5zou - Revision history

OCA at 09:02, 22 November 2023

2023-11-22T09:02:16Z

←Older revision		Revision as of 09:02, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5zou' size='340' side='right'caption='[[5zou]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='5zou' size='340' side='right'caption='[[5zou]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zou]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter~~ globiformis~~" (conn 1928) bergey et al. 1930~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZOU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zou]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZOU 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>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.68Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~TYQ~~:~~3-AMINO-6-HYDROXY-TYROSINE~~'>~~TYQ~~</scene><~~/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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYQ:3-AMINO-6-HYDROXY-TYROSINE'>TYQ</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Primary~~-~~amine_oxidase Primary~~-~~amine oxidase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.4.3.21 1.4.3.21]~~ </~~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=5zou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zou OCA], [https://pdbe.org/5zou PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zou RCSB], [https://www.ebi.ac.uk/pdbsum/5zou PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zou 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=5zou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zou OCA], [~~http~~://pdbe.org/5zou PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zou RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zou PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zou ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PAOX_ARTGO PAOX_ARTGO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5zou" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zou" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Copper amine oxidase 3D structures\|Copper amine oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arthrobacter globiformis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Primary-amine oxidase]]~~	+	[[Category: Baba S]]
-	[[Category: Baba, S]]	+	[[Category: Hayashi H]]
-	[[Category: Hayashi, H]]	+	[[Category: Kawano Y]]
-	[[Category: Kawano, Y]]	+	[[Category: Kumasaka T]]
-	[[Category: Kumasaka, T]]	+	[[Category: Murakawa T]]
-	[[Category: Murakawa, T]]	+	[[Category: Okajima T]]
-	[[Category: Okajima, T]]	+	[[Category: Tanizawa K]]
-	[[Category: Tanizawa, K]]	+	[[Category: Yamamoto M]]
-	[[Category: Yamamoto, M]]	+	[[Category: Yano T]]
-	[[Category: Yano, T]]	+
-	~~[[Category: Copper amine oxidase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Topaquinone]]~~	+
-	~~[[Category: Tpq~~]]	+

OCA at 21:22, 28 October 2020

2020-10-28T21:22:08Z

←Older revision		Revision as of 21:22, 28 October 2020
Line 1:		Line 1:

	==Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH6 at 288 K (1)==		==Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH6 at 288 K (1)==
-	<StructureSection load='5zou' size='340' side='right' caption='[[5zou]], [[Resolution\|resolution]] 1.68Å' scene=''>	+	<StructureSection load='5zou' size='340' side='right'caption='[[5zou]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zou]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZOU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zou]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZOU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYQ:3-AMINO-6-HYDROXY-TYROSINE'>TYQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYQ:3-AMINO-6-HYDROXY-TYROSINE'>TYQ</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Primary-amine_oxidase Primary-amine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 1.4.3.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Primary-amine_oxidase Primary-amine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 1.4.3.21] </span></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=5zou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zou OCA], [http://pdbe.org/5zou PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zou RCSB], [http://www.ebi.ac.uk/pdbsum/5zou PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zou 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=5zou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zou OCA], [http://pdbe.org/5zou PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zou RCSB], [http://www.ebi.ac.uk/pdbsum/5zou PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zou ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Primary-amine oxidase]]		[[Category: Primary-amine oxidase]]
	[[Category: Baba, S]]		[[Category: Baba, S]]

OCA at 06:16, 2 January 2019

2019-01-02T06:16:21Z

←Older revision		Revision as of 06:16, 2 January 2019
Line 3:		Line 3:
	<StructureSection load='5zou' size='340' side='right' caption='[[5zou]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='5zou' size='340' side='right' caption='[[5zou]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zou]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zou]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYQ:3-AMINO-6-HYDROXY-TYROSINE'>TYQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYQ:3-AMINO-6-HYDROXY-TYROSINE'>TYQ</scene></td></tr>
Line 9:		Line 9:
	<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=5zou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zou OCA], [http://pdbe.org/5zou PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zou RCSB], [http://www.ebi.ac.uk/pdbsum/5zou PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zou ProSAT]</span></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=5zou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zou OCA], [http://pdbe.org/5zou PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zou RCSB], [http://www.ebi.ac.uk/pdbsum/5zou PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zou ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the catalytic reaction of copper amine oxidase, the protein-derived redox cofactor topaquinone (TPQ) is reduced by an amine substrate to an aminoresorcinol form (TPQamr), which is in equilibrium with a semiquinone radical (TPQsq). The transition from TPQamr to TPQsq is an endothermic process, accompanied by a significant conformational change of the cofactor. We employed the humid air and glue-coating (HAG) method to capture the equilibrium mixture of TPQamr and TPQsq in noncryocooled crystals of the enzyme from Arthrobacter globiformis and found that the equilibrium shifts more toward TPQsq in crystals than in solution. Thermodynamic analyses of the temperature-dependent equilibrium also revealed that the transition to TPQsq is entropy-driven both in crystals and in solution, giving the thermodynamic parameters that led to experimental determination of the crystal packing effect. Furthermore, we demonstrate that the binding of product aldehyde to the hydrophobic pocket in the active site produces various equilibrium states among two forms of the product Schiff-base, TPQamr, and TPQsq, in a pH-dependent manner. The temperature-controlled HAG method provides a technique for thermodynamic analysis of conformational changes occurring in protein crystals that are hardly scrutinized by conventional cryogenic X-ray crystallography.
		+
		+	In crystallo thermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase.,Murakawa T, Baba S, Kawano Y, Hayashi H, Yano T, Kumasaka T, Yamamoto M, Tanizawa K, Okajima T Proc Natl Acad Sci U S A. 2018 Dec 18. pii: 1811837116. doi:, 10.1073/pnas.1811837116. PMID:30563857<ref>PMID:30563857</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zou" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:12, 19 December 2018

2018-12-19T08:12:26Z

←Older revision		Revision as of 08:12, 19 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zou ~~is ON HOLD until Paper Publication~~	+	==Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH6 at 288 K (1)==
-		+	<StructureSection load='5zou' size='340' side='right' caption='[[5zou]], [[Resolution\|resolution]] 1.68Å' scene=''>
-	~~Authors~~: ~~Murakawa, T~~.~~, Baba, S~~., ~~Kawano, Y~~.~~, Hayashi, H~~., ~~Yano, T~~., ~~Tanizawa~~, K., ~~Kumasaka, T~~., ~~Yamamoto, M~~., ~~Okajima, T~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zou]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZOU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZOU FirstGlance]. <br>
-	~~Description~~: ~~Copper~~ amine oxidase ~~from Arthrobacter globiformis anaerobically reduced by ethylamine at pH6 at 288 K (1)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYQ:3-AMINO-6-HYDROXY-TYROSINE'>TYQ</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Primary-amine_oxidase Primary-amine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 1.4.3.21] </span></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=5zou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zou OCA], [http://pdbe.org/5zou PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zou RCSB], [http://www.ebi.ac.uk/pdbsum/5zou PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zou ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Primary-amine oxidase]]
		+	[[Category: Baba, S]]
	[[Category: Hayashi, H]]		[[Category: Hayashi, H]]
	[[Category: Kawano, Y]]		[[Category: Kawano, Y]]
-	[[Category: ~~Baba~~, S]]	+	[[Category: Kumasaka, T]]
	[[Category: Murakawa, T]]		[[Category: Murakawa, T]]
-	[[Category: ~~Kumasaka~~, T]]	+	[[Category: Okajima, T]]
		+	[[Category: Tanizawa, K]]
	[[Category: Yamamoto, M]]		[[Category: Yamamoto, M]]
	[[Category: Yano, T]]		[[Category: Yano, T]]
-	[[Category: ~~Okajima, T~~]]	+	[[Category: Copper amine oxidase]]
-	[[Category: ~~Tanizawa, K~~]]	+	[[Category: Oxidoreductase]]
		+	[[Category: Topaquinone]]
		+	[[Category: Tpq]]

OCA at 03:48, 16 May 2018

2018-05-16T03:48:46Z

←Older revision		Revision as of 03:48, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Murakawa, T., Baba, S., Kawano, Y., Hayashi, H., Yano, T., Tanizawa, K., Kumasaka, T., Yamamoto, M., Okajima, T.		Authors: Murakawa, T., Baba, S., Kawano, Y., Hayashi, H., Yano, T., Tanizawa, K., Kumasaka, T., Yamamoto, M., Okajima, T.

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

2018-04-25T03:52:01Z

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

←Older revision

Revision as of 03:52, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zou is ON HOLD Authors: Murakawa, T., Baba, S., Kawano, Y., Hayashi, H., Yano, T., Tanizawa, K., Kumasaka, T., Yamamoto, M., Okajima, T. Descripti...

2018-04-25T03:51:59Z

New page: '''Unreleased structure''' The entry 5zou is ON HOLD Authors: Murakawa, T., Baba, S., Kawano, Y., Hayashi, H., Yano, T., Tanizawa, K., Kumasaka, T., Yamamoto, M., Okajima, T. Descripti...

New page

'''Unreleased structure'''

The entry 5zou is ON HOLD

Authors: Murakawa, T., Baba, S., Kawano, Y., Hayashi, H., Yano, T., Tanizawa, K., Kumasaka, T., Yamamoto, M., Okajima, T.

Description: Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH6 at 288 K (1)
[[Category: Unreleased Structures]]
[[Category: Hayashi, H]]
[[Category: Kawano, Y]]
[[Category: Baba, S]]
[[Category: Murakawa, T]]
[[Category: Kumasaka, T]]
[[Category: Yamamoto, M]]
[[Category: Yano, T]]
[[Category: Okajima, T]]
[[Category: Tanizawa, K]]