OCA at 16:35, 29 November 2023

OCA — Wed, 29 Nov 2023 16:35:02 GMT

←Older revision		Revision as of 16:35, 29 November 2023
Line 1:		Line 1:

	==Stenotrophomonas maltophilia DPP7 in complex with Asn-Tyr==		==Stenotrophomonas maltophilia DPP7 in complex with Asn-Tyr==
-	<StructureSection load='7dkd' size='340' side='right'caption='[[7dkd]]' scene=''>	+	<StructureSection load='7dkd' size='340' side='right'caption='[[7dkd]], [[Resolution\|resolution]] 1.92Å' 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=7DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dkd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Stenotrophomonas_maltophilia_R551-3 Stenotrophomonas maltophilia R551-3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DKD 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=7dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dkd OCA], [https://pdbe.org/7dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dkd RCSB], [https://www.ebi.ac.uk/pdbsum/7dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dkd 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]] 1.92Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</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=7dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dkd OCA], [https://pdbe.org/7dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dkd RCSB], [https://www.ebi.ac.uk/pdbsum/7dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dkd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B4SLK2_STRM5 B4SLK2_STRM5] Catalyzes the removal of dipeptides from the N-terminus of oligopeptides.[RuleBase:RU366067]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The emergence of drug-resistant bacteria has become a major problem worldwide. Bacterial dipeptidyl peptidases 7 and 11 (DPP7s and DPP11s), belonging to the family-S46 peptidases, are important enzymes for bacterial growth and are not present in mammals. Therefore, specific inhibitors for these peptidases are promising as potential antibiotics. While the molecular mechanisms underlining strict specificity at the S1 subsite of S46 peptidases have been well studied, those of relatively broad preference at the S2 subsite of these peptidases are unknown. In this study, we performed structural and biochemical analyses on DPP7 from Stenotrophomonas maltophilia (SmDPP7). SmDPP7 showed preference for the accommodation of hydrophobic amino acids at the S2 subsite in general, but as an exception, also for asparagine, a hydrophilic amino acid. Structural analyses of SmDPP7 revealed that this exceptional preference to asparagine is caused by a hydrogen bonding network at the bottom of the S2 subsite. The residues in the S2 subsite are well conserved among S46 peptidases as compared with those in the S1 subsite. We expect that our findings will contribute toward the development of a universal inhibitor of S46 peptidases.
		+
		+	Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.,Nakamura A, Suzuki Y, Sakamoto Y, Roppongi S, Kushibiki C, Yonezawa N, Takahashi M, Shida Y, Gouda H, Nonaka T, Tanaka N, Ogasawara W Sci Rep. 2021 Apr 12;11(1):7929. doi: 10.1038/s41598-021-86965-x. PMID:33846449<ref>PMID:33846449</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dkd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dipeptidyl peptidase 3D structures\|Dipeptidyl peptidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Stenotrophomonas maltophilia R551-3]]
	[[Category: Gouda H]]		[[Category: Gouda H]]
	[[Category: Honma N]]		[[Category: Honma N]]

OCA at 14:28, 3 November 2021

OCA — Wed, 03 Nov 2021 14:28:39 GMT

←Older revision		Revision as of 14:28, 3 November 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7dkd is ~~ON HOLD until Paper Publication~~	+	==Stenotrophomonas maltophilia DPP7 in complex with Asn-Tyr==
-		+	<StructureSection load='7dkd' size='340' side='right'caption='[[7dkd]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DKD FirstGlance]. <br>
-	~~Description~~:	+	</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=7dkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dkd OCA], [https://pdbe.org/7dkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dkd RCSB], [https://www.ebi.ac.uk/pdbsum/7dkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dkd ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gouda H]]
		+	[[Category: Honma N]]
		+	[[Category: Kushibiki C]]
		+	[[Category: Nakamura A]]
		+	[[Category: Nonaka T]]
		+	[[Category: Ogasawara W]]
		+	[[Category: Roppongi S]]
		+	[[Category: Sakamoto Y]]
		+	[[Category: Shida Y]]
		+	[[Category: Suzuki Y]]
		+	[[Category: Takahashi M]]
		+	[[Category: Tanaka N]]
		+	[[Category: Yonezawa N]]

OCA at 13:13, 3 March 2021

OCA — Wed, 03 Mar 2021 13:13:51 GMT

←Older revision		Revision as of 13:13, 3 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dkd is ON HOLD	+	The entry 7dkd is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7dkd" [edit=sysop:move=sysop]

OCA — Wed, 02 Dec 2020 05:42:53 GMT

Protected "7dkd" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:42, 2 December 2020

OCA: New page: '''Unreleased structure''' The entry 7dkd is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Dec 2020 05:42:52 GMT

New page: '''Unreleased structure''' The entry 7dkd is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7dkd is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7dkd - Revision history

OCA at 16:35, 29 November 2023

OCA at 14:28, 3 November 2021

OCA at 13:13, 3 March 2021

OCA: Protected "7dkd" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7dkd is ON HOLD Authors: Description: Category: Unreleased Structures