6dqq - Revision history

OCA at 14:36, 13 March 2024

OCA — Wed, 13 Mar 2024 14:36:22 GMT

←Older revision		Revision as of 14:36, 13 March 2024
Line 1:		Line 1:

	==Crystal structure of Haemophilus influenzae OppA complex with endogenous peptide==		==Crystal structure of Haemophilus influenzae OppA complex with endogenous peptide==
-	<StructureSection load='6dqq' size='340' side='right' caption='[[6dqq]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='6dqq' size='340' side='right'caption='[[6dqq]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dqq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Haei8 Haei8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DQQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DQQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dqq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_86-028NP Haemophilus influenzae 86-028NP] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DQQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DQQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.85Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~oppA, NTHI1292 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=281310 HAEI8])~~</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=SO4:SULFATE+ION'>SO4</scene></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=6dqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dqq OCA], [~~http~~://pdbe.org/6dqq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dqq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dqq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dqq 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=6dqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dqq OCA], [https://pdbe.org/6dqq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dqq RCSB], [https://www.ebi.ac.uk/pdbsum/6dqq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dqq ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q4QLH0_HAEI8 Q4QLH0_HAEI8]
-	In nontypeable Haemophilus influenzae (NTHi), the oligopeptide-binding protein OppA serves as the substrate-binding protein (SBP) responsible for peptide import. As a heme auxotroph, NTHi also uses host hemoproteins as an iron source. OppA is a member of the Cluster C SBP family, and unlike other SBP families, some members recognize two distinctly different substrates. DppA (dipeptide), MppA (murein tripeptide), and SapA (antimicrobial peptides) are Cluster C proteins known to also transport heme. However, the ability of OppA to participate in heme binding and how Cluster C proteins accommodate these heme and peptide substrates are unclear. Here, we solved the crystal structure of nthiOppA in complex with hydrophobic peptides of various sizes. The hexapeptide complex revealed the flexibility of nthiOppA's binding cavity to expand and accommodate a longer peptide substrate while maintaining similar protein-peptide interactions used to bind smaller peptides. Additionally, we observed the multifunctional heme binding of nthiOppA, and using surface plasmon resonance (SPR), we established heme specificity and affinity of the four Cluster C proteins in NTHi. Ligand-docking studies predicted a distinct heme-specific cleft in the nthiOppA substrate-binding pocket, and SPR competition assays confirmed that heme does not directly compete with peptides in this pocket. Additionally, we noted that the individual nthiOppA domains differentially contribute to substrate binding, with one domain playing a dominant role in heme binding and the other in peptide binding. ~~Our results identified multi-substrate specificity of nthiOppA and distinguished the roles of NTHi Cluster C proteins in the heme-uptake pathway of this bacterial pathogen~~.	+

-	Oligopeptide-binding protein from nontypeable Haemophilus influenzae has ligand-specific sites to accommodate peptides and heme in the binding pocket.,Tanaka KJ, Pinkett HW J Biol Chem. 2018 Nov 19. pii: RA118.004479. doi: 10.1074/jbc.RA118.004479. PMID:30455346<ref>PMID:30455346</ref>	+	==See Also==
-		+	*[[ABC transporter 3D structures\|ABC transporter 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6dqq" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Haei8~~]]	+	[[Category: Haemophilus influenzae 86-028NP]]
-	[[Category: ~~Pinkett, H W~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Tanaka, K J~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Abc transporter~~]]	+	[[Category: Pinkett HW]]
-	[[Category: ~~Peptide binding protein]]~~	+	[[Category: Tanaka KJ]]
-	~~[[Category: Substrate-binding protein~~]]	+

OCA at 07:03, 5 December 2018

OCA — Wed, 05 Dec 2018 07:03:32 GMT

←Older revision		Revision as of 07:03, 5 December 2018
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	<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=6dqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dqq OCA], [http://pdbe.org/6dqq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dqq RCSB], [http://www.ebi.ac.uk/pdbsum/6dqq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dqq 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=6dqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dqq OCA], [http://pdbe.org/6dqq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dqq RCSB], [http://www.ebi.ac.uk/pdbsum/6dqq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dqq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In nontypeable Haemophilus influenzae (NTHi), the oligopeptide-binding protein OppA serves as the substrate-binding protein (SBP) responsible for peptide import. As a heme auxotroph, NTHi also uses host hemoproteins as an iron source. OppA is a member of the Cluster C SBP family, and unlike other SBP families, some members recognize two distinctly different substrates. DppA (dipeptide), MppA (murein tripeptide), and SapA (antimicrobial peptides) are Cluster C proteins known to also transport heme. However, the ability of OppA to participate in heme binding and how Cluster C proteins accommodate these heme and peptide substrates are unclear. Here, we solved the crystal structure of nthiOppA in complex with hydrophobic peptides of various sizes. The hexapeptide complex revealed the flexibility of nthiOppA's binding cavity to expand and accommodate a longer peptide substrate while maintaining similar protein-peptide interactions used to bind smaller peptides. Additionally, we observed the multifunctional heme binding of nthiOppA, and using surface plasmon resonance (SPR), we established heme specificity and affinity of the four Cluster C proteins in NTHi. Ligand-docking studies predicted a distinct heme-specific cleft in the nthiOppA substrate-binding pocket, and SPR competition assays confirmed that heme does not directly compete with peptides in this pocket. Additionally, we noted that the individual nthiOppA domains differentially contribute to substrate binding, with one domain playing a dominant role in heme binding and the other in peptide binding. Our results identified multi-substrate specificity of nthiOppA and distinguished the roles of NTHi Cluster C proteins in the heme-uptake pathway of this bacterial pathogen.
		+
		+	Oligopeptide-binding protein from nontypeable Haemophilus influenzae has ligand-specific sites to accommodate peptides and heme in the binding pocket.,Tanaka KJ, Pinkett HW J Biol Chem. 2018 Nov 19. pii: RA118.004479. doi: 10.1074/jbc.RA118.004479. PMID:30455346<ref>PMID:30455346</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dqq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 20:27, 2 December 2018

OCA — Sun, 02 Dec 2018 20:27:20 GMT

←Older revision		Revision as of 20:27, 2 December 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6dqq is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Haemophilus influenzae OppA complex with endogenous peptide==
-		+	<StructureSection load='6dqq' size='340' side='right' caption='[[6dqq]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dqq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haei8 Haei8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DQQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DQQ FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oppA, NTHI1292 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=281310 HAEI8])</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=6dqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dqq OCA], [http://pdbe.org/6dqq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dqq RCSB], [http://www.ebi.ac.uk/pdbsum/6dqq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dqq ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Haei8]]
		+	[[Category: Pinkett, H W]]
		+	[[Category: Tanaka, K J]]
		+	[[Category: Abc transporter]]
		+	[[Category: Peptide binding protein]]
		+	[[Category: Substrate-binding protein]]

OCA at 05:40, 4 July 2018

OCA — Wed, 04 Jul 2018 05:40:38 GMT

←Older revision		Revision as of 05:40, 4 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 20 Jun 2018 04:09:29 GMT

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

←Older revision

Revision as of 04:09, 20 June 2018

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

OCA — Wed, 20 Jun 2018 04:09:27 GMT

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

New page

'''Unreleased structure'''

The entry 6dqq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]