6cpu - Revision history

OCA at 14:29, 13 March 2024

2024-03-13T14:29:44Z

← Older revision		Revision as of 14:29, 13 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CPU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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]] 1.8Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [https://pdbe.org/6cpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [https://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu 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=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [https://pdbe.org/6cpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [https://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q8NJP9_CANAX Q8NJP9_CANAX]		[https://www.uniprot.org/uniprot/Q8NJP9_CANAX Q8NJP9_CANAX]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The cAMP signaling system plays important roles in the physiological processes of pathogen yeast Candida albicans, but its functional mechanism has not been well illustrated. Here, we report the enzymatic characterization and crystal structures of C. albicans phosphodiesterase 2 (caPDE2) in the unliganded and 3-isobutyl-1-methylxanthine-complexed forms. caPDE2 is a monomer in liquid and crystal states and specifically hydrolyzes cAMP with a KM of 35 nM. It does not effectively hydrolyze cGMP as shown by the 1.32 x 10(5)-fold specificity of cAMP/cGMP. The crystal structure of caPDE2 shows significant differences from those of human PDEs. First, the N-terminal fragment of caPDE2 (residues 1-201) tightly associates with the catalytic domain to form a rigid molecular entity, implying its stable molecular conformation for C. albicans to resist environmental stresses. Second, the M-loop, a critical fragment for binding of the substrate and inhibitors to human PDEs, is not a part of the caPDE2 active site. This feature of caPDE2 may provide a structural basis for the design of selective inhibitors for the treatment of yeast infection.

	Crystal Structures of Candida albicans Phosphodiesterase 2 and Implications for Its Biological Functions.,Yao T, Huang Y, Zhang M, Chen Y, Pei H, Shi J, Wang H, Wang Y, Ke H Biochemistry. 2018 Oct 23;57(42):6070-6077. doi: 10.1021/acs.biochem.8b00707., Epub 2018 Oct 4. PMID:30231198<ref>PMID:30231198</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6cpu" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]		*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:31, 30 September 2022

2022-09-30T04:31:49Z

← Older revision		Revision as of 04:31, 30 September 2022
Line 3:		Line 3:
	<StructureSection load='6cpu' size='340' side='right'caption='[[6cpu]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6cpu' size='340' side='right'caption='[[6cpu]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_11006_[[monilia_stellatoidea]] Atcc 11006 [[monilia stellatoidea]]~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Candida_albicans Candida albicans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CPU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5476 ATCC 11006 [[Monilia stellatoidea]]])</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=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [https://pdbe.org/6cpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [https://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu 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=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [~~http~~://pdbe.org/6cpu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q8NJP9_CANAX Q8NJP9_CANAX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Candida albicans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ke, H]]		[[Category: Ke H]]
	[[Category: Wang, y]]		[[Category: Wang y]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Yeast phosphodiesterase-2~~]]

OCA at 10:49, 1 January 2020

2020-01-01T10:49:07Z

← Older revision		Revision as of 10:49, 1 January 2020
Line 3:		Line 3:
	<StructureSection load='6cpu' size='340' side='right'caption='[[6cpu]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6cpu' size='340' side='right'caption='[[6cpu]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11006_[[~~candida_stellatoidea~~]] Atcc 11006 [[~~candida~~ stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11006_[[monilia_stellatoidea]] Atcc 11006 [[monilia stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CPU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5476 ATCC 11006 [[~~Candida~~ stellatoidea]]])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5476 ATCC 11006 [[Monilia stellatoidea]]])</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=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [http://pdbe.org/6cpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [http://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu 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=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [http://pdbe.org/6cpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [http://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The cAMP signaling system plays important roles in the physiological processes of pathogen yeast Candida albicans, but its functional mechanism has not been well illustrated. Here, we report the enzymatic characterization and crystal structures of C. albicans phosphodiesterase 2 (caPDE2) in the unliganded and 3-isobutyl-1-methylxanthine-complexed forms. caPDE2 is a monomer in liquid and crystal states and specifically hydrolyzes cAMP with a KM of 35 nM. It does not effectively hydrolyze cGMP as shown by the 1.32 x 10(5)-fold specificity of cAMP/cGMP. The crystal structure of caPDE2 shows significant differences from those of human PDEs. First, the N-terminal fragment of caPDE2 (residues 1-201) tightly associates with the catalytic domain to form a rigid molecular entity, implying its stable molecular conformation for C. albicans to resist environmental stresses. Second, the M-loop, a critical fragment for binding of the substrate and inhibitors to human PDEs, is not a part of the caPDE2 active site. This feature of caPDE2 may provide a structural basis for the design of selective inhibitors for the treatment of yeast infection.

			Crystal Structures of Candida albicans Phosphodiesterase 2 and Implications for Its Biological Functions.,Yao T, Huang Y, Zhang M, Chen Y, Pei H, Shi J, Wang H, Wang Y, Ke H Biochemistry. 2018 Oct 23;57(42):6070-6077. doi: 10.1021/acs.biochem.8b00707., Epub 2018 Oct 4. PMID:30231198<ref>PMID:30231198</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6cpu" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:46, 10 April 2019

2019-04-10T07:46:17Z

← Older revision		Revision as of 07:46, 10 April 2019
Line 1:		Line 1:

	==Crystal structure of yeast caPDE2==		==Crystal structure of yeast caPDE2==
	<StructureSection load='6cpu' size='340' side='right' caption='[[6cpu]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6cpu' size='340' side='right'caption='[[6cpu]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11006_[[candida_stellatoidea]] Atcc 11006 [[candida stellatoidea]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CPU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5476 ATCC 11006 [[Candida stellatoidea]]])</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=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [http://pdbe.org/6cpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [http://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu 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=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [http://pdbe.org/6cpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [http://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Ke, H]]		[[Category: Ke, H]]
	[[Category: Wang, y]]		[[Category: Wang, y]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Yeast phosphodiesterase-2]]		[[Category: Yeast phosphodiesterase-2]]

OCA at 06:37, 21 February 2019

2019-02-21T06:37:09Z

← Older revision		Revision as of 06:37, 21 February 2019
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6cpu ~~is ON HOLD until Paper Publication~~		==Crystal structure of yeast caPDE2==
			<StructureSection load='6cpu' size='340' side='right' caption='[[6cpu]], [[Resolution\|resolution]] 1.80Å' scene=''>
	~~Authors~~: ~~Ke, H~~.~~, Wang, y~~.		== Structural highlights ==
			<table><tr><td colspan='2'>[[6cpu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CPU FirstGlance]. <br>
	~~Description~~: ~~Crystal structure of yeast caPDE2~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	[[~~Category~~: ~~Unreleased Structures~~]]		<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=6cpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cpu OCA], [http://pdbe.org/6cpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cpu RCSB], [http://www.ebi.ac.uk/pdbsum/6cpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cpu ProSAT]</span></td></tr>
	[[~~Category~~: ~~Wang~~, Y]]		</table>
			__TOC__
			</StructureSection>
	[[Category: Ke, H]]		[[Category: Ke, H]]
			[[Category: Wang, y]]
			[[Category: Hydrolase]]
			[[Category: Yeast phosphodiesterase-2]]

OCA at 12:25, 11 April 2018

2018-04-11T12:25:48Z

← Older revision		Revision as of 12:25, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6cpu is ON HOLD		The entry 6cpu is ON HOLD until Paper Publication

	Authors: Ke, H., Wang, y.		Authors: Ke, H., Wang, y.

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

2018-03-21T06:13:27Z

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

← Older revision	Revision as of 06:13, 21 March 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6cpu is ON HOLD Authors: Ke, H., Wang, y. Description: Crystal structure of yeast caPDE2 Category: Unreleased Structures Category: Wang, Y ...

2018-03-21T06:13:26Z

New page: '''Unreleased structure''' The entry 6cpu is ON HOLD Authors: Ke, H., Wang, y. Description: Crystal structure of yeast caPDE2 Category: Unreleased Structures Category: Wang, Y ...

New page

'''Unreleased structure'''

The entry 6cpu is ON HOLD

Authors: Ke, H., Wang, y.

Description: Crystal structure of yeast caPDE2
[[Category: Unreleased Structures]]
[[Category: Wang, Y]]
[[Category: Ke, H]]