6pu3 - Revision history

OCA at 07:35, 11 October 2023

2023-10-11T07:35:53Z

←Older revision		Revision as of 07:35, 11 October 2023
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	<StructureSection load='6pu3' size='340' side='right'caption='[[6pu3]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6pu3' size='340' side='right'caption='[[6pu3]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pu3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PU3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PU3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pu3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PU3 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[~~6ofq~~\|~~6ofq~~]]</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='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=6pu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pu3 OCA], [~~http~~://pdbe.org/6pu3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pu3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pu3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pu3 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=6pu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pu3 OCA], [https://pdbe.org/6pu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pu3 RCSB], [https://www.ebi.ac.uk/pdbsum/6pu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pu3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A3Q9Y393_HELPX A0A3Q9Y393_HELPX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6pu3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6pu3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ABC transporter 3D structures\|ABC transporter 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Helicobacter pylori]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barlow~~, C K~~]]	+	[[Category: Barlow CK]]
-	[[Category: Khan~~, M F~~]]	+	[[Category: Khan MF]]
-	[[Category: Machuca~~, M A~~]]	+	[[Category: Machuca MA]]
-	[[Category: Rahman~~, M M~~]]	+	[[Category: Rahman MM]]
-	[[Category: Roujeinikova, A]]	+	[[Category: Roujeinikova A]]
-	[[Category: Schittenhelm~~, R B]]~~	+	[[Category: Schittenhelm RB]]
-	~~[[Category: Dppa]]~~	+
-	~~[[Category: Periplasmic binding protein]]~~	+
-	~~[[Category: Periplasmic peptide binding protein]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Type ii~~]]	+

OCA at 06:05, 21 August 2019

2019-08-21T06:05:36Z

←Older revision		Revision as of 06:05, 21 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6pu3 is ~~ON HOLD until Paper~~ Publication	+	==ABC transporter-associated periplasmic binding protein DppA from Helicobacter pylori==
		+	<StructureSection load='6pu3' size='340' side='right'caption='[[6pu3]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6pu3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PU3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PU3 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ofq\|6ofq]]</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=6pu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pu3 OCA], [http://pdbe.org/6pu3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pu3 RCSB], [http://www.ebi.ac.uk/pdbsum/6pu3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pu3 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The gastric pathogen Helicobacter pylori has limited ability to use carbohydrates as a carbon source, relying instead on exogenous amino acids and peptides. Uptake of certain peptides by H. pylori requires an ABC transporter annotated dipeptide permease (Dpp). The transporter specificity is determined by its cognate substrate-binding protein DppA that captures ligands in the periplasm and delivers them to the permease. Here, we show that, unlike previously characterized DppA proteins, H. pylori DppA binds, with micromolar affinity, peptides of diverse amino acid sequences, ranging between two and eight residues in length. We present analysis of the 1.45-A resolution crystal structure of its complex with the tetrapeptide STSA, which provides a structural rationale for the observed broad specificity. Analysis of the molecular surface revealed a ligand-binding pocket that is large enough to accommodate peptides of up to nine residues in length. The structure suggests that H. pylori DppA is able to recognize a wide range of peptide sequences by forming interactions primarily with the peptide main-chain atoms. The loop that terminates the peptide-binding pocket in DppAs from other bacteria is significantly shorter in the H. pylori protein, providing an explanation for its ability to bind longer peptides. The subsites accommodating the two N-terminal residues of the peptide ligand make the most contribution to the protein-ligand binding energy, in agreement with the observation that dipeptides bind with affinity close to that of longer peptides.IMPORTANCE The World Health Organization listed Helicobacter pylori as a high priority pathogen for antibiotic development. The potential of using peptide transporters in drug design is well recognized. We discovered that the substrate-binding protein of the ABC transporter for peptides termed dipeptide permease, is an unusual member of its family in that it directly binds peptides of diverse amino acid sequences, ranging between two and eight residues in length. We also provided a structural rationale for the observed broad specificity. Since the ability to import peptides as a source of carbon is critical for H. pylori, our findings will inform drug design strategies based on inhibition or fusion of membrane-impermeant antimicrobials with peptides.

-	~~Authors:~~ Rahman~~, M.M.~~, Machuca~~, M.A.~~, Khan~~, M.F.~~, Barlow~~, C.K.~~, Schittenhelm~~, R.B.~~, Roujeinikova, A.	+	Molecular basis of unexpected specificity of ABC transporter-associated substrate-binding protein DppA from Helicobacter pylori.,Rahman MM, Machuca MA, Khan MF, Barlow CK, Schittenhelm RB, Roujeinikova A J Bacteriol. 2019 Jul 29. pii: JB.00400-19. doi: 10.1128/JB.00400-19. PMID:31358613<ref>PMID:31358613</ref>

-	~~Description: ABC transporter~~-~~associated periplasmic binding protein DppA from Helicobacter pylori~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Khan, M.F]]	+	<div class="pdbe-citations 6pu3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Barlow, C K]]
		+	[[Category: Khan, M F]]
		+	[[Category: Machuca, M A]]
		+	[[Category: Rahman, M M]]
	[[Category: Roujeinikova, A]]		[[Category: Roujeinikova, A]]
-	[[Category: ~~Barlow~~, ~~C.K~~]]	+	[[Category: Schittenhelm, R B]]
-	[[Category: ~~Rahman, M.M~~]]	+	[[Category: Dppa]]
-	[[Category: ~~Schittenhelm, R.B~~]]	+	[[Category: Periplasmic binding protein]]
-	[[Category: ~~Machuca, M.A~~]]	+	[[Category: Periplasmic peptide binding protein]]
		+	[[Category: Transport protein]]
		+	[[Category: Type ii]]

OCA: Protected "6pu3" [edit=sysop:move=sysop]

2019-07-24T04:35:09Z

Protected "6pu3" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:35, 24 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pu3 is ON HOLD until Paper Publication Authors: Rahman, M.M., Machuca, M.A., Khan, M.F., Barlow, C.K., Schittenhelm, R.B., Roujeinikova, A. Descri...

2019-07-24T04:35:07Z

New page: '''Unreleased structure''' The entry 6pu3 is ON HOLD until Paper Publication Authors: Rahman, M.M., Machuca, M.A., Khan, M.F., Barlow, C.K., Schittenhelm, R.B., Roujeinikova, A. Descri...

New page

'''Unreleased structure'''

The entry 6pu3 is ON HOLD until Paper Publication

Authors: Rahman, M.M., Machuca, M.A., Khan, M.F., Barlow, C.K., Schittenhelm, R.B., Roujeinikova, A.

Description: ABC transporter-associated periplasmic binding protein DppA from Helicobacter pylori
[[Category: Unreleased Structures]]
[[Category: Khan, M.F]]
[[Category: Roujeinikova, A]]
[[Category: Barlow, C.K]]
[[Category: Rahman, M.M]]
[[Category: Schittenhelm, R.B]]
[[Category: Machuca, M.A]]