6yag - Revision history

OCA at 13:22, 24 January 2024

OCA — Wed, 24 Jan 2024 13:22:57 GMT

←Older revision		Revision as of 13:22, 24 January 2024
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	==Crystal structure of PnrA from S. pneumoniae in complex with thymidine==		==Crystal structure of PnrA from S. pneumoniae in complex with thymidine==
-	<StructureSection load='6yag' size='340' side='right'caption='[[6yag]]' scene=''>	+	<StructureSection load='6yag' size='340' side='right'caption='[[6yag]], [[Resolution\|resolution]] 2.55Å' 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=6YAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YAG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yag]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YAG 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=6yag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yag OCA], [https://pdbe.org/6yag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yag RCSB], [https://www.ebi.ac.uk/pdbsum/6yag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yag 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]] 2.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</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=6yag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yag OCA], [https://pdbe.org/6yag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yag RCSB], [https://www.ebi.ac.uk/pdbsum/6yag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yag ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H2UPF3_STRPN A0A0H2UPF3_STRPN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nucleotides are important for RNA and DNA synthesis and, despite a de novo synthesis by bacteria, uptake systems are crucial. Streptococcus pneumoniae, a facultative human pathogen, produces a surface-exposed nucleoside-binding protein, PnrA, as part of an ABC transporter system. Here we demonstrate the binding affinity of PnrA to nucleosides adenosine, guanosine, cytidine, thymidine and uridine by microscale thermophoresis and indicate the consumption of adenosine and guanosine by (1)H NMR spectroscopy. In a series of five crystal structures we revealed the PnrA structure and provide insights into how PnrA can bind purine and pyrimidine ribonucleosides but with preference for purine ribonucleosides. Crystal structures of PnrA:nucleoside complexes unveil a clear pattern of interactions in which both the N- and C- domains of PnrA contribute. The ribose moiety is strongly recognized through a conserved network of H-bond interactions, while plasticity in loop 27-36 is essential to bind purine- or pyrimidine-based nucleosides. Further, we deciphered the role of PnrA in pneumococcal fitness in infection experiments. Phagocytosis experiments did not show a clear difference in phagocytosis between PnrA-deficient and wild-type pneumococci. In the acute pneumonia infection model the deficiency of PnrA attenuated moderately virulence of the mutant, which is indicated by a delay in the development of severe lung infections. Importantly, we confirmed the loss of fitness in co-infections, where the wild-type out-competed the pnrA-mutant. In conclusion, we present the PnrA structure in complex with individual nucleosides and show that the consumption of adenosine and guanosine under infection conditions is required for virulence.
		+
		+	Crystal Structure and Pathophysiological Role of the Pneumococcal Nucleoside-binding Protein PnrA.,Abdullah MR, Batuecas MT, Jennert F, Voss F, Westhoff P, Kohler TP, Molina R, Hirschmann S, Lalk M, Hermoso JA, Hammerschmidt S J Mol Biol. 2021 Jan 22;433(2):166723. doi: 10.1016/j.jmb.2020.11.022. Epub 2020 , Nov 23. PMID:33242497<ref>PMID:33242497</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yag" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Streptococcus pneumoniae]]
	[[Category: Batuecas MT]]		[[Category: Batuecas MT]]
	[[Category: Hermoso JA]]		[[Category: Hermoso JA]]

OCA at 10:56, 10 February 2021

OCA — Wed, 10 Feb 2021 10:56:19 GMT

←Older revision		Revision as of 10:56, 10 February 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6yag ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of PnrA from S. pneumoniae in complex with thymidine==
-		+	<StructureSection load='6yag' size='340' side='right'caption='[[6yag]]' scene=''>
-	~~Authors~~: ~~Batuecas~~, M.T., ~~Hermoso~~, J.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YAG FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of PnrA from S~~. ~~pneumoniae in complex with thymidine~~	+	</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=6yag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yag OCA], [https://pdbe.org/6yag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yag RCSB], [https://www.ebi.ac.uk/pdbsum/6yag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yag ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Hermoso, J.A~~]]	+	__TOC__
-	[[Category: ~~Batuecas, M.T~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Batuecas MT]]
		+	[[Category: Hermoso JA]]

OCA at 08:32, 27 March 2020

OCA — Fri, 27 Mar 2020 08:32:43 GMT

←Older revision		Revision as of 08:32, 27 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Batuecas, M.T., Hermoso, J.A.		Authors: Batuecas, M.T., Hermoso, J.A.

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

OCA — Wed, 18 Mar 2020 08:41:31 GMT

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

←Older revision

Revision as of 08:41, 18 March 2020

OCA: New page: '''Unreleased structure''' The entry 6yag is ON HOLD Authors: Batuecas, M.T., Hermoso, J.A. Description: Crystal structure of PnrA from S. pneumoniae in complex with thymidine [[Catego...

OCA — Wed, 18 Mar 2020 08:41:30 GMT

New page: '''Unreleased structure''' The entry 6yag is ON HOLD Authors: Batuecas, M.T., Hermoso, J.A. Description: Crystal structure of PnrA from S. pneumoniae in complex with thymidine [[Catego...

New page

'''Unreleased structure'''

The entry 6yag is ON HOLD

Authors: Batuecas, M.T., Hermoso, J.A.

Description: Crystal structure of PnrA from S. pneumoniae in complex with thymidine
[[Category: Unreleased Structures]]
[[Category: Hermoso, J.A]]
[[Category: Batuecas, M.T]]