6mh9 - Revision history

OCA at 06:31, 11 October 2023

OCA — Wed, 11 Oct 2023 06:31:45 GMT

←Older revision		Revision as of 06:31, 11 October 2023
Line 1:		Line 1:

	==The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein A121I mutant to 2.02 Angstrom resolution==		==The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein A121I mutant to 2.02 Angstrom resolution==
-	<StructureSection load='6mh9' size='340' side='right'caption='[[6mh9]]' scene=''>	+	<StructureSection load='6mh9' size='340' side='right'caption='[[6mh9]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MH9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mh9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MH9 FirstGlance]. <br>
-	</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=6mh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mh9 OCA], [https://pdbe.org/6mh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mh9 RCSB], [https://www.ebi.ac.uk/pdbsum/6mh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mh9 ProSAT]</span></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]] 2.02Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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=6mh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mh9 OCA], [https://pdbe.org/6mh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mh9 RCSB], [https://www.ebi.ac.uk/pdbsum/6mh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mh9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YU230_STAAU YU230_STAAU] May bind long-chain fatty acids, such as palmitate, and may play a role in lipid transport or fatty acid metabolism.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein-FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a "closed" FakB1 state to an "open" state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic alpha-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.
		+
		+	Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes.,Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW J Biol Chem. 2022 Mar;298(3):101676. doi: 10.1016/j.jbc.2022.101676. Epub 2022, Feb 3. PMID:35122790<ref>PMID:35122790</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mh9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Staphylococcus aureus]]
	[[Category: Cuypers MG]]		[[Category: Cuypers MG]]
	[[Category: Ericson M]]		[[Category: Ericson M]]

OCA at 14:41, 31 August 2022

OCA — Wed, 31 Aug 2022 14:41:45 GMT

←Older revision		Revision as of 14:41, 31 August 2022
Line 1:		Line 1:

	==The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein A121I mutant to 2.02 Angstrom resolution==		==The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein A121I mutant to 2.02 Angstrom resolution==
-	<StructureSection load='6mh9' size='340' side='right'caption='[[6mh9]]~~, [[Resolution\|resolution]] 2.02Å~~' scene=''>	+	<StructureSection load='6mh9' size='340' side='right'caption='[[6mh9]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[6mh9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MH9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MH9 FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>~~	+	</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=6mh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mh9 OCA], [https://pdbe.org/6mh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mh9 RCSB], [https://www.ebi.ac.uk/pdbsum/6mh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mh9 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5uto\|5uto]]</div></td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTN44_08795, CV021_09110, EP54_02745, EQ90_03735, ERS072840_01626, HMPREF3211_01094 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=6mh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mh9 OCA], [https://pdbe.org/6mh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mh9 RCSB], [https://www.ebi.ac.uk/pdbsum/6mh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mh9 ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein-FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a "closed" FakB1 state to an "open" state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic alpha-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.
-
-	Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes.,Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW J Biol Chem. 2022 Mar;298(3):101676. doi: 10.1016/j.jbc.2022.101676. Epub 2022, Feb 3. PMID:35122790<ref>PMID:35122790</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6mh9" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cuypers~~, M G~~]]	+	[[Category: Cuypers MG]]
-	[[Category: Ericson, M]]	+	[[Category: Ericson M]]
-	[[Category: Rock~~, C O~~]]	+	[[Category: Rock CO]]
-	[[Category: Subramanian, C]]	+	[[Category: Subramanian C]]
-	[[Category: White~~, S W]]~~	+	[[Category: White SW]]
-	~~[[Category: Fakb1]]~~	+
-	~~[[Category: Mutant transferase]]~~	+
-	~~[[Category: Staphylococcus aureus]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:22, 12 May 2022

OCA — Thu, 12 May 2022 06:22:48 GMT

←Older revision		Revision as of 06:22, 12 May 2022
Line 3:		Line 3:
	<StructureSection load='6mh9' size='340' side='right'caption='[[6mh9]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='6mh9' size='340' side='right'caption='[[6mh9]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mh9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MH9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MH9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mh9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MH9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uto\|5uto]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5uto\|5uto]]</div></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=6mh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mh9 OCA], [~~http~~://pdbe.org/6mh9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mh9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mh9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mh9 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BTN44_08795, CV021_09110, EP54_02745, EQ90_03735, ERS072840_01626, HMPREF3211_01094 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=6mh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mh9 OCA], [https://pdbe.org/6mh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mh9 RCSB], [https://www.ebi.ac.uk/pdbsum/6mh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mh9 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein-FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a "closed" FakB1 state to an "open" state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic alpha-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.
		+
		+	Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes.,Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW J Biol Chem. 2022 Mar;298(3):101676. doi: 10.1016/j.jbc.2022.101676. Epub 2022, Feb 3. PMID:35122790<ref>PMID:35122790</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mh9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:03, 13 November 2019

OCA — Wed, 13 Nov 2019 11:03:10 GMT

←Older revision		Revision as of 11:03, 13 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6mh9 ~~is ON HOLD until Paper Publication~~	+	==The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein A121I mutant to 2.02 Angstrom resolution==
-		+	<StructureSection load='6mh9' size='340' side='right'caption='[[6mh9]], [[Resolution\|resolution]] 2.02Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mh9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MH9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MH9 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uto\|5uto]]</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=6mh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mh9 OCA], [http://pdbe.org/6mh9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mh9 RCSB], [http://www.ebi.ac.uk/pdbsum/6mh9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mh9 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cuypers, M G]]
		+	[[Category: Ericson, M]]
		+	[[Category: Rock, C O]]
		+	[[Category: Subramanian, C]]
		+	[[Category: White, S W]]
		+	[[Category: Fakb1]]
		+	[[Category: Mutant transferase]]
		+	[[Category: Staphylococcus aureus]]
		+	[[Category: Transferase]]

OCA at 10:30, 16 January 2019

OCA — Wed, 16 Jan 2019 10:30:27 GMT

←Older revision		Revision as of 10:30, 16 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6mh9 is ON HOLD	+	The entry 6mh9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6mh9" [edit=sysop:move=sysop]

OCA — Wed, 26 Sep 2018 06:32:03 GMT

Protected "6mh9" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:32, 26 September 2018

OCA: New page: '''Unreleased structure''' The entry 6mh9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Sep 2018 06:32:02 GMT

New page: '''Unreleased structure''' The entry 6mh9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6mh9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]