6k2l - Revision history

OCA at 10:40, 27 March 2024

OCA — Wed, 27 Mar 2024 10:40:56 GMT

←Older revision		Revision as of 10:40, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6k2l' size='340' side='right'caption='[[6k2l]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6k2l' size='340' side='right'caption='[[6k2l]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k2l]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"aeromonas_liquefaciens"_kluyver_and_van_niel_1936 "aeromonas liquefaciens" kluyver and van niel 1936~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K2L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K2L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k2l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeromonas_hydrophila Aeromonas hydrophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K2L FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</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]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>B7E00_09475, BWQ95_19695 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~644~~ "~~Aeromonas liquefaciens~~" ~~Kluyver and van Niel 1936])~~</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></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=6k2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k2l OCA], [~~http~~://pdbe.org/6k2l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k2l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k2l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k2l 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=6k2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k2l OCA], [https://pdbe.org/6k2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k2l RCSB], [https://www.ebi.ac.uk/pdbsum/6k2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k2l ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0KMJ5_AERHH A0KMJ5_AERHH]
-	Siderophores acquire iron from hosts under iron-limiting conditions and play an essential role in the survival of microorganisms. Siderophore-interacting proteins (SIPs) from microbes release iron from the siderophore complex by reducing ferric iron to ferrous iron, but the molecular mechanism of iron reduction remains unclear. To better understand the molecular mechanism of SIPs, we herein report the crystal structure of Aeromonas hydrophila SIP (AhSIP) in complex with flavin adenine dinucleotide (FAD) as a cofactor. AhSIP consists of an N-terminal FAD binding domain and a C-terminal NADH binding domain, which are connected by a linker region. AhSIP showed unique structural differences in the orientation of the cofactor binding lobes when compared with SIP homologs. This study identified a cluster of three basic residues (Lys48, His259 and Arg262) in AhSIP distributed around a potential substrate binding pocket. In addition, AhSIP, containing the NADH binding motif E(L)VL-X3-GE, belongs to the group I subfamily. Our results show the diverse cofactor and substrate binding sites of the SIP family.	+
-		+
-	Crystal structure of the Siderophore-interacting protein SIP from Aeromonas hydrophila.,Shang F, Lan J, Wang L, Liu W, Chen Y, Chen J, Ha NC, Quan C, Nam KH, Xu Y Biochem Biophys Res Commun. 2019 Oct 29;519(1):~~23-28. doi:, 10.1016~~/~~j.bbrc.2019.08.085. Epub 2019 Aug 30. PMID:31477273<ref>PMID:31477273<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6k2l" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aeromonas liquefaciens kluyver and van niel 1936]]
-	[[Category: Large Structures]]
-	[[Category: Lan, J]]
-	[[Category: Liu, W]]
-	[[Category: Shang, F]]
-	[[Category: Xu, Y]]
	[[Category: Aeromonas hydrophila]]		[[Category: Aeromonas hydrophila]]
-	[[Category: ~~Flavoprotein~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Siderophore-interacting protein~~]]	+	[[Category: Lan J]]
-	[[Category: ~~Sip~~]]	+	[[Category: Liu W]]
		+	[[Category: Shang F]]
		+	[[Category: Xu Y]]

OCA at 10:13, 18 March 2020

OCA — Wed, 18 Mar 2020 10:13:18 GMT

←Older revision		Revision as of 10:13, 18 March 2020
Line 3:		Line 3:
	<StructureSection load='6k2l' size='340' side='right'caption='[[6k2l]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6k2l' size='340' side='right'caption='[[6k2l]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k2l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K2L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K2L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k2l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aeromonas_liquefaciens"_kluyver_and_van_niel_1936 "aeromonas liquefaciens" kluyver and van niel 1936]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K2L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K2L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B7E00_09475, BWQ95_19695 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644 "Aeromonas liquefaciens" Kluyver and van Niel 1936])</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=6k2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k2l OCA], [http://pdbe.org/6k2l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k2l RCSB], [http://www.ebi.ac.uk/pdbsum/6k2l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k2l 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=6k2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k2l OCA], [http://pdbe.org/6k2l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k2l RCSB], [http://www.ebi.ac.uk/pdbsum/6k2l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k2l ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Siderophores acquire iron from hosts under iron-limiting conditions and play an essential role in the survival of microorganisms. Siderophore-interacting proteins (SIPs) from microbes release iron from the siderophore complex by reducing ferric iron to ferrous iron, but the molecular mechanism of iron reduction remains unclear. To better understand the molecular mechanism of SIPs, we herein report the crystal structure of Aeromonas hydrophila SIP (AhSIP) in complex with flavin adenine dinucleotide (FAD) as a cofactor. AhSIP consists of an N-terminal FAD binding domain and a C-terminal NADH binding domain, which are connected by a linker region. AhSIP showed unique structural differences in the orientation of the cofactor binding lobes when compared with SIP homologs. This study identified a cluster of three basic residues (Lys48, His259 and Arg262) in AhSIP distributed around a potential substrate binding pocket. In addition, AhSIP, containing the NADH binding motif E(L)VL-X3-GE, belongs to the group I subfamily. Our results show the diverse cofactor and substrate binding sites of the SIP family.
		+
		+	Crystal structure of the Siderophore-interacting protein SIP from Aeromonas hydrophila.,Shang F, Lan J, Wang L, Liu W, Chen Y, Chen J, Ha NC, Quan C, Nam KH, Xu Y Biochem Biophys Res Commun. 2019 Oct 29;519(1):23-28. doi:, 10.1016/j.bbrc.2019.08.085. Epub 2019 Aug 30. PMID:31477273<ref>PMID:31477273</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6k2l" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aeromonas liquefaciens kluyver and van niel 1936]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Lan, J]]		[[Category: Lan, J]]

OCA at 05:38, 12 June 2019

OCA — Wed, 12 Jun 2019 05:38:03 GMT

←Older revision		Revision as of 05:38, 12 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6k2l is ~~ON HOLD until Jun 11 2020~~	+	==Crystal structure of the Siderophore-interacting protein SipS from Aeromonas hydrophila==
-		+	<StructureSection load='6k2l' size='340' side='right'caption='[[6k2l]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors~~: ~~Shang~~, F., ~~Lan~~, J., ~~Liu, W~~., ~~Xu, Y~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6k2l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K2L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K2L FirstGlance]. <br>
-	~~Description: Crystal structure of the Siderophore-interacting protein SipS from Aeromonas hydrophila~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6k2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k2l OCA], [http://pdbe.org/6k2l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k2l RCSB], [http://www.ebi.ac.uk/pdbsum/6k2l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k2l ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lan, J]]
		+	[[Category: Liu, W]]
	[[Category: Shang, F]]		[[Category: Shang, F]]
-	[[Category: Liu, W]]
	[[Category: Xu, Y]]		[[Category: Xu, Y]]
-	[[Category: ~~Lan, J~~]]	+	[[Category: Aeromonas hydrophila]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Siderophore-interacting protein]]
		+	[[Category: Sip]]

OCA at 20:57, 5 June 2019

OCA — Wed, 05 Jun 2019 20:57:52 GMT

←Older revision		Revision as of 20:57, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k2l is ON HOLD	+	The entry 6k2l is ON HOLD until Jun 11 2020

	Authors: Shang, F., Lan, J., Liu, W., Xu, Y.		Authors: Shang, F., Lan, J., Liu, W., Xu, Y.
Line 7:		Line 7:
	Description: Crystal structure of the Siderophore-interacting protein SipS from Aeromonas hydrophila		Description: Crystal structure of the Siderophore-interacting protein SipS from Aeromonas hydrophila
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Lan, J]]
	[[Category: Shang, F]]		[[Category: Shang, F]]
	[[Category: Liu, W]]		[[Category: Liu, W]]
	[[Category: Xu, Y]]		[[Category: Xu, Y]]
		+	[[Category: Lan, J]]

OCA: Protected "6k2l" [edit=sysop:move=sysop]

OCA — Wed, 22 May 2019 03:56:02 GMT

Protected "6k2l" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:56, 22 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k2l is ON HOLD Authors: Shang, F., Lan, J., Liu, W., Xu, Y. Description: Crystal structure of the Siderophore-interacting protein SipS from Aeromo...

OCA — Wed, 22 May 2019 03:56:00 GMT

New page: '''Unreleased structure''' The entry 6k2l is ON HOLD Authors: Shang, F., Lan, J., Liu, W., Xu, Y. Description: Crystal structure of the Siderophore-interacting protein SipS from Aeromo...

New page

'''Unreleased structure'''

The entry 6k2l is ON HOLD

Authors: Shang, F., Lan, J., Liu, W., Xu, Y.

Description: Crystal structure of the Siderophore-interacting protein SipS from Aeromonas hydrophila
[[Category: Unreleased Structures]]
[[Category: Lan, J]]
[[Category: Shang, F]]
[[Category: Liu, W]]
[[Category: Xu, Y]]