5k53 - Revision history

OCA at 10:39, 27 September 2023

OCA — Wed, 27 Sep 2023 10:39:51 GMT

←Older revision		Revision as of 10:39, 27 September 2023
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	<StructureSection load='5k53' size='340' side='right'caption='[[5k53]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5k53' size='340' side='right'caption='[[5k53]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k53]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Oscillatoria_sp. Oscillatoria sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K53 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K53 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k53]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oscillatoria_sp. Oscillatoria sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K53 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K53 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>~~, ~~<scene name='pdbligand=STE:STEARIC+ACID'>STE</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5k52\|5k52]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</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=5k53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k53 OCA], [~~http~~://pdbe.org/5k53 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k53 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k53 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k53 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=5k53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k53 OCA], [https://pdbe.org/5k53 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k53 RCSB], [https://www.ebi.ac.uk/pdbsum/5k53 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k53 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1D5B390_9CYAN A0A1D5B390_9CYAN] Catalyzes the decarbonylation of fatty aldehydes to alkanes.[HAMAP-Rule:MF_00931]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Oscillatoria sp]]		[[Category: Oscillatoria sp]]
-	[[Category: Kim, H-.W]]	+	[[Category: Kim H-W]]
-	[[Category: Park~~, A K]]~~	+	[[Category: Park AK]]
-	~~[[Category: Ferritin-like di-iron protein]]~~	+
-	~~[[Category: Metal binding protein~~]]	+

OCA at 09:19, 25 June 2020

OCA — Thu, 25 Jun 2020 09:19:08 GMT

←Older revision		Revision as of 09:19, 25 June 2020
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	==Crystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011==		==Crystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011==
-	<StructureSection load='5k53' size='340' side='right' caption='[[5k53]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5k53' size='340' side='right'caption='[[5k53]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k53]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K53 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K53 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k53]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Oscillatoria_sp. Oscillatoria sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K53 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K53 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k52\|5k52]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k52\|5k52]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5k53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k53 OCA], [http://pdbe.org/5k53 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k53 RCSB], [http://www.ebi.ac.uk/pdbsum/5k53 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k53 ProSAT]</span></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=5k53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k53 OCA], [http://pdbe.org/5k53 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k53 RCSB], [http://www.ebi.ac.uk/pdbsum/5k53 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k53 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Oscillatoria sp]]
	[[Category: Kim, H-.W]]		[[Category: Kim, H-.W]]
	[[Category: Park, A K]]		[[Category: Park, A K]]
	[[Category: Ferritin-like di-iron protein]]		[[Category: Ferritin-like di-iron protein]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]

OCA at 21:10, 10 September 2016

OCA — Sat, 10 Sep 2016 21:10:38 GMT

←Older revision		Revision as of 21:10, 10 September 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5k53 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011==
		+	<StructureSection load='5k53' size='340' side='right' caption='[[5k53]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k53]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K53 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K53 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k52\|5k52]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k53 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k53 OCA], [http://pdbe.org/5k53 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k53 RCSB], [http://www.ebi.ac.uk/pdbsum/5k53 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k53 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cyanobacterial aldehyde deformylating oxygenase (cADO) is a key enzyme that catalyzes the unusual deformylation of aliphatic aldehydes for alkane biosynthesis and can be applied to the production of biofuel in vitro and in vivo. In this study, we determined crystal structures of two ADOs from Limnothrix sp. KNUA012 (LiADO) and Oscillatoria sp. KNUA011 (OsADO). The structures of LiADO and OsADO resembled those of typical cADOs, consisting of eight alpha-helices found in ferritin-like di-iron proteins. However, structural comparisons revealed that while the LiADO active site was vacant of iron and substrates, the OsADO active site was fully occupied, containing both a coordinated metal ion and substrate. Previous reports indicated that helix 5 is capable of adopting two distinct conformations depending upon the existence of bound iron. We observed that helix 5 of OsADO with an iron bound in the active site presented as a long helix, whereas helix 5 of LiADO, which lacked iron in the active site, presented two conformations (one long and two short helices), indicating that an equilibrium exists between the two states in solution. Furthermore, acquisition of a structure having a fully occupied active site is unique in the absence of higher iron concentrations as compared with other cADO structures, wherein low affinity for iron complicates the acquisition of crystal structures with bound iron. An in-depth analysis of the ADO apo-enzyme, the enzyme with substrate bound, and the enzyme with both iron and substrate bound provided novel insight into substrate-binding modes in the absence of a coordinated metal ion and suggested a separate two-step binding mechanism for substrate and iron co-factors. Moreover, our results provided a comprehensive structural basis for conformational changes induced by binding of the substrate and co-factor.

-	~~Authors: Park, A~~.K., Kim, H-.W.	+	Crystal structures of aldehyde deformylating oxygenase from Limnothrix sp. KNUA012 and Oscillatoria sp. KNUA011.,Park AK, Kim IS, Jeon BW, Roh SJ, Ryu MY, Baek HR, Jo SW, Kim YS, Park H, Lee JH, Yoon HS, Kim HW Biochem Biophys Res Commun. 2016 Aug 26;477(3):395-400. doi:, 10.1016/j.bbrc.2016.06.090. Epub 2016 Jun 18. PMID:27329814<ref>PMID:27329814</ref>

-	~~Description: Crystal structures~~ of ~~aldehyde deformylating oxygenase from Oscillatoria sp~~. ~~KNUA011~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Park, A.K]]~~	+	<div class="pdbe-citations 5k53" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kim, H-.W]]		[[Category: Kim, H-.W]]
		+	[[Category: Park, A K]]
		+	[[Category: Ferritin-like di-iron protein]]
		+	[[Category: Metal binding protein]]

OCA at 00:01, 13 July 2016

OCA — Wed, 13 Jul 2016 00:01:07 GMT

←Older revision		Revision as of 00:01, 13 July 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k53 is ON HOLD	+	The entry 5k53 is ON HOLD until Paper Publication

	Authors: Park, A.K., Kim, H-.W.		Authors: Park, A.K., Kim, H-.W.

OCA: Protected "5k53" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:20:22 GMT

Protected "5k53" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:20, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k53 is ON HOLD Authors: Park, A.K., Kim, H-.W. Description: Crystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011 [...

OCA — Wed, 01 Jun 2016 14:20:21 GMT

New page: '''Unreleased structure''' The entry 5k53 is ON HOLD Authors: Park, A.K., Kim, H-.W. Description: Crystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011 [...

New page

'''Unreleased structure'''

The entry 5k53 is ON HOLD

Authors: Park, A.K., Kim, H-.W.

Description: Crystal structures of aldehyde deformylating oxygenase from Oscillatoria sp. KNUA011
[[Category: Unreleased Structures]]
[[Category: Park, A.K]]
[[Category: Kim, H-.W]]