4y1q - Revision history

OCA at 15:33, 8 November 2023

OCA — Wed, 08 Nov 2023 15:33:26 GMT

←Older revision		Revision as of 15:33, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4y1q]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_IP_32953 Yersinia pseudotuberculosis IP 32953]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y1Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[4y1q]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_IP_32953 Yersinia pseudotuberculosis IP 32953]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y1Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 3.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [https://pdbe.org/4y1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [https://www.ebi.ac.uk/pdbsum/4y1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1q 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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [https://pdbe.org/4y1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [https://www.ebi.ac.uk/pdbsum/4y1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1q ProSAT]</span></td></tr>
	</table>		</table>

OCA at 18:03, 26 April 2023

OCA — Wed, 26 Apr 2023 18:03:17 GMT

←Older revision		Revision as of 18:03, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4y1q' size='340' side='right'caption='[[4y1q]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='4y1q' size='340' side='right'caption='[[4y1q]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y1q]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Yerps Yerps~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Y1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y1q]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_IP_32953 Yersinia pseudotuberculosis IP 32953]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y1Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xzd\|4xzd]]</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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [https://pdbe.org/4y1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [https://www.ebi.ac.uk/pdbsum/4y1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1q ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HasA, YPTB0114 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273123 YERPS])~~</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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [~~http~~://pdbe.org/4y1q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4y1q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1q ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q66G68_YERPS Q66G68_YERPS]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Yerps~~]]	+	[[Category: Yersinia pseudotuberculosis IP 32953]]
-	[[Category: Hino, T]]	+	[[Category: Hino T]]
-	[[Category: Kanadani, M]]	+	[[Category: Kanadani M]]
-	[[Category: Nagano, S]]	+	[[Category: Nagano S]]
-	[[Category: Ozaki, S]]	+	[[Category: Ozaki S]]
-	[[Category: Sato, T]]	+	[[Category: Sato T]]
-	~~[[Category: Heme acquisition system]]~~	+
-	~~[[Category: Heme binding protein]]~~	+
-	~~[[Category: Hemophore~~]]	+

OCA at 00:14, 6 June 2019

OCA — Thu, 06 Jun 2019 00:14:36 GMT

←Older revision		Revision as of 00:14, 6 June 2019
Line 1:		Line 1:
		+
	==Crystal Structure of HasA mutant Y75A monomer from Yersinia pseudotuberculosis==		==Crystal Structure of HasA mutant Y75A monomer from Yersinia pseudotuberculosis==
-	<StructureSection load='4y1q' size='340' side='right' caption='[[4y1q]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='4y1q' size='340' side='right'caption='[[4y1q]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y1q]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y1q]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Yerps Yerps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y1Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xzd\|4xzd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xzd\|4xzd]]</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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [http://pdbe.org/4y1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [http://www.ebi.ac.uk/pdbsum/4y1q PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HasA, YPTB0114 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273123 YERPS])</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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [http://pdbe.org/4y1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [http://www.ebi.ac.uk/pdbsum/4y1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1q ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Yerps]]
	[[Category: Hino, T]]		[[Category: Hino, T]]
	[[Category: Kanadani, M]]		[[Category: Kanadani, M]]

OCA at 04:50, 7 January 2016

OCA — Thu, 07 Jan 2016 04:50:20 GMT

←Older revision		Revision as of 04:50, 7 January 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xzd\|4xzd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xzd\|4xzd]]</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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [http://www.ebi.ac.uk/pdbsum/4y1q PDBsum]</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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [http://pdbe.org/4y1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [http://www.ebi.ac.uk/pdbsum/4y1q PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4y1q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:33, 12 August 2015

OCA — Wed, 12 Aug 2015 14:33:18 GMT

←Older revision		Revision as of 14:33, 12 August 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal Structure of HasA mutant Y75A monomer from Yersinia pseudotuberculosis==
		+	<StructureSection load='4y1q' size='340' side='right' caption='[[4y1q]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4y1q]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y1Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xzd\|4xzd]]</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=4y1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y1q RCSB], [http://www.ebi.ac.uk/pdbsum/4y1q PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Some Gram-negative pathogens utilize an extracellular heme-binding protein called hemophore to satisfy their needs for iron, a metal element essential for most living things. We report here crystal structures of heme acquisition system A from Yersinia pseudotuberculosis (HasAypt) and its Y75A mutant. The wild-type HasAypt structure revealed that the heme iron is coordinated with Tyr75 and a water molecule. The heme-bound water molecule makes extensive hydrogen bond network that includes Arg40 and Arg144 on the distal heme pocket. Arg40, highly conserved for HasAs from Yersinia species, forms a salt bridge with the propionate side chain of heme, and makes pi-pi stacking and hydrophobic interactions with porphyrin plane. Interestingly, similar Arg-heme interactions are also found for periplasmic heme transporter, PhuT, suggesting that this is an example of a convergent evolution and one of the important interactions for bacterial heme transportation. Heme titration, heme binding kinetics, and the crystal structures of wild-type and Y75A proteins show that, although Tyr75 is primarily important for heme capturing, other interactions with Arg40, Arg144, and hydrophobic residues also contribute for heme acquisition. We also found that HasAypt can form a dimer in solution. The structure of the domain-swapped Y75A HasAypt dimer shows the presence of two low-spin heme molecules coordinated with His84 and His140, and displacement of the Arg40 loop of dimeric Y75A HasAypt results in deformation of the heme-binding pocket. A similar rearrangement of the distal heme loop might occur in heme transfer from HasAypt to HasRypt.

-	The ~~entry 4y1q is ON HOLD until Paper Publication~~	+	The crystal structure of heme acquisition system A from Yersinia pseudotuberculosis (HasA): Roles of the axial ligand Tyr75 and two distal arginines in heme binding.,Kanadani M, Sato T, Hino T, Nagano S, Ozaki SI J Inorg Biochem. 2015 Jul 18. pii: S0162-0134(15)30034-9. doi:, 10.1016/j.jinorgbio.2015.07.007. PMID:26210321<ref>PMID:26210321</ref>

-	~~Authors: Nagano~~, S.~~, Hino, T., Kanadani, M., Ozaki,~~ S.~~, Sato, T~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal Structure of HasA mutant Y75A monomer from Yersinia pseudotuberculosis~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Hino, T]]		[[Category: Hino, T]]
		+	[[Category: Kanadani, M]]
		+	[[Category: Nagano, S]]
	[[Category: Ozaki, S]]		[[Category: Ozaki, S]]
	[[Category: Sato, T]]		[[Category: Sato, T]]
-	[[Category: ~~Nagano, S~~]]	+	[[Category: Heme acquisition system]]
-	[[Category: ~~Kanadani, M~~]]	+	[[Category: Heme binding protein]]
		+	[[Category: Hemophore]]

OCA at 12:35, 25 February 2015

OCA — Wed, 25 Feb 2015 12:35:39 GMT

←Older revision		Revision as of 12:35, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y1q is ON HOLD	+	The entry 4y1q is ON HOLD until Paper Publication

-	Authors: ~~Shingo~~ Nagano, ~~Tomoya~~ Hino, ~~Masahiro~~ Kanadani, ~~Shin-ichi~~ Ozaki, ~~Takehiro~~ Sato	+	Authors: Nagano, S., Hino, T., Kanadani, M., Ozaki, S., Sato, T.

	Description: Crystal Structure of HasA mutant Y75A monomer from Yersinia pseudotuberculosis		Description: Crystal Structure of HasA mutant Y75A monomer from Yersinia pseudotuberculosis
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Shingo Nagano, Tomoya~~ Hino, ~~Masahiro Kanadani, Shin-Ichi~~ Ozaki, ~~Takehiro~~ Sato]]	+	[[Category: Hino, T]]
		+	[[Category: Ozaki, S]]
		+	[[Category: Sato, T]]
		+	[[Category: Nagano, S]]
		+	[[Category: Kanadani, M]]

OCA: Protected "4y1q" [edit=sysop:move=sysop]

OCA — Wed, 18 Feb 2015 11:54:44 GMT

Protected "4y1q" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:54, 18 February 2015

OCA: New page: '''Unreleased structure''' The entry 4y1q is ON HOLD Authors: Shingo Nagano, Tomoya Hino, Masahiro Kanadani, Shin-ichi Ozaki, Takehiro Sato Description: Crystal Structure of HasA mutan...

OCA — Wed, 18 Feb 2015 11:54:43 GMT

New page: '''Unreleased structure''' The entry 4y1q is ON HOLD Authors: Shingo Nagano, Tomoya Hino, Masahiro Kanadani, Shin-ichi Ozaki, Takehiro Sato Description: Crystal Structure of HasA mutan...

New page

'''Unreleased structure'''

The entry 4y1q is ON HOLD

Authors: Shingo Nagano, Tomoya Hino, Masahiro Kanadani, Shin-ichi Ozaki, Takehiro Sato

Description: Crystal Structure of HasA mutant Y75A monomer from Yersinia pseudotuberculosis
[[Category: Unreleased Structures]]
[[Category: Shingo Nagano, Tomoya Hino, Masahiro Kanadani, Shin-Ichi Ozaki, Takehiro Sato]]