6r2h - Revision history

OCA at 11:51, 1 February 2024

2024-02-01T11:51:33Z

←Older revision		Revision as of 11:51, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6r2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Prevotella_intermedia Prevotella intermedia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R2H FirstGlance]. <br>		<table><tr><td colspan='2'>[[6r2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Prevotella_intermedia Prevotella intermedia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R2H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.46Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6r2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r2h OCA], [https://pdbe.org/6r2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r2h RCSB], [https://www.ebi.ac.uk/pdbsum/6r2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r2h 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=6r2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r2h OCA], [https://pdbe.org/6r2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r2h RCSB], [https://www.ebi.ac.uk/pdbsum/6r2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r2h ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:03, 21 December 2022

2022-12-21T10:03:03Z

←Older revision		Revision as of 10:03, 21 December 2022
Line 3:		Line 3:
	<StructureSection load='6r2h' size='340' side='right'caption='[[6r2h]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='6r2h' size='340' side='right'caption='[[6r2h]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r2h]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_25611 Atcc 25611~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R2H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R2H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Prevotella_intermedia Prevotella intermedia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R2H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BWX40_10235 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28131 ATCC 25611])~~</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=6r2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r2h OCA], [https://pdbe.org/6r2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r2h RCSB], [https://www.ebi.ac.uk/pdbsum/6r2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r2h 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=6r2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r2h OCA], [~~http~~://pdbe.org/6r2h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r2h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r2h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r2h ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1P8JNE7_PREIN A0A1P8JNE7_PREIN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25611]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Antonyuk, S V]]
-	[[Category: Bielecki, M]]
-	[[Category: Capper, M]]
-	[[Category: Olczak, M]]
-	[[Category: Olczak, T]]
-	[[Category: Strange, R W]]
-	[[Category: Heme]]
-	[[Category: Heme-binding protein]]
-	[[Category: Hemophore]]
-	[[Category: Hmuy]]
-	[[Category: Metal binding protein]]
-	[[Category: Phylogeny]]
-	[[Category: Porphyromonas gingivali]]
	[[Category: Prevotella intermedia]]		[[Category: Prevotella intermedia]]
-	[[Category: ~~Sequence evolution~~]]	+	[[Category: Antonyuk SV]]
		+	[[Category: Bielecki M]]
		+	[[Category: Capper M]]
		+	[[Category: Olczak M]]
		+	[[Category: Olczak T]]
		+	[[Category: Strange RW]]

OCA at 04:43, 13 February 2020

2020-02-13T04:43:30Z

←Older revision		Revision as of 04:43, 13 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6r2h is ~~ON HOLD~~	+	==Crystal structure of Apo PinO from Porphyromonas gingivitis==
		+	<StructureSection load='6r2h' size='340' side='right'caption='[[6r2h]], [[Resolution\|resolution]] 2.46Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r2h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25611 Atcc 25611]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R2H FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BWX40_10235 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28131 ATCC 25611])</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=6r2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r2h OCA], [http://pdbe.org/6r2h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r2h RCSB], [http://www.ebi.ac.uk/pdbsum/6r2h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r2h ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	As part of the infective process, Porphyromonas gingivalis must acquire heme which is indispensable for life and enables the microorganism to survive and multiply at the infection site. This oral pathogenic bacterium uses a newly discovered novel hmu heme uptake system with a leading role played by the HmuY hemophore-like protein, responsible for acquiring heme and increasing virulence of this periodontopathogen. We demonstrated that Prevotella intermedia produces two HmuY homologs, termed PinO and PinA. Both proteins were produced at higher mRNA and protein levels when the bacterium grew under low-iron/heme conditions. PinO and PinA bound heme, but preferentially under reducing conditions, and in a manner different from that of the P. gingivalis HmuY. The analysis of the three-dimensional structures confirmed differences between apo-PinO and apo-HmuY, mainly in the fold forming the heme-binding pocket. Instead of two histidine residues coordinating heme iron in P. gingivalis HmuY, PinO and PinA could use one methionine residue to fulfill this function, with potential support of additional methionine residue/s. The P. intermedia proteins sequestered heme only from the host albumin-heme complex under reducing conditions. Our findings suggest that HmuY-like family might comprise proteins subjected during evolution to significant diversification, resulting in different heme coordination modes. The newer data presented in this manuscript on HmuY homologs produced by P. intermedia sheds more light on the novel mechanism of heme uptake, could be helpful in discovering their biological function, and in developing novel therapeutic approaches.

-	~~Authors: Antonyuk, S.V~~., Bielecki, M., Strange, ~~R.W.~~, ~~Capper~~, M., ~~Olczak~~, T., ~~Olczak~~, M.	+	Prevotella intermedia produces two proteins homologous to Porphyromonas gingivalis HmuY but with different heme coordination mode.,Bielecki M, Antonyuk S, Strange RW, Sieminska K, Smalley JW, Mackiewicz P, Smiga M, Cowan M, Capper MJ, Slezak P, Olczak M, Olczak T Biochem J. 2020 Jan 31;477(2):381-405. doi: 10.1042/BCJ20190607. PMID:31899475<ref>PMID:31899475</ref>

-	~~Description: Crystal structure~~ of ~~Apo PinO from Porphyromonas gingivitis~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Olczak, T~~]]	+	<div class="pdbe-citations 6r2h" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Olczak~~, M]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 25611]]
		+	[[Category: Large Structures]]
		+	[[Category: Antonyuk, S V]]
	[[Category: Bielecki, M]]		[[Category: Bielecki, M]]
-	[[Category: Antonyuk, S.V]]
	[[Category: Capper, M]]		[[Category: Capper, M]]
-	[[Category: Strange, R.W]]	+	[[Category: Olczak, M]]
		+	[[Category: Olczak, T]]
		+	[[Category: Strange, R W]]
		+	[[Category: Heme]]
		+	[[Category: Heme-binding protein]]
		+	[[Category: Hemophore]]
		+	[[Category: Hmuy]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Phylogeny]]
		+	[[Category: Porphyromonas gingivali]]
		+	[[Category: Prevotella intermedia]]
		+	[[Category: Sequence evolution]]

OCA: Protected "6r2h" [edit=sysop:move=sysop]

2019-03-27T05:12:56Z

Protected "6r2h" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:12, 27 March 2019

OCA: New page: '''Unreleased structure''' The entry 6r2h is ON HOLD Authors: Antonyuk, S.V., Bielecki, M., Strange, R.W., Capper, M., Olczak, T., Olczak, M. Description: Crystal structure of Apo PinO...

2019-03-27T05:12:55Z

New page: '''Unreleased structure''' The entry 6r2h is ON HOLD Authors: Antonyuk, S.V., Bielecki, M., Strange, R.W., Capper, M., Olczak, T., Olczak, M. Description: Crystal structure of Apo PinO...

New page

'''Unreleased structure'''

The entry 6r2h is ON HOLD

Authors: Antonyuk, S.V., Bielecki, M., Strange, R.W., Capper, M., Olczak, T., Olczak, M.

Description: Crystal structure of Apo PinO from Porphyromonas gingivitis
[[Category: Unreleased Structures]]
[[Category: Olczak, T]]
[[Category: Olczak, M]]
[[Category: Bielecki, M]]
[[Category: Antonyuk, S.V]]
[[Category: Capper, M]]
[[Category: Strange, R.W]]