8iat - Revision history

OCA at 19:53, 29 May 2024

OCA — Wed, 29 May 2024 19:53:45 GMT

←Older revision		Revision as of 19:53, 29 May 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q8DQ84_STRR6 Q8DQ84_STRR6]		[https://www.uniprot.org/uniprot/Q8DQ84_STRR6 Q8DQ84_STRR6]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycolysis is the primary metabolic pathway in the strictly fermentative Streptococcus pneumoniae, which is a major human pathogen associated with antibiotic resistance. Pyruvate kinase (PYK) is the last enzyme in this pathway that catalyzes the production of pyruvate from phosphoenolpyruvate (PEP) and plays a crucial role in controlling carbon flux; however, while S. pneumoniae PYK (SpPYK) is indispensable for growth, surprisingly little is known about its functional properties. Here, we report that compromising mutations in SpPYK confers resistance to the antibiotic fosfomycin, which inhibits the peptidoglycan synthesis enzyme MurA, implying a direct link between PYK and cell wall biogenesis. The crystal structures of SpPYK in the apo and ligand-bound states reveal key interactions that contribute to its conformational change as well as residues responsible for the recognition of PEP and the allosteric activator fructose 1,6-bisphosphate (FBP). Strikingly, FBP binding was observed at a location distinct from previously reported PYK effector binding sites. Furthermore, we show that SpPYK could be engineered to become more responsive to glucose 6-phosphate instead of FBP by sequence and structure-guided mutagenesis of the effector binding site. Together, our work sheds light on the regulatory mechanism of SpPYK and lays the groundwork for antibiotic development that targets this essential enzyme.
		+
		+	Functional and structural characterization of Streptococcus pneumoniae pyruvate kinase involved in fosfomycin resistance.,Taguchi A, Nakashima R, Nishino K J Biol Chem. 2023 Jul;299(7):104892. doi: 10.1016/j.jbc.2023.104892. Epub 2023 , Jun 5. PMID:37286036<ref>PMID:37286036</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 8iat" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pyruvate kinase 3D structures\|Pyruvate kinase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:23, 19 July 2023

OCA — Wed, 19 Jul 2023 06:23:27 GMT

←Older revision		Revision as of 06:23, 19 July 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8iat]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IAT FirstGlance]. <br>		<table><tr><td colspan='2'>[[8iat]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IAT 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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.8Å</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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=8iat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8iat OCA], [https://pdbe.org/8iat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8iat RCSB], [https://www.ebi.ac.uk/pdbsum/8iat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8iat 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=8iat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8iat OCA], [https://pdbe.org/8iat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8iat RCSB], [https://www.ebi.ac.uk/pdbsum/8iat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8iat ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:20, 14 June 2023

OCA — Wed, 14 Jun 2023 08:20:33 GMT

←Older revision		Revision as of 08:20, 14 June 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8iat is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate==
-		+	<StructureSection load='8iat' size='340' side='right'caption='[[8iat]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~: ~~Nakashima~~, R., ~~Taguchi~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[8iat]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IAT FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate~~	+	</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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8iat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8iat OCA], [https://pdbe.org/8iat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8iat RCSB], [https://www.ebi.ac.uk/pdbsum/8iat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8iat ProSAT]</span></td></tr>
-	[[Category: ~~Taguchi, A~~]]	+	</table>
-	[[Category: Nakashima, R]]	+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8DQ84_STRR6 Q8DQ84_STRR6]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Streptococcus pneumoniae R6]]
		+	[[Category: Nakashima R]]
		+	[[Category: Taguchi A]]

OCA at 08:01, 15 March 2023

OCA — Wed, 15 Mar 2023 08:01:33 GMT

←Older revision		Revision as of 08:01, 15 March 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8iat is ON HOLD	+	The entry 8iat is ON HOLD until Paper Publication

	Authors: Nakashima, R., Taguchi, A.		Authors: Nakashima, R., Taguchi, A.

OCA: Protected "8iat" [edit=sysop:move=sysop]

OCA — Wed, 15 Feb 2023 09:03:50 GMT

Protected "8iat" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:03, 15 February 2023

OCA: New page: '''Unreleased structure''' The entry 8iat is ON HOLD Authors: Nakashima, R., Taguchi, A. Description: Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxal...

OCA — Wed, 15 Feb 2023 09:03:47 GMT

New page: '''Unreleased structure''' The entry 8iat is ON HOLD Authors: Nakashima, R., Taguchi, A. Description: Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxal...

New page

'''Unreleased structure'''

The entry 8iat is ON HOLD

Authors: Nakashima, R., Taguchi, A.

Description: Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate
[[Category: Unreleased Structures]]
[[Category: Taguchi, A]]
[[Category: Nakashima, R]]