5yp2 - Revision history

OCA at 08:34, 22 November 2023

OCA — Wed, 22 Nov 2023 08:34:39 GMT

←Older revision		Revision as of 08:34, 22 November 2023
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	<StructureSection load='5yp2' size='340' side='right'caption='[[5yp2]], [[Resolution\|resolution]] 2.13Å' scene=''>		<StructureSection load='5yp2' size='340' side='right'caption='[[5yp2]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yp2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YP2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YP2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yp2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoxanthomonas_mexicana Pseudoxanthomonas mexicana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YP2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=8YC:(2S~~,~~5R)-1-~~[2-[~~[1-(hydroxymethyl)cyclopentyl~~]~~amino~~]~~ethanoyl]pyrrolidine-~~2~~,5-dicarbonitrile'>8YC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.13Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[~~5yp1\|5yp1~~]]~~, [[5yp3\|5yp3]~~], ~~[[5yp4\|5yp4]]</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8YC:(2S,5R)-1-[2-[[1-(hydroxymethyl)cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile'>8YC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_IV Dipeptidyl-peptidase IV], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.5 3.4.14.5]~~ </~~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=5yp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yp2 OCA], [https://pdbe.org/5yp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yp2 RCSB], [https://www.ebi.ac.uk/pdbsum/5yp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yp2 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5yp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yp2 OCA], [~~http~~://pdbe.org/5yp2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yp2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yp2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yp2 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DAP4_PSEMX DAP4_PSEMX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dipeptidyl-peptidase IV]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fuimoto, M]]	+	[[Category: Pseudoxanthomonas mexicana]]
-	[[Category: Honma, N]]	+	[[Category: Fuimoto M]]
-	[[Category: Iizuka, I]]	+	[[Category: Honma N]]
-	[[Category: Morisawa, S]]	+	[[Category: Iizuka I]]
-	[[Category: Nakamura, A]]	+	[[Category: Morisawa S]]
-	[[Category: Nonaka, T]]	+	[[Category: Nakamura A]]
-	[[Category: Ogasawara, W]]	+	[[Category: Nonaka T]]
-	[[Category: Roppongi, S]]	+	[[Category: Ogasawara W]]
-	[[Category: Sakamoto, Y]]	+	[[Category: Roppongi S]]
-	[[Category: Shida, Y]]	+	[[Category: Sakamoto Y]]
-	[[Category: Suzuki, Y]]	+	[[Category: Shida Y]]
-	[[Category: Tanaka, N]]	+	[[Category: Suzuki Y]]
-	[[Category: Tateoka, C]]	+	[[Category: Tanaka N]]
-	~~[[Category: Clan sc s9]]~~	+	[[Category: Tateoka C]]
-	~~[[Category: Dap iv]]~~	+
-	~~[[Category: Dpp4]]~~	+
-	~~[[Category: Dpp8]]~~	+
-	~~[[Category: Dpp9]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidase~~]]	+

OCA at 09:24, 21 October 2020

OCA — Wed, 21 Oct 2020 09:24:14 GMT

←Older revision		Revision as of 09:24, 21 October 2020
Line 1:		Line 1:

	==Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24==		==Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24==
-	<StructureSection load='5yp2' size='340' side='right' caption='[[5yp2]], [[Resolution\|resolution]] 2.13Å' scene=''>	+	<StructureSection load='5yp2' size='340' side='right'caption='[[5yp2]], [[Resolution\|resolution]] 2.13Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yp2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YP2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YP2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yp2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YP2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YP2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8YC:(2S,5R)-1-[2-[[1-(hydroxymethyl)cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile'>8YC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8YC:(2S,5R)-1-[2-[[1-(hydroxymethyl)cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile'>8YC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yp1\|5yp1]], [[5yp3\|5yp3]], [[5yp4\|5yp4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yp1\|5yp1]], [[5yp3\|5yp3]], [[5yp4\|5yp4]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_IV Dipeptidyl-peptidase IV], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.5 3.4.14.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_IV Dipeptidyl-peptidase IV], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.5 3.4.14.5] </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=5yp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yp2 OCA], [http://pdbe.org/5yp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yp2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yp2 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yp2 OCA], [http://pdbe.org/5yp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yp2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yp2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Dipeptidyl-peptidase IV]]		[[Category: Dipeptidyl-peptidase IV]]
		+	[[Category: Large Structures]]
	[[Category: Fuimoto, M]]		[[Category: Fuimoto, M]]
	[[Category: Honma, N]]		[[Category: Honma, N]]

OCA at 07:22, 22 February 2018

OCA — Thu, 22 Feb 2018 07:22:01 GMT

←Older revision		Revision as of 07:22, 22 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yp2 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24==
		+	<StructureSection load='5yp2' size='340' side='right' caption='[[5yp2]], [[Resolution\|resolution]] 2.13Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yp2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YP2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8YC:(2S,5R)-1-[2-[[1-(hydroxymethyl)cyclopentyl]amino]ethanoyl]pyrrolidine-2,5-dicarbonitrile'>8YC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5yp1\|5yp1]], [[5yp3\|5yp3]], [[5yp4\|5yp4]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_IV Dipeptidyl-peptidase IV], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.5 3.4.14.5] </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=5yp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yp2 OCA], [http://pdbe.org/5yp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yp2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yp2 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dipeptidyl peptidase IV (DPP IV, DPP4, or DAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position. The substrate recognition mechanism has been fully elucidated for mammalian DPP IV by crystal structure analyses but not for bacterial orthologues. Here, we report the crystal structures of a bacterial DPP IV (PmDAP IV) in its free form and in complexes with two kinds of dipeptides as well as with a non-peptidyl inhibitor at 1.90 to 2.47 A resolution. Acyl-enzyme intermediates were observed for the dipeptide complexes of PmDAP IV, whereas tetrahedral intermediates were reported for the oligopeptide complexes of mammalian DPP IVs. This variation reflects the different structural environments of the active site Arg residues, which are involved in the recognition of a substrate carbonyl group, of mammalian and bacterial enzymes. A phylogenetic analysis revealed that PmDAP IV is a closer relative of dipeptidyl peptidases 8 and 9 (DPP8 and DPP9, DPP IV-family enzymes) than DPP IV. These results provide new insights into the substrate recognition mechanism of bacterial DAP IVs and may assist in the development of selective inhibitors for DAP IVs from pathogenic asaccharolytic bacteria, which utilise proteins or peptides as an energy source.

-	~~Authors:~~ Roppongi, S., Suzuki, Y., Tateoka, C~~., Fuimoto~~, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara, W., Tanaka, N., Sakamoto, Y., Nonaka, T.	+	Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.,Roppongi S, Suzuki Y, Tateoka C, Fujimoto M, Morisawa S, Iizuka I, Nakamura A, Honma N, Shida Y, Ogasawara W, Tanaka N, Sakamoto Y, Nonaka T Sci Rep. 2018 Feb 9;8(1):2714. doi: 10.1038/s41598-018-21056-y. PMID:29426867<ref>PMID:29426867</ref>

-	~~Description: Crystal structure~~ of ~~dipeptidyl~~ peptidase IV ~~(DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yp2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dipeptidyl-peptidase IV]]
		+	[[Category: Fuimoto, M]]
		+	[[Category: Honma, N]]
		+	[[Category: Iizuka, I]]
		+	[[Category: Morisawa, S]]
		+	[[Category: Nakamura, A]]
		+	[[Category: Nonaka, T]]
	[[Category: Ogasawara, W]]		[[Category: Ogasawara, W]]
-	[[Category: ~~Tanaka~~, N]]	+	[[Category: Roppongi, S]]
	[[Category: Sakamoto, Y]]		[[Category: Sakamoto, Y]]
		+	[[Category: Shida, Y]]
	[[Category: Suzuki, Y]]		[[Category: Suzuki, Y]]
		+	[[Category: Tanaka, N]]
	[[Category: Tateoka, C]]		[[Category: Tateoka, C]]
-	[[Category: ~~Roppongi, S~~]]	+	[[Category: Clan sc s9]]
-	[[Category: ~~Shida, Y~~]]	+	[[Category: Dap iv]]
-	[[Category: ~~Nakamura, A~~]]	+	[[Category: Dpp4]]
-	[[Category: ~~Morisawa, S~~]]	+	[[Category: Dpp8]]
-	[[Category: ~~Honma, N~~]]	+	[[Category: Dpp9]]
-	[[Category: ~~Nonaka, T~~]]	+	[[Category: Hydrolase]]
-	[[Category: ~~Iizuka, I]]~~	+	[[Category: Peptidase]]
-	~~[[Category: Fuimoto, M~~]]	+

OCA at 04:55, 7 February 2018

OCA — Wed, 07 Feb 2018 04:55:59 GMT

←Older revision		Revision as of 04:55, 7 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yp2 is ON HOLD	+	The entry 5yp2 is ON HOLD until Paper Publication

	Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara, W., Tanaka, N., Sakamoto, Y., Nonaka, T.		Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara, W., Tanaka, N., Sakamoto, Y., Nonaka, T.

OCA at 17:09, 24 January 2018

OCA — Wed, 24 Jan 2018 17:09:20 GMT

←Older revision		Revision as of 17:09, 24 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yp2 is ON HOLD ~~until Paper Publication~~	+	The entry 5yp2 is ON HOLD

	Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara, W., Tanaka, N., Sakamoto, Y., Nonaka, T.		Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara, W., Tanaka, N., Sakamoto, Y., Nonaka, T.

OCA at 05:45, 13 December 2017

OCA — Wed, 13 Dec 2017 05:45:25 GMT

←Older revision		Revision as of 05:45, 13 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yp2 is ON HOLD	+	The entry 5yp2 is ON HOLD until Paper Publication

	Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara, W., Tanaka, N., Sakamoto, Y., Nonaka, T.		Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara, W., Tanaka, N., Sakamoto, Y., Nonaka, T.

OCA: Protected "5yp2" [edit=sysop:move=sysop]

OCA — Wed, 08 Nov 2017 06:27:51 GMT

Protected "5yp2" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:27, 8 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yp2 is ON HOLD Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara...

OCA — Wed, 08 Nov 2017 06:27:50 GMT

New page: '''Unreleased structure''' The entry 5yp2 is ON HOLD Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara...

New page

'''Unreleased structure'''

The entry 5yp2 is ON HOLD

Authors: Roppongi, S., Suzuki, Y., Tateoka, C., Fuimoto, M., Morisawa, S., Iizuka, I., Nakamura, A., Honma, N., Shida, Y., Ogasawara, W., Tanaka, N., Sakamoto, Y., Nonaka, T.

Description: Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24
[[Category: Unreleased Structures]]
[[Category: Ogasawara, W]]
[[Category: Tanaka, N]]
[[Category: Sakamoto, Y]]
[[Category: Suzuki, Y]]
[[Category: Tateoka, C]]
[[Category: Roppongi, S]]
[[Category: Shida, Y]]
[[Category: Nakamura, A]]
[[Category: Morisawa, S]]
[[Category: Honma, N]]
[[Category: Nonaka, T]]
[[Category: Iizuka, I]]
[[Category: Fuimoto, M]]