5xsi - Revision history

OCA at 10:20, 27 March 2024

2024-03-27T10:20:16Z

←Older revision		Revision as of 10:20, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5xsi' size='340' side='right'caption='[[5xsi]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5xsi' size='340' side='right'caption='[[5xsi]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xsi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XSI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xsi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XSI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.2Å</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=5xsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsi OCA], [~~http~~://pdbe.org/5xsi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xsi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xsi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsi ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5xsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsi OCA], [https://pdbe.org/5xsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xsi RCSB], [https://www.ebi.ac.uk/pdbsum/5xsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsi ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A0U1MUE2_STAAU A0A0U1MUE2_STAAU]
-	The Asp-His-His and Asp-His-His-associated (DHH/DHHA1) domain-containing phosphodiesterases (PDEs) that catalyze degradation of cyclic di-adenosine monophosphate (c-di-AMP) could be subdivided into two subfamilies based on the final product [5'-phosphadenylyl-adenosine (5'-pApA) or AMP]. In a previous study, we revealed that Rv2837c, a stand-alone DHH/DHHA1 PDE, employs a 5'-pApA internal flipping mechanism to produce AMPs. However, why the membrane-bound DHH/DHHA1 PDE can only degrade c-di-AMP to 5'-pApA remains obscure. Here, we report the crystal structure of the DHH/DHHA1 domain of GdpP (GdpP-C), and structures in complex with c-di-AMP, cyclic di-guanosine monophosphate (c-di-GMP), and 5'-pApA. Structural analysis reveals that GdpP-C binds nucleotide substrates quite differently from how Rv2837c does in terms of substrate-binding position. Accordingly, the nucleotide-binding site of the DHH/DHHA1 PDEs is organized into three (C, G, and R) subsites. For GdpP-C, in the C and G sites c-di-AMP binds and degrades into 5'-pApA, and its G site determines nucleotide specificity. To further degrade into AMPs, 5'-pApA must slide into the C and R sites for flipping and hydrolysis as in Rv2837c. Subsequent mutagenesis and enzymatic studies of GdpP-C and Rv2837c uncover the complete flipping process and reveal a unified catalytic mechanism for members of both DHH/DHHA1 PDE subfamilies.	+
-		+
-	Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase.,Wang F, He Q, Su K, Wei T, Xu S, Gu L Biochem J. 2018 Jan 5;475(1):~~191-205. doi: 10.1042~~/~~BCJ20170739. PMID:29203646<ref>PMID:29203646</ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5xsi" 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>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gu, L~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Wang, F~~]]	+	[[Category: Gu L]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Wang F]]
-	~~[[Category: Phosphodiesterase~~]]	+

OCA at 06:58, 14 October 2020

2020-10-14T06:58:10Z

←Older revision		Revision as of 06:58, 14 October 2020
Line 1:		Line 1:

	==The catalytic domain of GdpP==		==The catalytic domain of GdpP==
-	<StructureSection load='5xsi' size='340' side='right' caption='[[5xsi]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5xsi' size='340' side='right'caption='[[5xsi]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xsi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XSI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xsi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XSI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=5xsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsi OCA], [http://pdbe.org/5xsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsi RCSB], [http://www.ebi.ac.uk/pdbsum/5xsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsi 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=5xsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsi OCA], [http://pdbe.org/5xsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsi RCSB], [http://www.ebi.ac.uk/pdbsum/5xsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 5xsi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xsi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gu, L]]		[[Category: Gu, L]]
	[[Category: Wang, F]]		[[Category: Wang, F]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Phosphodiesterase]]		[[Category: Phosphodiesterase]]

OCA at 05:54, 31 January 2018

2018-01-31T05:54:06Z

←Older revision		Revision as of 05:54, 31 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5xsi is ~~ON HOLD until Jun 14 2019~~	+	==The catalytic domain of GdpP==
		+	<StructureSection load='5xsi' size='340' side='right' caption='[[5xsi]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xsi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XSI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=5xsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsi OCA], [http://pdbe.org/5xsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsi RCSB], [http://www.ebi.ac.uk/pdbsum/5xsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Asp-His-His and Asp-His-His-associated (DHH/DHHA1) domain-containing phosphodiesterases (PDEs) that catalyze degradation of cyclic di-adenosine monophosphate (c-di-AMP) could be subdivided into two subfamilies based on the final product [5'-phosphadenylyl-adenosine (5'-pApA) or AMP]. In a previous study, we revealed that Rv2837c, a stand-alone DHH/DHHA1 PDE, employs a 5'-pApA internal flipping mechanism to produce AMPs. However, why the membrane-bound DHH/DHHA1 PDE can only degrade c-di-AMP to 5'-pApA remains obscure. Here, we report the crystal structure of the DHH/DHHA1 domain of GdpP (GdpP-C), and structures in complex with c-di-AMP, cyclic di-guanosine monophosphate (c-di-GMP), and 5'-pApA. Structural analysis reveals that GdpP-C binds nucleotide substrates quite differently from how Rv2837c does in terms of substrate-binding position. Accordingly, the nucleotide-binding site of the DHH/DHHA1 PDEs is organized into three (C, G, and R) subsites. For GdpP-C, in the C and G sites c-di-AMP binds and degrades into 5'-pApA, and its G site determines nucleotide specificity. To further degrade into AMPs, 5'-pApA must slide into the C and R sites for flipping and hydrolysis as in Rv2837c. Subsequent mutagenesis and enzymatic studies of GdpP-C and Rv2837c uncover the complete flipping process and reveal a unified catalytic mechanism for members of both DHH/DHHA1 PDE subfamilies.

-	~~Authors: Feng, W~~., ~~Lichuan~~, G.	+	Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase.,Wang F, He Q, Su K, Wei T, Xu S, Gu L Biochem J. 2018 Jan 5;475(1):191-205. doi: 10.1042/BCJ20170739. PMID:29203646<ref>PMID:29203646</ref>

-	~~Description: The catalytic domain~~ of ~~GdpP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Lichuan~~, G]]	+	<div class="pdbe-citations 5xsi" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Feng, W~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gu, L]]
		+	[[Category: Wang, F]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phosphodiesterase]]

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

2017-09-27T15:44:12Z

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

←Older revision

Revision as of 15:44, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xsi is ON HOLD until Jun 14 2019 Authors: Feng, W., Lichuan, G. Description: The catalytic domain of GdpP Category: Unreleased Structures [[Ca...

2017-09-27T15:44:10Z

New page: '''Unreleased structure''' The entry 5xsi is ON HOLD until Jun 14 2019 Authors: Feng, W., Lichuan, G. Description: The catalytic domain of GdpP Category: Unreleased Structures [[Ca...

New page

'''Unreleased structure'''

The entry 5xsi is ON HOLD until Jun 14 2019

Authors: Feng, W., Lichuan, G.

Description: The catalytic domain of GdpP
[[Category: Unreleased Structures]]
[[Category: Lichuan, G]]
[[Category: Feng, W]]