5xgw - Revision history

OCA at 10:18, 27 March 2024

2024-03-27T10:18:32Z

←Older revision		Revision as of 10:18, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5xgw' size='340' side='right'caption='[[5xgw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5xgw' size='340' side='right'caption='[[5xgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xgw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XGW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xgw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Colwellia_psychrerythraea_34H Colwellia psychrerythraea 34H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XGW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5xgx\|5xgx]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5xgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgw OCA], [~~http~~://pdbe.org/5xgw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xgw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xgw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgw 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=5xgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgw OCA], [https://pdbe.org/5xgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xgw RCSB], [https://www.ebi.ac.uk/pdbsum/5xgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q484B6_COLP3 Q484B6_COLP3]] Catalyzes the hydrolytic cleavage of a subset of L-isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins damaged by L-isoaspartyl residues formation.[PIRNR:PIRNR001238]	+	[https://www.uniprot.org/uniprot/Q484B6_COLP3 Q484B6_COLP3] Catalyzes the hydrolytic cleavage of a subset of L-isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins damaged by L-isoaspartyl residues formation.[PIRNR:PIRNR001238]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the beta-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with beta-isoaspartyl lysine, at 1.85-A and 2.33-A resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site. A structural comparison with Escherichia coli isoaspartyl dipeptidase (EcoIadA) revealed a major difference in the structure of the active site. For metal ion coordination, CpsIadA has a Glu166 residue in the active site, whereas EcoIadA has a post-translationally carbamylated-lysine 162 residue. Site-directed mutagenesis studies confirmed that the Glu166 residue is critical for CpsIadA enzymatic activity. This residue substitution from lysine to glutamate induces the protrusion of the beta12-alpha8 loop into the active site to compensate for the loss of length of the side chain. In addition, the alpha3-beta9 loop of CpsIadA adopts a different conformation compared to EcoIadA, which induces a change in the structure of the substrate-binding pocket. Despite CpsIadA having a different active-site residue composition and substrate-binding pocket, there is only a slight difference in CpsIadA substrate specificity compared with EcoIadA. Comparative sequence analysis classified IadA-containing bacteria and archaea into two groups based on the active-site residue composition, with Type I IadAs having a glutamate residue and Type II IadAs having a carbamylated-lysine residue. CpsIadA has maximal activity at pH 8-8.5 and 45 degrees C, and was completely inactivated at 60 degrees C. Despite being isolated from a psychrophilic bacteria, CpsIadA is thermostable probably owing to its octameric structure. This is the first conclusive description of the structure and properties of a Type I IadA.	+
-		+
-	Crystal structure and functional characterization of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea strain 34H.,Park SH, Lee CW, Lee SG, Shin SC, Kim HJ, Park H, Lee JH PLoS One. 2017 Jul 19;12(7):e0181705. doi: 10.1371/journal.pone.0181705., eCollection 2017. PMID:28723955<ref>PMID:28723955</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5xgw" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Isoaspartyl dipeptidase\|Isoaspartyl dipeptidase]]		*[[Isoaspartyl dipeptidase\|Isoaspartyl dipeptidase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Colwellia psychrerythraea 34H]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lee~~, C W~~]]	+	[[Category: Lee CW]]
-	[[Category: Lee~~, J H~~]]	+	[[Category: Lee JH]]
-	[[Category: Park~~, S H]]~~	+	[[Category: Park SH]]
-	~~[[Category: Colwellia psychrerythraea]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Iada]]~~	+
-	~~[[Category: Isoaspartyl dipeptidase~~]]	+

OCA at 06:49, 14 October 2020

2020-10-14T06:49:26Z

←Older revision		Revision as of 06:49, 14 October 2020
Line 1:		Line 1:

	==Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H==		==Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H==
-	<StructureSection load='5xgw' size='340' side='right' caption='[[5xgw]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5xgw' size='340' side='right'caption='[[5xgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xgw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XGW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xgw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XGW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xgx\|5xgx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xgx\|5xgx]]</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=5xgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgw OCA], [http://pdbe.org/5xgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xgw RCSB], [http://www.ebi.ac.uk/pdbsum/5xgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgw 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=5xgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgw OCA], [http://pdbe.org/5xgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xgw RCSB], [http://www.ebi.ac.uk/pdbsum/5xgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5xgw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xgw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Isoaspartyl dipeptidase\|Isoaspartyl dipeptidase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lee, C W]]		[[Category: Lee, C W]]
	[[Category: Lee, J H]]		[[Category: Lee, J H]]

OCA at 05:41, 20 June 2018

2018-06-20T05:41:28Z

←Older revision		Revision as of 05:41, 20 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xgw is ~~ON HOLD~~	+	==Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H==
		+	<StructureSection load='5xgw' size='340' side='right' caption='[[5xgw]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xgw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XGW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xgx\|5xgx]]</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=5xgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgw OCA], [http://pdbe.org/5xgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xgw RCSB], [http://www.ebi.ac.uk/pdbsum/5xgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q484B6_COLP3 Q484B6_COLP3]] Catalyzes the hydrolytic cleavage of a subset of L-isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins damaged by L-isoaspartyl residues formation.[PIRNR:PIRNR001238]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the beta-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with beta-isoaspartyl lysine, at 1.85-A and 2.33-A resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site. A structural comparison with Escherichia coli isoaspartyl dipeptidase (EcoIadA) revealed a major difference in the structure of the active site. For metal ion coordination, CpsIadA has a Glu166 residue in the active site, whereas EcoIadA has a post-translationally carbamylated-lysine 162 residue. Site-directed mutagenesis studies confirmed that the Glu166 residue is critical for CpsIadA enzymatic activity. This residue substitution from lysine to glutamate induces the protrusion of the beta12-alpha8 loop into the active site to compensate for the loss of length of the side chain. In addition, the alpha3-beta9 loop of CpsIadA adopts a different conformation compared to EcoIadA, which induces a change in the structure of the substrate-binding pocket. Despite CpsIadA having a different active-site residue composition and substrate-binding pocket, there is only a slight difference in CpsIadA substrate specificity compared with EcoIadA. Comparative sequence analysis classified IadA-containing bacteria and archaea into two groups based on the active-site residue composition, with Type I IadAs having a glutamate residue and Type II IadAs having a carbamylated-lysine residue. CpsIadA has maximal activity at pH 8-8.5 and 45 degrees C, and was completely inactivated at 60 degrees C. Despite being isolated from a psychrophilic bacteria, CpsIadA is thermostable probably owing to its octameric structure. This is the first conclusive description of the structure and properties of a Type I IadA.

-	~~Authors: Lee, J.H~~., Lee, ~~C.W.~~, Park, S.H.	+	Crystal structure and functional characterization of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea strain 34H.,Park SH, Lee CW, Lee SG, Shin SC, Kim HJ, Park H, Lee JH PLoS One. 2017 Jul 19;12(7):e0181705. doi: 10.1371/journal.pone.0181705., eCollection 2017. PMID:28723955<ref>PMID:28723955</ref>

-	~~Description: Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Lee, C.W]]	+	<div class="pdbe-citations 5xgw" style="background-color:#fffaf0;"></div>
-	[[Category: Lee, J.H]]	+	== References ==
-	[[Category: Park, S.H]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lee, C W]]
		+	[[Category: Lee, J H]]
		+	[[Category: Park, S H]]
		+	[[Category: Colwellia psychrerythraea]]
		+	[[Category: Hydrolase]]
		+	[[Category: Iada]]
		+	[[Category: Isoaspartyl dipeptidase]]

OCA at 15:27, 27 September 2017

2017-09-27T15:27:53Z

←Older revision		Revision as of 15:27, 27 September 2017
Line 7:		Line 7:
	Description: Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H		Description: Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Park, S.H]]
	[[Category: Lee, C.W]]		[[Category: Lee, C.W]]
	[[Category: Lee, J.H]]		[[Category: Lee, J.H]]
		+	[[Category: Park, S.H]]

OCA at 12:11, 4 May 2017

2017-05-04T12:11:17Z

←Older revision		Revision as of 12:11, 4 May 2017
Line 3:		Line 3:
	The entry 5xgw is ON HOLD		The entry 5xgw is ON HOLD

-	Authors: Lee. J.H., Lee. C.W., Park. S.H.	+	Authors: Lee, J.H., Lee, C.W., Park, S.H.

	Description: Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H		Description: Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Park. S.H]]	+	[[Category: Park, S.H]]
-	[[Category: Lee. ~~J.H~~]]	+	[[Category: Lee, C.W]]
-	[[Category: Lee. ~~C.W~~]]	+	[[Category: Lee, J.H]]

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

2017-04-27T13:03:59Z

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

←Older revision

Revision as of 13:03, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xgw is ON HOLD Authors: Lee. J.H., Lee. C.W., Park. S.H. Description: Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H [[Category...

2017-04-27T13:03:58Z

New page: '''Unreleased structure''' The entry 5xgw is ON HOLD Authors: Lee. J.H., Lee. C.W., Park. S.H. Description: Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H [[Category...

New page

'''Unreleased structure'''

The entry 5xgw is ON HOLD

Authors: Lee. J.H., Lee. C.W., Park. S.H.

Description: Isoaspartyl dipeptidase from Colwellia psychrerythraea strain 34H
[[Category: Unreleased Structures]]
[[Category: Park. S.H]]
[[Category: Lee. J.H]]
[[Category: Lee. C.W]]