4iuk - Revision history

OCA at 11:59, 1 March 2024

2024-03-01T11:59:56Z

←Older revision		Revision as of 11:59, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4iuk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_carnosus_subsp._carnosus_TM300 Staphylococcus carnosus subsp. carnosus TM300]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IUK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4iuk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_carnosus_subsp._carnosus_TM300 Staphylococcus carnosus subsp. carnosus TM300]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IUK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 2.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=4iuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iuk OCA], [https://pdbe.org/4iuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iuk RCSB], [https://www.ebi.ac.uk/pdbsum/4iuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iuk 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=4iuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iuk OCA], [https://pdbe.org/4iuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iuk RCSB], [https://www.ebi.ac.uk/pdbsum/4iuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iuk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/B9DL91_STACT B9DL91_STACT]		[https://www.uniprot.org/uniprot/B9DL91_STACT B9DL91_STACT]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Staphylococci are able to use nitrate as an alternative electron acceptor during anaerobic respiration. The regulation of energy metabolism is dependent on the presence of oxygen and nitrate. Under anaerobic conditions, staphylococci employ the nitrate regulatory element (Nre) for transcriptional activation of genes involved in reduction and transport of nitrate and nitrite. Of the three proteins that constitute the Nre system, NreB has been characterized as an oxygen sensor kinase and NreC has been characterized as its cognate response regulator. Here, we present structural and functional data that establish NreA as a new type of nitrate receptor. The structure of NreA with bound nitrate was solved at 2.35A resolution, revealing a GAF domain fold. Isothermal titration calorimetry experiments showed that NreA binds nitrate with low micromolar affinity (KD=22muM). Two crystal forms for NreA were obtained, with either bound nitrate or iodide. While the binding site is hydrophobic, two helix dipoles and polar interactions contribute to specific binding of the ions. The expression of nitrate reductase (NarGHI) was examined using a narG-lip (lipase) reporter gene assay in vivo. Expression was regulated by the presence of NreA and nitrate. Structure-guided mutations of NreA reduced its nitrate binding affinity and also affected the gene expression, thus providing support for the function of NreA as a nitrate receptor.
-
-	The NreA Protein Functions as a Nitrate Receptor in the Staphylococcal Nitrate Regulation System.,Niemann V, Koch-Singenstreu M, Neu A, Nilkens S, Gotz F, Unden G, Stehle T J Mol Biol. 2013 Dec 31. pii: S0022-2836(13)00813-9. doi:, 10.1016/j.jmb.2013.12.026. PMID:24389349<ref>PMID:24389349</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4iuk" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:12, 16 November 2022

2022-11-16T21:12:01Z

←Older revision		Revision as of 21:12, 16 November 2022
Line 1:		Line 1:

	==Crystal structure of NreA of Staphylococcus carnosus with bound nitrate==		==Crystal structure of NreA of Staphylococcus carnosus with bound nitrate==
-	<StructureSection load='4iuk' size='340' side='right' caption='[[4iuk]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='4iuk' size='340' side='right'caption='[[4iuk]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4iuk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Stact Stact~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IUK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4iuk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_carnosus_subsp._carnosus_TM300 Staphylococcus carnosus subsp. carnosus TM300]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IUK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nreA, Sca_1890, SCA_1890 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=396513 STACT])</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=4iuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iuk OCA], [https://pdbe.org/4iuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iuk RCSB], [https://www.ebi.ac.uk/pdbsum/4iuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iuk 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=4iuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iuk OCA], [~~http~~://pdbe.org/4iuk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4iuk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4iuk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4iuk ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B9DL91_STACT B9DL91_STACT]
	<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: ~~Stact~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Niemann, V~~]]	+	[[Category: Staphylococcus carnosus subsp. carnosus TM300]]
-	[[Category: ~~Stehle, T~~]]	+	[[Category: Niemann V]]
-	[[Category: ~~Cytosolic]]~~	+	[[Category: Stehle T]]
-	~~[[Category: Gaf domain]]~~	+
-	~~[[Category: Nitrate]]~~	+
-	~~[[Category: Nitrate binding]]~~	+
-	~~[[Category: Nitrate sensor]]~~	+
-	~~[[Category: Nitrate-binding protein]]~~	+
-	~~[[Category: Staphylococcus~~]]	+

OCA at 11:47, 4 August 2016

2016-08-04T11:47:16Z

←Older revision		Revision as of 11:47, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of NreA of Staphylococcus carnosus with bound nitrate==		==Crystal structure of NreA of Staphylococcus carnosus with bound nitrate==
	<StructureSection load='4iuk' size='340' side='right' caption='[[4iuk]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='4iuk' size='340' side='right' caption='[[4iuk]], [[Resolution\|resolution]] 2.35Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nreA, Sca_1890, SCA_1890 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=396513 STACT])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nreA, Sca_1890, SCA_1890 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=396513 STACT])</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=4iuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iuk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4iuk RCSB], [http://www.ebi.ac.uk/pdbsum/4iuk 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=4iuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iuk OCA], [http://pdbe.org/4iuk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4iuk RCSB], [http://www.ebi.ac.uk/pdbsum/4iuk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4iuk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4iuk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:44, 21 December 2014

2014-12-21T18:44:14Z

←Older revision		Revision as of 18:44, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4iuk\| PDB=4iuk \| SCENE= }}~~	+	==Crystal structure of NreA of Staphylococcus carnosus with bound nitrate==
-	===Crystal structure of NreA of Staphylococcus carnosus with bound nitrate===	+	<StructureSection load='4iuk' size='340' side='right' caption='[[4iuk]], [[Resolution\|resolution]] 2.35Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24389349}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4iuk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Stact Stact]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IUK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nreA, Sca_1890, SCA_1890 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=396513 STACT])</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=4iuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iuk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4iuk RCSB], [http://www.ebi.ac.uk/pdbsum/4iuk PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Staphylococci are able to use nitrate as an alternative electron acceptor during anaerobic respiration. The regulation of energy metabolism is dependent on the presence of oxygen and nitrate. Under anaerobic conditions, staphylococci employ the nitrate regulatory element (Nre) for transcriptional activation of genes involved in reduction and transport of nitrate and nitrite. Of the three proteins that constitute the Nre system, NreB has been characterized as an oxygen sensor kinase and NreC has been characterized as its cognate response regulator. Here, we present structural and functional data that establish NreA as a new type of nitrate receptor. The structure of NreA with bound nitrate was solved at 2.35A resolution, revealing a GAF domain fold. Isothermal titration calorimetry experiments showed that NreA binds nitrate with low micromolar affinity (KD=22muM). Two crystal forms for NreA were obtained, with either bound nitrate or iodide. While the binding site is hydrophobic, two helix dipoles and polar interactions contribute to specific binding of the ions. The expression of nitrate reductase (NarGHI) was examined using a narG-lip (lipase) reporter gene assay in vivo. Expression was regulated by the presence of NreA and nitrate. Structure-guided mutations of NreA reduced its nitrate binding affinity and also affected the gene expression, thus providing support for the function of NreA as a nitrate receptor.

-	~~==About this Structure==~~	+	The NreA Protein Functions as a Nitrate Receptor in the Staphylococcal Nitrate Regulation System.,Niemann V, Koch-Singenstreu M, Neu A, Nilkens S, Gotz F, Unden G, Stehle T J Mol Biol. 2013 Dec 31. pii: S0022-2836(13)00813-9. doi:, 10.1016/j.jmb.2013.12.026. PMID:24389349<ref>PMID:24389349</ref>
-	~~[[4iuk]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4IUK OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024389349</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Niemann, V.]]	+	== References ==
-	[[Category: Stehle, T.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Stact]]
		+	[[Category: Niemann, V]]
		+	[[Category: Stehle, T]]
	[[Category: Cytosolic]]		[[Category: Cytosolic]]
	[[Category: Gaf domain]]		[[Category: Gaf domain]]

OCA at 08:51, 5 February 2014

2014-02-05T08:51:47Z

←Older revision		Revision as of 08:51, 5 February 2014
Line 1:		Line 1:
	{{STRUCTURE_4iuk\| PDB=4iuk \| SCENE= }}		{{STRUCTURE_4iuk\| PDB=4iuk \| SCENE= }}
	===Crystal structure of NreA of Staphylococcus carnosus with bound nitrate===		===Crystal structure of NreA of Staphylococcus carnosus with bound nitrate===
		+	{{ABSTRACT_PUBMED_24389349}}

	==About this Structure==		==About this Structure==
	[[4iuk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUK OCA].		[[4iuk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUK OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024389349</ref><references group="xtra"/><references/>
	[[Category: Niemann, V.]]		[[Category: Niemann, V.]]
	[[Category: Stehle, T.]]		[[Category: Stehle, T.]]

OCA at 08:22, 15 January 2014

2014-01-15T08:22:48Z

←Older revision		Revision as of 08:22, 15 January 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4iuk\| PDB=4iuk \| SCENE= }}
		+	===Crystal structure of NreA of Staphylococcus carnosus with bound nitrate===

-	~~The entry~~ 4iuk is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4iuk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUK OCA].
-	~~Authors~~: Stehle, T.~~, Niemann, V.~~	+	[[Category: Niemann, V.]]
-		+	[[Category: Stehle, T.]]
-	~~Description~~: ~~Crystal structure of~~ [~~...~~] of Staphylococcus ~~carnosus with bound nitrate~~	+	[[Category: Cytosolic]]
		+	[[Category: Gaf domain]]
		+	[[Category: Nitrate]]
		+	[[Category: Nitrate binding]]
		+	[[Category: Nitrate sensor]]
		+	[[Category: Nitrate-binding protein]]
		+	[[Category: Staphylococcus]]

OCA at 10:51, 24 April 2013

2013-04-24T10:51:11Z

←Older revision		Revision as of 10:51, 24 April 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Stehle, T., Niemann, V.		Authors: Stehle, T., Niemann, V.

	Description: Crystal structure of [...] of Staphylococcus carnosus with bound nitrate		Description: Crystal structure of [...] of Staphylococcus carnosus with bound nitrate

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

2013-01-30T12:05:12Z

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

←Older revision

Revision as of 12:05, 30 January 2013

OCA: New page: '''Unreleased structure''' The entry 4iuk is ON HOLD Authors: Stehle, T., Niemann, V. Description: Crystal structure of [...] of Staphylococcus carnosus with bound nitrate

2013-01-30T12:05:11Z

New page: '''Unreleased structure''' The entry 4iuk is ON HOLD Authors: Stehle, T., Niemann, V. Description: Crystal structure of [...] of Staphylococcus carnosus with bound nitrate

New page

'''Unreleased structure'''

The entry 4iuk is ON HOLD

Authors: Stehle, T., Niemann, V.

Description: Crystal structure of [...] of Staphylococcus carnosus with bound nitrate