. Overall, BpBOD shows high homology with the fungal enzymes; however, it holds a unique surface-exposed disulfide bond between Cys229 and Cys322 residues. We present methodologies to orient the T1 site towards the electrode by coupling the reduced disulfide bond with maleimide moiety on the electrodes. The developed configurations were further investigated and revealed improved direct electron transfer rates with the electrodes. The work presented here may contribute to the construction of rationally designed bioanodes or biocathode configurations that are based on redox-active enzymes.
		+
		+	The Structure of Bilirubin Oxidase from Bacillus pumilus Reveals a Unique Disulfide Bond for Site-Specific Direct Electron Transfer.,Gihaz S, Herzallh NS, Cohen Y, Bachar O, Fishman A, Yehezkeli O Biosensors (Basel). 2022 Apr 19;12(5). pii: bios12050258. doi:, 10.3390/bios12050258. PMID:35624560<ref>PMID:35624560</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7z5p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus pumilus SAFR-032]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bachar O]]		[[Category: Bachar O]]

OCA at 14:40, 31 August 2022

OCA — Wed, 31 Aug 2022 14:40:22 GMT

←Older revision		Revision as of 14:40, 31 August 2022
Line 1:		Line 1:

	==Bilirubin oxidase from Bacillus pumilus==		==Bilirubin oxidase from Bacillus pumilus==
-	<StructureSection load='7z5p' size='340' side='right'caption='[[7z5p]]~~, [[Resolution\|resolution]] 2.99Å~~' scene=''>	+	<StructureSection load='7z5p' size='340' side='right'caption='[[7z5p]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7z5p]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z5P FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>~~	+	</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=7z5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z5p OCA], [https://pdbe.org/7z5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z5p RCSB], [https://www.ebi.ac.uk/pdbsum/7z5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z5p 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=7z5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z5p OCA], [https://pdbe.org/7z5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z5p RCSB], [https://www.ebi.ac.uk/pdbsum/7z5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z5p ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Efficient oxygen-reducing biocatalysts are essential for the development of biofuel cells or photo-bioelectrochemical applications. Bilirubin oxidase (BOD) is a promising biocatalyst for oxygen reduction processes at neutral pH and low overpotentials. BOD has been extensively investigated over the last few decades. While the enzyme's internal electron transfer process and methods to establish electrical communication with electrodes have been elucidated, a crystal structure of BOD from bacterial origin has never been determined. Here we present the first crystal structure of BOD from Bacillus pumilus (BpBOD) at 3.5 A resolution. Overall, BpBOD shows high homology with the fungal enzymes; however, it holds a unique surface-exposed disulfide bond between Cys229 and Cys322 residues. We present methodologies to orient the T1 site towards the electrode by coupling the reduced disulfide bond with maleimide moiety on the electrodes. The developed configurations were further investigated and revealed improved direct electron transfer rates with the electrodes. The work presented here may contribute to the construction of rationally designed bioanodes or biocathode configurations that are based on redox-active enzymes.
-
-	The Structure of Bilirubin Oxidase from Bacillus pumilus Reveals a Unique Disulfide Bond for Site-Specific Direct Electron Transfer.,Gihaz S, Herzallh NS, Cohen Y, Bachar O, Fishman A, Yehezkeli O Biosensors (Basel). 2022 Apr 19;12(5). pii: bios12050258. doi:, 10.3390/bios12050258. PMID:35624560<ref>PMID:35624560</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7z5p" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bachar, O]]	+	[[Category: Bachar O]]
-	[[Category: Cohen, Y]]	+	[[Category: Cohen Y]]
-	[[Category: Fishman, A]]	+	[[Category: Fishman A]]
-	[[Category: Gihaz, S]]	+	[[Category: Gihaz S]]
-	[[Category: Herzallh~~, N S~~]]	+	[[Category: Herzallh NS]]
-	[[Category: Yehezkeli, O]]	+	[[Category: Yehezkeli O]]
-	~~[[Category: Bacillus pumilus]]~~	+
-	~~[[Category: Bilirubin oxidase]]~~	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Oxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 05:38, 8 June 2022

OCA — Wed, 08 Jun 2022 05:38:05 GMT

←Older revision		Revision as of 05:38, 8 June 2022
Line 1:		Line 1:

	==Bilirubin oxidase from Bacillus pumilus==		==Bilirubin oxidase from Bacillus pumilus==
-	<StructureSection load='7z5p' size='340' side='right'caption='[[7z5p]]' scene=''>	+	<StructureSection load='7z5p' size='340' side='right'caption='[[7z5p]], [[Resolution\|resolution]] 2.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z5P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7z5p]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z5P FirstGlance]. <br>
-	</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=7z5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z5p OCA], [https://pdbe.org/7z5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z5p RCSB], [https://www.ebi.ac.uk/pdbsum/7z5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z5p ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=7z5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z5p OCA], [https://pdbe.org/7z5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z5p RCSB], [https://www.ebi.ac.uk/pdbsum/7z5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z5p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Efficient oxygen-reducing biocatalysts are essential for the development of biofuel cells or photo-bioelectrochemical applications. Bilirubin oxidase (BOD) is a promising biocatalyst for oxygen reduction processes at neutral pH and low overpotentials. BOD has been extensively investigated over the last few decades. While the enzyme's internal electron transfer process and methods to establish electrical communication with electrodes have been elucidated, a crystal structure of BOD from bacterial origin has never been determined. Here we present the first crystal structure of BOD from Bacillus pumilus (BpBOD) at 3.5 A resolution. Overall, BpBOD shows high homology with the fungal enzymes; however, it holds a unique surface-exposed disulfide bond between Cys229 and Cys322 residues. We present methodologies to orient the T1 site towards the electrode by coupling the reduced disulfide bond with maleimide moiety on the electrodes. The developed configurations were further investigated and revealed improved direct electron transfer rates with the electrodes. The work presented here may contribute to the construction of rationally designed bioanodes or biocathode configurations that are based on redox-active enzymes.
		+
		+	The Structure of Bilirubin Oxidase from Bacillus pumilus Reveals a Unique Disulfide Bond for Site-Specific Direct Electron Transfer.,Gihaz S, Herzallh NS, Cohen Y, Bachar O, Fishman A, Yehezkeli O Biosensors (Basel). 2022 Apr 19;12(5). pii: bios12050258. doi:, 10.3390/bios12050258. PMID:35624560<ref>PMID:35624560</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7z5p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bachar O]]	+	[[Category: Bachar, O]]
-	[[Category: Cohen Y]]	+	[[Category: Cohen, Y]]
-	[[Category: Fishman A]]	+	[[Category: Fishman, A]]
-	[[Category: Gihaz S]]	+	[[Category: Gihaz, S]]
-	[[Category: Herzallh NS]]	+	[[Category: Herzallh, N S]]
-	[[Category: Yehezkeli O]]	+	[[Category: Yehezkeli, O]]
		+	[[Category: Bacillus pumilus]]
		+	[[Category: Bilirubin oxidase]]
		+	[[Category: Electron transfer]]
		+	[[Category: Oxidase]]
		+	[[Category: Oxidoreductase]]

OCA at 06:22, 12 May 2022

OCA — Thu, 12 May 2022 06:22:04 GMT

←Older revision		Revision as of 06:22, 12 May 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7z5p is ~~ON HOLD~~	+	==Bilirubin oxidase from Bacillus pumilus==
-		+	<StructureSection load='7z5p' size='340' side='right'caption='[[7z5p]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z5P FirstGlance]. <br>
-	~~Description~~:	+	</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=7z5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z5p OCA], [https://pdbe.org/7z5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z5p RCSB], [https://www.ebi.ac.uk/pdbsum/7z5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z5p ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bachar O]]
		+	[[Category: Cohen Y]]
		+	[[Category: Fishman A]]
		+	[[Category: Gihaz S]]
		+	[[Category: Herzallh NS]]
		+	[[Category: Yehezkeli O]]

OCA: Protected "7z5p" [edit=sysop:move=sysop]

OCA — Wed, 16 Mar 2022 05:19:17 GMT

Protected "7z5p" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:19, 16 March 2022

OCA: New page: '''Unreleased structure''' The entry 7z5p is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 16 Mar 2022 05:19:17 GMT

New page: '''Unreleased structure''' The entry 7z5p is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7z5p is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]