4xzy - Revision history

OCA at 15:32, 8 November 2023

2023-11-08T15:32:39Z

←Older revision		Revision as of 15:32, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xzy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XZY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xzy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XZY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [https://pdbe.org/4xzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [https://www.ebi.ac.uk/pdbsum/4xzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xzy 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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [https://pdbe.org/4xzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [https://www.ebi.ac.uk/pdbsum/4xzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xzy ProSAT]</span></td></tr>
	</table>		</table>

OCA at 18:00, 26 April 2023

2023-04-26T18:00:24Z

←Older revision		Revision as of 18:00, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xzy' size='340' side='right'caption='[[4xzy]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4xzy' size='340' side='right'caption='[[4xzy]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xzy]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_33277 Atcc 33277~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XZY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xzy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XZY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x01\|4x01]], [[4x02\|4x02]], [[4x04\|4x04]], [[4x06\|4x06]]</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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [https://pdbe.org/4xzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [https://www.ebi.ac.uk/pdbsum/4xzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xzy ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EG14_04230 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 ATCC 33277])~~</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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [~~http~~://pdbe.org/4xzy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xzy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xzy ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPP11_PORG3 DPP11_PORG3] Catalyzes the removal of dipeptides from the N-terminus of oligopeptides. Shows a strict specificity for acidic residues (Asp or Glu) in the P1 position, and has a hydrophobic residue preference at the P2 position. Preferentially cleaves the synthetic substrate Leu-Asp-methylcoumaryl-7-amide (Leu-Asp-MCA) as compared to Leu-Glu-MCA. Is involved in amino acid metabolism and bacterial growth of asaccharolytic P.gingivalis, that utilizes amino acids from extracellular proteinaceous nutrients as energy and carbon sources.<ref>PMID:21896480</ref> <ref>PMID:23246913</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 33277]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fujimoto, M]]	+	[[Category: Porphyromonas gingivalis]]
-	[[Category: Iizuka, I]]	+	[[Category: Fujimoto M]]
-	[[Category: Nonaka, T]]	+	[[Category: Iizuka I]]
-	[[Category: Ogasawara, W]]	+	[[Category: Nonaka T]]
-	[[Category: Roppongi, S]]	+	[[Category: Ogasawara W]]
-	[[Category: Sakamoto, Y]]	+	[[Category: Roppongi S]]
-	[[Category: Suzuki, Y]]	+	[[Category: Sakamoto Y]]
-	[[Category: Tanaka, N]]	+	[[Category: Suzuki Y]]
-	[[Category: Tateoka, C]]	+	[[Category: Tanaka N]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Tateoka C]]
-	~~[[Category: Wild type~~]]	+

OCA at 08:41, 5 February 2020

2020-02-05T08:41:49Z

←Older revision		Revision as of 08:41, 5 February 2020
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Dipeptidyl peptidase\|Dipeptidyl peptidase]]	+	*[[Dipeptidyl peptidase 3D structures\|Dipeptidyl peptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:03, 6 June 2019

2019-06-06T00:03:17Z

←Older revision		Revision as of 00:03, 6 June 2019
Line 1:		Line 1:

	==Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis==		==Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis==
-	<StructureSection load='4xzy' size='340' side='right' caption='[[4xzy]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='4xzy' size='340' side='right'caption='[[4xzy]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xzy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XZY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xzy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33277 Atcc 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XZY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x01\|4x01]], [[4x02\|4x02]], [[4x04\|4x04]], [[4x06\|4x06]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x01\|4x01]], [[4x02\|4x02]], [[4x04\|4x04]], [[4x06\|4x06]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EG14_04230 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=837 ATCC 33277])</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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [http://pdbe.org/4xzy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [http://www.ebi.ac.uk/pdbsum/4xzy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xzy 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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [http://pdbe.org/4xzy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [http://www.ebi.ac.uk/pdbsum/4xzy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xzy ProSAT]</span></td></tr>
	</table>		</table>
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4xzy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xzy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dipeptidyl peptidase\|Dipeptidyl peptidase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33277]]
		+	[[Category: Large Structures]]
	[[Category: Fujimoto, M]]		[[Category: Fujimoto, M]]
	[[Category: Iizuka, I]]		[[Category: Iizuka, I]]

OCA at 13:24, 19 April 2017

2017-04-19T13:24:55Z

←Older revision		Revision as of 13:24, 19 April 2017
Line 1:		Line 1:
		+
	==Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis==		==Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis==
	<StructureSection load='4xzy' size='340' side='right' caption='[[4xzy]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4xzy' size='340' side='right' caption='[[4xzy]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x01\|4x01]], [[4x02\|4x02]], [[4x04\|4x04]], [[4x06\|4x06]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x01\|4x01]], [[4x02\|4x02]], [[4x04\|4x04]], [[4x06\|4x06]]</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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [http://www.ebi.ac.uk/pdbsum/4xzy PDBsum]</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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [http://pdbe.org/4xzy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [http://www.ebi.ac.uk/pdbsum/4xzy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xzy ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4xzy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:21, 15 July 2015

2015-07-15T13:21:23Z

←Older revision		Revision as of 13:21, 15 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis==
		+	<StructureSection load='4xzy' size='340' side='right' caption='[[4xzy]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xzy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XZY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XZY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x01\|4x01]], [[4x02\|4x02]], [[4x04\|4x04]], [[4x06\|4x06]]</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=4xzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xzy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xzy RCSB], [http://www.ebi.ac.uk/pdbsum/4xzy PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double beta-barrel fold and a recently identified regulatory alpha-helical domain. Crystal structure analyses, docking studies, and biochemical studies revealed that the side chain of Arg673 in the S1 subsite is essential for recognition of the Asp/Glu side chain at the P1 position of the bound substrate. Because S46 peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we anticipate that DPP11s could be utilised as targets for antibiotics. In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms.

-	~~The entry 4xzy is ON HOLD until Paper Publication~~	+	Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.,Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Yamada M, Ohta K, Gouda H, Nonaka T, Ogasawara W, Tanaka N Sci Rep. 2015 Jun 9;5:11151. doi: 10.1038/srep11151. PMID:26057589<ref>PMID:26057589</ref>

-	~~Authors: Sakamoto~~, Y.~~, Suzuki, Y~~.~~, Iizuka, I~~.~~, Tateoka, C., Roppongi, S.,~~ Fujimoto, M~~., Nonaka, T., Ogasawara, W., Tanaka, N.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: ~~Tateoka~~, C]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Fujimoto, M]]
		+	[[Category: Iizuka, I]]
		+	[[Category: Nonaka, T]]
		+	[[Category: Ogasawara, W]]
	[[Category: Roppongi, S]]		[[Category: Roppongi, S]]
-	[[Category: Nonaka, T]]
	[[Category: Sakamoto, Y]]		[[Category: Sakamoto, Y]]
-	[[Category: ~~Ogasawara~~, ~~W]]~~	+	[[Category: Suzuki, Y]]
-	~~[[Category: Iizuka, I~~]]	+
	[[Category: Tanaka, N]]		[[Category: Tanaka, N]]
-	[[Category: ~~Suzuki~~, Y]]	+	[[Category: Tateoka, C]]
-	[[Category: ~~Fujimoto, M~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Wild type]]

OCA at 10:09, 11 March 2015

2015-03-11T10:09:59Z

←Older revision		Revision as of 10:09, 11 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xzy is ON HOLD	+	The entry 4xzy is ON HOLD until Paper Publication

	Authors: Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Nonaka, T., Ogasawara, W., Tanaka, N.		Authors: Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Nonaka, T., Ogasawara, W., Tanaka, N.

OCA: Protected "4xzy" [edit=sysop:move=sysop]

2015-02-12T10:56:03Z

Protected "4xzy" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:56, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xzy is ON HOLD Authors: Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Nonaka, T., Ogasawara, W., Tanaka, N. Descr...

2015-02-12T10:56:02Z

New page: '''Unreleased structure''' The entry 4xzy is ON HOLD Authors: Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Nonaka, T., Ogasawara, W., Tanaka, N. Descr...

New page

'''Unreleased structure'''

The entry 4xzy is ON HOLD

Authors: Sakamoto, Y., Suzuki, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Nonaka, T., Ogasawara, W., Tanaka, N.

Description:
[[Category: Unreleased Structures]]
[[Category: Tateoka, C]]
[[Category: Roppongi, S]]
[[Category: Nonaka, T]]
[[Category: Sakamoto, Y]]
[[Category: Ogasawara, W]]
[[Category: Iizuka, I]]
[[Category: Tanaka, N]]
[[Category: Suzuki, Y]]
[[Category: Fujimoto, M]]