5ds7 - Revision history

OCA at 12:26, 6 March 2024

2024-03-06T12:26:02Z

←Older revision		Revision as of 12:26, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/D5X329_THIK1 D5X329_THIK1]		[https://www.uniprot.org/uniprot/D5X329_THIK1 D5X329_THIK1]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e., bicarbonate and CO2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and CO2, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around alpha-type carboxysome operons, we characterize a protein that is conserved across these operons but has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.
-
-	A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein.,Wheatley NM, Eden KD, Ngo J, Rosinski JS, Sawaya MR, Cascio D, Collazo M, Hoveida H, Hubbell WL, Yeates TO J Mol Biol. 2016 Oct 9;428(20):4013-4030. doi: 10.1016/j.jmb.2016.07.015. Epub, 2016 Jul 25. PMID:27464895<ref>PMID:27464895</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5ds7" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:57, 28 June 2023

2023-06-28T21:57:24Z

←Older revision		Revision as of 21:57, 28 June 2023
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	<StructureSection load='5ds7' size='340' side='right'caption='[[5ds7]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5ds7' size='340' side='right'caption='[[5ds7]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ds7]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thik1 Thik1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DS7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ds7]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thiomonas_intermedia_K12 Thiomonas intermedia K12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DS7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene~~>, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5drk\|5drk]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Tint_0114 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=75379 THIK1])~~</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=5ds7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds7 OCA], [https://pdbe.org/5ds7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ds7 RCSB], [https://www.ebi.ac.uk/pdbsum/5ds7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds7 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=5ds7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds7 OCA], [~~http~~://pdbe.org/5ds7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ds7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ds7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds7 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D5X329_THIK1 D5X329_THIK1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thik1~~]]	+	[[Category: Thiomonas intermedia K12]]
-	[[Category: Cascio, D]]	+	[[Category: Cascio D]]
-	[[Category: Ngo, J]]	+	[[Category: Ngo J]]
-	[[Category: Sawaya~~, M R~~]]	+	[[Category: Sawaya MR]]
-	[[Category: Wheatley~~, N M~~]]	+	[[Category: Wheatley NM]]
-	[[Category: Yeates~~, T O]]~~	+	[[Category: Yeates TO]]
-	~~[[Category: Acetate binding]]~~	+
-	~~[[Category: Adp hydrolysis]]~~	+
-	~~[[Category: Bicarbonate]]~~	+
-	~~[[Category: Carbon regulatory pii protein]]~~	+
-	~~[[Category: Cpii]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Nitrogen regulatory pii protein]]~~	+
-	~~[[Category: Nucleotide binding~~]]	+

OCA at 07:34, 23 October 2019

2019-10-23T07:34:09Z

←Older revision		Revision as of 07:34, 23 October 2019
Line 1:		Line 1:

	==2.0 A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound AMP==		==2.0 A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound AMP==
-	<StructureSection load='5ds7' size='340' side='right' caption='[[5ds7]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5ds7' size='340' side='right'caption='[[5ds7]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ds7]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ds7]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thik1 Thik1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5drk\|5drk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5drk\|5drk]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tint_0114 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=75379 THIK1])</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=5ds7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds7 OCA], [http://pdbe.org/5ds7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds7 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds7 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=5ds7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds7 OCA], [http://pdbe.org/5ds7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds7 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds7 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e., bicarbonate and CO2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and CO2, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around alpha-type carboxysome operons, we characterize a protein that is conserved across these operons but has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.
		+
		+	A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein.,Wheatley NM, Eden KD, Ngo J, Rosinski JS, Sawaya MR, Cascio D, Collazo M, Hoveida H, Hubbell WL, Yeates TO J Mol Biol. 2016 Oct 9;428(20):4013-4030. doi: 10.1016/j.jmb.2016.07.015. Epub, 2016 Jul 25. PMID:27464895<ref>PMID:27464895</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ds7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Thik1]]
	[[Category: Cascio, D]]		[[Category: Cascio, D]]
	[[Category: Ngo, J]]		[[Category: Ngo, J]]

OCA at 17:05, 3 October 2016

2016-10-03T17:05:19Z

←Older revision		Revision as of 17:05, 3 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5ds7 is ON HOLD until Paper Publication~~	+	==2.0 A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound AMP==
-		+	<StructureSection load='5ds7' size='340' side='right' caption='[[5ds7]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors: Wheatley, N.M., Ngo, J., Cascio, D., Sawaya, M.R., Yeates, T.O.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ds7]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS7 FirstGlance]. <br>
-	~~Description:~~ 2.0 A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound AMP	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5drk\|5drk]]</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=5ds7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds7 OCA], [http://pdbe.org/5ds7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds7 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds7 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cascio, D]]
	[[Category: Ngo, J]]		[[Category: Ngo, J]]
-	[[Category: Sawaya, M.R]]	+	[[Category: Sawaya, M R]]
-	[[Category: Yeates, T.O]]	+	[[Category: Wheatley, N M]]
-	[[Category: ~~Cascio, D~~]]	+	[[Category: Yeates, T O]]
-	[[Category: ~~Wheatley, N.M~~]]	+	[[Category: Acetate binding]]
		+	[[Category: Adp hydrolysis]]
		+	[[Category: Bicarbonate]]
		+	[[Category: Carbon regulatory pii protein]]
		+	[[Category: Cpii]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Nitrogen regulatory pii protein]]
		+	[[Category: Nucleotide binding]]

OCA at 04:02, 22 October 2015

2015-10-22T04:02:22Z

←Older revision		Revision as of 04:02, 22 October 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ds7 is ON HOLD	+	The entry 5ds7 is ON HOLD until Paper Publication

	Authors: Wheatley, N.M., Ngo, J., Cascio, D., Sawaya, M.R., Yeates, T.O.		Authors: Wheatley, N.M., Ngo, J., Cascio, D., Sawaya, M.R., Yeates, T.O.

OCA: Protected "5ds7" [edit=sysop:move=sysop]

2015-09-30T13:27:09Z

Protected "5ds7" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:27, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5ds7 is ON HOLD Authors: Wheatley, N.M., Ngo, J., Cascio, D., Sawaya, M.R., Yeates, T.O. Description: 2.0 A Structure of CPII, a nitrogen regulator...

2015-09-30T13:27:08Z

New page: '''Unreleased structure''' The entry 5ds7 is ON HOLD Authors: Wheatley, N.M., Ngo, J., Cascio, D., Sawaya, M.R., Yeates, T.O. Description: 2.0 A Structure of CPII, a nitrogen regulator...

New page

'''Unreleased structure'''

The entry 5ds7 is ON HOLD

Authors: Wheatley, N.M., Ngo, J., Cascio, D., Sawaya, M.R., Yeates, T.O.

Description: 2.0 A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound AMP
[[Category: Unreleased Structures]]
[[Category: Ngo, J]]
[[Category: Sawaya, M.R]]
[[Category: Yeates, T.O]]
[[Category: Cascio, D]]
[[Category: Wheatley, N.M]]