7d9g - Revision history

OCA at 16:28, 29 November 2023

2023-11-29T16:28:59Z

←Older revision		Revision as of 16:28, 29 November 2023
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	<StructureSection load='7d9g' size='340' side='right'caption='[[7d9g]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='7d9g' size='340' side='right'caption='[[7d9g]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7d9g]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D9G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7d9g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D9G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<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]] 2.4Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Spermidine_dehydrogenase Spermidine dehydrogenase]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.6 1.5.99.6]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=7d9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d9g OCA], [https://pdbe.org/7d9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d9g RCSB], [https://www.ebi.ac.uk/pdbsum/7d9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d9g 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=7d9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d9g OCA], [https://pdbe.org/7d9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d9g RCSB], [https://www.ebi.ac.uk/pdbsum/7d9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d9g ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9HXS8_PSEAE Q9HXS8_PSEAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Spermidine dehydrogenase~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Bartlam, M]]	+	[[Category: Bartlam M]]
-	[[Category: Che, S]]	+	[[Category: Che S]]
-	[[Category: Zhang, Q]]	+	[[Category: Zhang Q]]
-	~~[[Category: Heme-containing monoamine oxidase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pseudomonas aeruginosa pao1]]~~	+
-	~~[[Category: Spdh~~]]	+

OCA at 03:03, 21 April 2022

2022-04-21T03:03:44Z

←Older revision		Revision as of 03:03, 21 April 2022
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	==SpdH Spermidine dehydrogenase native structure==		==SpdH Spermidine dehydrogenase native structure==
-	<StructureSection load='7d9g' size='340' side='right'caption='[[7d9g]]' scene=''>	+	<StructureSection load='7d9g' size='340' side='right'caption='[[7d9g]], [[Resolution\|resolution]] 2.40Å' 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=7D9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D9G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7d9g]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D9G 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=7d9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d9g OCA], [https://pdbe.org/7d9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d9g RCSB], [https://www.ebi.ac.uk/pdbsum/7d9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d9g 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Spermidine_dehydrogenase Spermidine dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.6 1.5.99.6] </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=7d9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d9g OCA], [https://pdbe.org/7d9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d9g RCSB], [https://www.ebi.ac.uk/pdbsum/7d9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d9g ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The opportunistic pathogen Pseudomonas aeruginosa can utilize polyamines (including putrescine, cadaverine, 4-aminobutyrate, spermidine, and spermine) as its sole source of carbon and nitrogen. Spermidine dehydrogenase (SpdH) is a component of one of the two polyamine utilization pathways identified in P. aeruginosa, but little is known about its structure and function. Here, we report the first crystal structure of SpdH from P. aeruginosa to 1.85 A resolution. The resulting core structure confirms that SpdH belongs to the polyamine oxidase (PAO) family with flavin-binding and substrate-binding domains. A unique N-terminal extension wraps around the flavin-binding domain of SpdH and is required for heme binding, placing a heme cofactor in close proximity to the FAD cofactor. Structural and mutational analysis reveals that residues in the putative active site at the re side of the FAD isoalloxazine ring form part of the catalytic machinery. PaSpdH features an unusual active site and lacks the conserved lysine that forms part of a lysine-water-flavin N5 atom interaction in other PAO enzymes characterized to date. Mutational analysis further confirms that heme is required for catalytic activity. This work provides an important starting point for understanding the role of SpdH, which occurs universally in P. aeruginosa strains, in polyamine metabolism.
		+
		+	Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold.,Che S, Liang Y, Chen Y, Wu W, Liu R, Zhang Q, Bartlam M FEBS J. 2021 Nov 6. doi: 10.1111/febs.16264. PMID:34741591<ref>PMID:34741591</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7d9g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bartlam M]]	+	[[Category: Spermidine dehydrogenase]]
-	[[Category: Che S]]	+	[[Category: Bartlam, M]]
-	[[Category: Zhang Q]]	+	[[Category: Che, S]]
		+	[[Category: Zhang, Q]]
		+	[[Category: Heme-containing monoamine oxidase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pseudomonas aeruginosa pao1]]
		+	[[Category: Spdh]]

OCA at 13:34, 17 November 2021

2021-11-17T13:34:57Z

←Older revision		Revision as of 13:34, 17 November 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7d9g ~~is ON HOLD until Nov 13 2022~~	+	==SpdH Spermidine dehydrogenase native structure==
-		+	<StructureSection load='7d9g' size='340' side='right'caption='[[7d9g]]' scene=''>
-	~~Authors~~: ~~Che~~, S., ~~Zhang~~, Q., ~~Bartlam~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D9G FirstGlance]. <br>
-	~~Description: SpdH Spermidine dehydrogenase native structure~~	+	</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=7d9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d9g OCA], [https://pdbe.org/7d9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d9g RCSB], [https://www.ebi.ac.uk/pdbsum/7d9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d9g ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Che, S~~]]	+	__TOC__
-	[[Category: ~~Bartlam, M~~]]	+	</StructureSection>
-	[[Category: Zhang, Q]]	+	[[Category: Large Structures]]
		+	[[Category: Bartlam M]]
		+	[[Category: Che S]]
		+	[[Category: Zhang Q]]

OCA at 05:23, 22 September 2021

2021-09-22T05:23:41Z

←Older revision		Revision as of 05:23, 22 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7d9g is ON HOLD	+	The entry 7d9g is ON HOLD until Nov 13 2022

	Authors: Che, S., Zhang, Q., Bartlam, M.		Authors: Che, S., Zhang, Q., Bartlam, M.

OCA at 04:56, 11 August 2021

2021-08-11T04:56:02Z

←Older revision		Revision as of 04:56, 11 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7d9g is ON HOLD ~~until Paper Publication~~	+	The entry 7d9g is ON HOLD

	Authors: Che, S., Zhang, Q., Bartlam, M.		Authors: Che, S., Zhang, Q., Bartlam, M.
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	Description: SpdH Spermidine dehydrogenase native structure		Description: SpdH Spermidine dehydrogenase native structure
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Bartlam, M]]
	[[Category: Che, S]]		[[Category: Che, S]]
		+	[[Category: Bartlam, M]]
	[[Category: Zhang, Q]]		[[Category: Zhang, Q]]

OCA at 07:59, 18 November 2020

2020-11-18T07:59:54Z

←Older revision		Revision as of 07:59, 18 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7d9g is ON HOLD until ~~Dec 08 2021~~	+	The entry 7d9g is ON HOLD until Paper Publication

	Authors: Che, S., Zhang, Q., Bartlam, M.		Authors: Che, S., Zhang, Q., Bartlam, M.

OCA at 05:27, 4 November 2020

2020-11-04T05:27:49Z

←Older revision		Revision as of 05:27, 4 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7d9g is ON HOLD	+	The entry 7d9g is ON HOLD until Dec 08 2021

	Authors: Che, S., Zhang, Q., Bartlam, M.		Authors: Che, S., Zhang, Q., Bartlam, M.

OCA: Protected "7d9g" [edit=sysop:move=sysop]

2020-10-21T06:45:37Z

Protected "7d9g" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:45, 21 October 2020

OCA: New page: '''Unreleased structure''' The entry 7d9g is ON HOLD Authors: Che, S., Zhang, Q., Bartlam, M. Description: SpdH Spermidine dehydrogenase native structure [[Category: Unreleased Structu...

2020-10-21T06:45:36Z

New page: '''Unreleased structure''' The entry 7d9g is ON HOLD Authors: Che, S., Zhang, Q., Bartlam, M. Description: SpdH Spermidine dehydrogenase native structure [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 7d9g is ON HOLD

Authors: Che, S., Zhang, Q., Bartlam, M.

Description: SpdH Spermidine dehydrogenase native structure
[[Category: Unreleased Structures]]
[[Category: Bartlam, M]]
[[Category: Che, S]]
[[Category: Zhang, Q]]