5zpa - Revision history

OCA at 09:02, 22 November 2023

OCA — Wed, 22 Nov 2023 09:02:53 GMT

←Older revision		Revision as of 09:02, 22 November 2023
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	==Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 283 K (2)==		==Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 283 K (2)==
-	<StructureSection load='5zpa' size='340' side='right' caption='[[5zpa]], [[Resolution\|resolution]] 1.69Å' scene=''>	+	<StructureSection load='5zpa' size='340' side='right'caption='[[5zpa]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zpa]] 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=5ZPA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zpa]] 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=5ZPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZPA 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~~></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]] 1.689Å</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=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=5zpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zpa OCA], [https://pdbe.org/5zpa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zpa RCSB], [https://www.ebi.ac.uk/pdbsum/5zpa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zpa 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=5zpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zpa OCA], [~~http~~://pdbe.org/5zpa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zpa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zpa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zpa 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 5zpa" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zpa" 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: ~~Primary-amine oxidase~~]]	+	[[Category: Arthrobacter globiformis]]
-	[[Category: Baba, S]]	+	[[Category: Large Structures]]
-	[[Category: Hayashi, H]]	+	[[Category: Baba S]]
-	[[Category: Kawano, Y]]	+	[[Category: Hayashi H]]
-	[[Category: Kumasaka, T]]	+	[[Category: Kawano Y]]
-	[[Category: Murakawa, T]]	+	[[Category: Kumasaka T]]
-	[[Category: Okajima, T]]	+	[[Category: Murakawa T]]
-	[[Category: Tanizawa, K]]	+	[[Category: Okajima T]]
-	[[Category: Yamamoto, M]]	+	[[Category: Tanizawa K]]
-	[[Category: Yano, T]]	+	[[Category: Yamamoto M]]
-	~~[[Category: Copper amine oxidase]]~~	+	[[Category: Yano T]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Topaquinone]]~~	+
-	~~[[Category: Tpq~~]]	+

OCA at 09:41, 13 February 2019

OCA — Wed, 13 Feb 2019 09:41:45 GMT

←Older revision		Revision as of 09:41, 13 February 2019
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	<StructureSection load='5zpa' size='340' side='right' caption='[[5zpa]], [[Resolution\|resolution]] 1.69Å' scene=''>		<StructureSection load='5zpa' size='340' side='right' caption='[[5zpa]], [[Resolution\|resolution]] 1.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zpa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZPA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zpa]] 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=5ZPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZPA 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></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></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=5zpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zpa OCA], [http://pdbe.org/5zpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zpa RCSB], [http://www.ebi.ac.uk/pdbsum/5zpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zpa 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=5zpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zpa OCA], [http://pdbe.org/5zpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zpa RCSB], [http://www.ebi.ac.uk/pdbsum/5zpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zpa 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 5zpa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:13, 19 December 2018

OCA — Wed, 19 Dec 2018 08:13:46 GMT

←Older revision		Revision as of 08:13, 19 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zpa is ~~ON HOLD until Paper Publication~~	+	==Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 283 K (2)==
-		+	<StructureSection load='5zpa' size='340' side='right' caption='[[5zpa]], [[Resolution\|resolution]] 1.69Å' 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'>[[5zpa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZPA FirstGlance]. <br>
-	~~Description~~: ~~Copper~~ amine oxidase ~~from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 6 at 283 K (2)~~	+	</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></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=5zpa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zpa OCA], [http://pdbe.org/5zpa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zpa RCSB], [http://www.ebi.ac.uk/pdbsum/5zpa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zpa ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Primary-amine oxidase]]
		+	[[Category: Baba, S]]
	[[Category: Hayashi, H]]		[[Category: Hayashi, H]]
-	[[Category: Baba, S]]
-	[[Category: Yamamoto, M]]
-	[[Category: Yano, T]]
-	[[Category: Tanizawa, K]]
	[[Category: Kawano, Y]]		[[Category: Kawano, Y]]
		+	[[Category: Kumasaka, T]]
	[[Category: Murakawa, T]]		[[Category: Murakawa, T]]
-	[[Category: Kumasaka, T]]
	[[Category: Okajima, T]]		[[Category: Okajima, T]]
		+	[[Category: Tanizawa, K]]
		+	[[Category: Yamamoto, M]]
		+	[[Category: Yano, T]]
		+	[[Category: Copper amine oxidase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Topaquinone]]
		+	[[Category: Tpq]]

OCA at 05:48, 23 May 2018

OCA — Wed, 23 May 2018 05:48:21 GMT

←Older revision		Revision as of 05:48, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zpa is ON HOLD	+	The entry 5zpa 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.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hayashi, H]]		[[Category: Hayashi, H]]
-	[[Category: Kawano, Y]]
	[[Category: Baba, S]]		[[Category: Baba, S]]
-	[[Category: Murakawa, T]]
-	[[Category: Kumasaka, T]]
	[[Category: Yamamoto, M]]		[[Category: Yamamoto, M]]
	[[Category: Yano, T]]		[[Category: Yano, T]]
-	[[Category: Okajima, T]]
	[[Category: Tanizawa, K]]		[[Category: Tanizawa, K]]
		+	[[Category: Kawano, Y]]
		+	[[Category: Murakawa, T]]
		+	[[Category: Kumasaka, T]]
		+	[[Category: Okajima, T]]

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

OCA — Wed, 25 Apr 2018 03:52:53 GMT

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

←Older revision

Revision as of 03:52, 25 April 2018

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

OCA — Wed, 25 Apr 2018 03:52:51 GMT

New page: '''Unreleased structure''' The entry 5zpa 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 5zpa 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 pH 6 at 283 K (2)
[[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]]