5o5c - Revision history

OCA at 19:08, 29 November 2023

OCA — Wed, 29 Nov 2023 19:08:40 GMT

←Older revision		Revision as of 19:08, 29 November 2023
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	==The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora==		==The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora==
-	<StructureSection load='5o5c' size='340' side='right' caption='[[5o5c]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5o5c' size='340' side='right'caption='[[5o5c]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o5c]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Erwac Erwac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O5C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o5c]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Erwinia_amylovora_CFBP1430 Erwinia amylovora CFBP1430]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O5C FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=PLP:PYRIDOXAL~~-~~5-PHOSPHATE'>PLP</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]] 2.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~dfoJ, EAMY_3238 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=665029 ERWAC])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></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=5o5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5c OCA], [~~http~~://pdbe.org/5o5c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o5c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o5c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5c 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=5o5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5c OCA], [https://pdbe.org/5o5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o5c RCSB], [https://www.ebi.ac.uk/pdbsum/5o5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5c ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D4I245_ERWAC D4I245_ERWAC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Erwac~~]]	+	[[Category: Erwinia amylovora CFBP1430]]
-	[[Category: Bartho~~, J D~~]]	+	[[Category: Large Structures]]
-	[[Category: Bellini, D]]	+	[[Category: Bartho JD]]
-	[[Category: Benini, S]]	+	[[Category: Bellini D]]
-	[[Category: Demitri, N]]	+	[[Category: Benini S]]
-	[[Category: Polsinelli, I]]	+	[[Category: Demitri N]]
-	[[Category: Salomone-Stagni, M]]	+	[[Category: Polsinelli I]]
-	[[Category: Walsh~~, M A]]~~	+	[[Category: Salomone-Stagni M]]
-	~~[[Category: Aspartate aminotransferase family type 1 fold subclass ii]]~~	+	[[Category: Walsh MA]]
-	~~[[Category: E c. 4 1.1 18]]~~	+
-	~~[[Category: Group ii plp-dependent enzyme]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Siderophore biosynthesis~~]]	+

OCA at 07:37, 23 May 2018

OCA — Wed, 23 May 2018 07:37:21 GMT

←Older revision		Revision as of 07:37, 23 May 2018
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	<StructureSection load='5o5c' size='340' side='right' caption='[[5o5c]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5o5c' size='340' side='right' caption='[[5o5c]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o5c]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o5c]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Erwac Erwac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5C FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dfoJ, EAMY_3238 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=665029 ERWAC])</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=5o5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5c OCA], [http://pdbe.org/5o5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5c RCSB], [http://www.ebi.ac.uk/pdbsum/5o5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5c 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=5o5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5c OCA], [http://pdbe.org/5o5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5c RCSB], [http://www.ebi.ac.uk/pdbsum/5o5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5c ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Erwac]]
	[[Category: Bartho, J D]]		[[Category: Bartho, J D]]
	[[Category: Bellini, D]]		[[Category: Bellini, D]]

OCA at 06:19, 28 February 2018

OCA — Wed, 28 Feb 2018 06:19:20 GMT

←Older revision		Revision as of 06:19, 28 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5o5c is ~~ON HOLD~~	+	==The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora==
		+	<StructureSection load='5o5c' size='340' side='right' caption='[[5o5c]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5o5c]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5C FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></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=5o5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5c OCA], [http://pdbe.org/5o5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5c RCSB], [http://www.ebi.ac.uk/pdbsum/5o5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5c ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Gram-negative bacterium Erwinia amylovora is the etiological agent of fire blight, a devastating disease which affects Rosaceae such as apple, pear and quince. The siderophore desferrioxamine E plays an important role in bacterial pathogenesis by scavenging iron from the host. DfoJ, DfoA and DfoC are the enzymes responsible for desferrioxamine production starting from lysine. We have determined the crystal structures of each enzyme in the desferrioxamine E pathway and demonstrate that the biosynthesis involves the concerted action of DfoJ, followed by DfoA and lastly DfoC. These data provide the first crystal structures of a Group II pyridoxal-dependent lysine decarboxylase, a cadaverine monooxygenase and a desferrioxamine synthetase. DfoJ is a homodimer made up of three domains. Each monomer contributes to the completion of the active site, which is positioned at the dimer interface. DfoA is the first structure of a cadaverine monooxygenase. It forms homotetramers whose subunits are built by two domains: one for FAD and one for NADP(+) binding, the latter of which is formed by two subdomains. We propose a model for substrate binding and the role of residues 43-47 as gate keepers for FAD binding and the role of Arg97 in cofactors turnover. DfoC is the first structure of a desferrioxamine synthetase and the first of a multi-enzyme siderophore synthetase coupling an acyltransferase domain with a Non-Ribosomal Peptide Synthetase (NRPS)-Independent Siderophore domain (NIS).

-	~~Authors:~~ Salomone-Stagni, M., Bartho~~, J.D.~~, Polsinelli, I., Bellini, D., Walsh~~, M.A.~~, Demitri, N., Benini, S.	+	A complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora.,Salomone-Stagni M, Bartho JD, Polsinelli I, Bellini D, Walsh MA, Demitri N, Benini S J Struct Biol. 2018 Feb 8. pii: S1047-8477(18)30029-7. doi:, 10.1016/j.jsb.2018.02.002. PMID:29428557<ref>PMID:29428557</ref>

-	~~Description: The crystal structure of DfoJ~~, the ~~desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5o5c" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bartho, J D]]
	[[Category: Bellini, D]]		[[Category: Bellini, D]]
-	[[Category: Walsh, M.A]]
-	[[Category: Demitri, N]]
-	[[Category: Salomone-Stagni, M]]
	[[Category: Benini, S]]		[[Category: Benini, S]]
		+	[[Category: Demitri, N]]
	[[Category: Polsinelli, I]]		[[Category: Polsinelli, I]]
-	[[Category: ~~Bartho~~, J.D]]	+	[[Category: Salomone-Stagni, M]]
		+	[[Category: Walsh, M A]]
		+	[[Category: Aspartate aminotransferase family type 1 fold subclass ii]]
		+	[[Category: E c. 4 1.1 18]]
		+	[[Category: Group ii plp-dependent enzyme]]
		+	[[Category: Lyase]]
		+	[[Category: Siderophore biosynthesis]]

OCA at 05:52, 6 December 2017

OCA — Wed, 06 Dec 2017 05:52:47 GMT

←Older revision		Revision as of 05:52, 6 December 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5o5c is ON HOLD ~~until Paper Publication~~	+	The entry 5o5c is ON HOLD

	Authors: Salomone-Stagni, M., Bartho, J.D., Polsinelli, I., Bellini, D., Walsh, M.A., Demitri, N., Benini, S.		Authors: Salomone-Stagni, M., Bartho, J.D., Polsinelli, I., Bellini, D., Walsh, M.A., Demitri, N., Benini, S.
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	Description: The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora		Description: The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Polsinelli~~, I]]	+	[[Category: Bellini, D]]
	[[Category: Walsh, M.A]]		[[Category: Walsh, M.A]]
	[[Category: Demitri, N]]		[[Category: Demitri, N]]
-	[[Category: Benini, S]]
-	[[Category: Bellini, D]]
	[[Category: Salomone-Stagni, M]]		[[Category: Salomone-Stagni, M]]
		+	[[Category: Benini, S]]
		+	[[Category: Polsinelli, I]]
	[[Category: Bartho, J.D]]		[[Category: Bartho, J.D]]

OCA: Protected "5o5c" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:03:19 GMT

Protected "5o5c" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:03, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5o5c is ON HOLD until Paper Publication Authors: Salomone-Stagni, M., Bartho, J.D., Polsinelli, I., Bellini, D., Walsh, M.A., Demitri, N., Benini, S...

OCA — Wed, 27 Sep 2017 12:03:18 GMT

New page: '''Unreleased structure''' The entry 5o5c is ON HOLD until Paper Publication Authors: Salomone-Stagni, M., Bartho, J.D., Polsinelli, I., Bellini, D., Walsh, M.A., Demitri, N., Benini, S...

New page

'''Unreleased structure'''

The entry 5o5c is ON HOLD until Paper Publication

Authors: Salomone-Stagni, M., Bartho, J.D., Polsinelli, I., Bellini, D., Walsh, M.A., Demitri, N., Benini, S.

Description: The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora
[[Category: Unreleased Structures]]
[[Category: Polsinelli, I]]
[[Category: Walsh, M.A]]
[[Category: Demitri, N]]
[[Category: Benini, S]]
[[Category: Bellini, D]]
[[Category: Salomone-Stagni, M]]
[[Category: Bartho, J.D]]