5jg8 - Revision history

OCA at 11:02, 6 September 2023

OCA — Wed, 06 Sep 2023 11:02:58 GMT

←Older revision		Revision as of 11:02, 6 September 2023
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	<StructureSection load='5jg8' size='340' side='right'caption='[[5jg8]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5jg8' size='340' side='right'caption='[[5jg8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jg8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JG8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JG8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jg8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JG8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.8Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SMPD1, ASM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=5jg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jg8 OCA], [https://pdbe.org/5jg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jg8 RCSB], [https://www.ebi.ac.uk/pdbsum/5jg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jg8 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=5jg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jg8 OCA], [~~http~~://pdbe.org/5jg8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jg8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jg8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jg8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/ASM_HUMAN ASM_HUMAN]] Niemann-Pick disease type A;Niemann-Pick disease type B. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/ASM_HUMAN ASM_HUMAN] Niemann-Pick disease type A;Niemann-Pick disease type B. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ASM_HUMAN ASM_HUMAN]] Converts sphingomyelin to ceramide (PubMed:1840600, PubMed:18815062). Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.<ref>PMID:1840600</ref> <ref>PMID:18815062</ref> Isoform 2 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref> Isoform 3 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref>	+	[https://www.uniprot.org/uniprot/ASM_HUMAN ASM_HUMAN] Converts sphingomyelin to ceramide (PubMed:1840600, PubMed:18815062). Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.<ref>PMID:1840600</ref> <ref>PMID:18815062</ref> Isoform 2 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref> Isoform 3 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref>
	<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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Sphingomyelin phosphodiesterase]]~~	+	[[Category: Prive GG]]
-	[[Category: Prive~~, G G~~]]	+	[[Category: Xiong ZJ]]
-	[[Category: Xiong~~, Z J]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lysosomal hydrolase]]~~	+
-	~~[[Category: Neimann-pick disease]]~~	+
-	~~[[Category: Saposin]]~~	+
-	~~[[Category: Sphingolipid~~]]	+

OCA at 07:47, 10 June 2020

OCA — Wed, 10 Jun 2020 07:47:53 GMT

←Older revision		Revision as of 07:47, 10 June 2020
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	==Crystal structure of human acid sphingomyelinase==		==Crystal structure of human acid sphingomyelinase==
-	<StructureSection load='5jg8' size='340' side='right' caption='[[5jg8]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5jg8' size='340' side='right'caption='[[5jg8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jg8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JG8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JG8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jg8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JG8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JG8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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">SMPD1, ASM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=5jg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jg8 OCA], [http://pdbe.org/5jg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jg8 RCSB], [http://www.ebi.ac.uk/pdbsum/5jg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jg8 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=5jg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jg8 OCA], [http://pdbe.org/5jg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jg8 RCSB], [http://www.ebi.ac.uk/pdbsum/5jg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jg8 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 28:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]
	[[Category: Prive, G G]]		[[Category: Prive, G G]]

OCA at 05:20, 9 September 2016

OCA — Fri, 09 Sep 2016 05:20:14 GMT

←Older revision		Revision as of 05:20, 9 September 2016
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5jg8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jg8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sphingomyelinase\|Sphingomyelinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:02, 13 July 2016

OCA — Wed, 13 Jul 2016 18:02:40 GMT

←Older revision		Revision as of 18:02, 13 July 2016
Line 12:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ASM_HUMAN ASM_HUMAN]] Converts sphingomyelin to ceramide (PubMed:1840600, PubMed:18815062). Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.<ref>PMID:1840600</ref> <ref>PMID:18815062</ref> Isoform 2 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref> Isoform 3 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref>		[[http://www.uniprot.org/uniprot/ASM_HUMAN ASM_HUMAN]] Converts sphingomyelin to ceramide (PubMed:1840600, PubMed:18815062). Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.<ref>PMID:1840600</ref> <ref>PMID:18815062</ref> Isoform 2 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref> Isoform 3 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Acid sphingomyelinase (ASM) is a lysosomal phosphodiesterase that catalyzes the hydrolysis of sphingomyelin to produce ceramide and phosphocholine. While other lysosomal sphingolipid hydrolases require a saposin activator protein for full activity, the ASM polypeptide incorporates a built-in N-terminal saposin domain and does not require an external activator protein. Here, we report the crystal structure of human ASM and describe the organization of the three main regions of the enzyme: the N-terminal saposin domain, the proline-rich connector, and the catalytic domain. The saposin domain is tightly associated along an edge of the large, bowl-shaped catalytic domain and adopts an open form that exposes a hydrophobic concave surface approximately 30A from the catalytic center. The calculated electrostatic potential of the enzyme is electropositive at the acidic pH of the lysosome, consistent with the strict requirement for the presence of acidic lipids in target membranes. Docking studies indicate that sphingomyelin binds with the ceramide-phosphate group positioned at the binuclear zinc center and molecular dynamic simulations indicate that the intrinsic flexibility of the saposin domain is important for monomer-dimer exchange and for membrane interactions. Overall, ASM uses a combination of electrostatic and hydrophobic interactions to cause local disruptions of target bilayers in order to bring the lipid headgroup to the catalytic center in a membrane-bound reaction.
		+
		+	Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis.,Xiong ZJ, Huang J, Poda G, Pomes R, Prive GG J Mol Biol. 2016 Jun 24. pii: S0022-2836(16)30220-0. doi:, 10.1016/j.jmb.2016.06.012. PMID:27349982<ref>PMID:27349982</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jg8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:07, 13 July 2016

OCA — Wed, 13 Jul 2016 03:07:09 GMT

←Older revision		Revision as of 03:07, 13 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~5jg8~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of human acid sphingomyelinase==
-		+	<StructureSection load='5jg8' size='340' side='right' caption='[[5jg8]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jg8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JG8 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=5jg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jg8 OCA], [http://pdbe.org/5jg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jg8 RCSB], [http://www.ebi.ac.uk/pdbsum/5jg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jg8 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/ASM_HUMAN ASM_HUMAN]] Niemann-Pick disease type A;Niemann-Pick disease type B. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ASM_HUMAN ASM_HUMAN]] Converts sphingomyelin to ceramide (PubMed:1840600, PubMed:18815062). Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.<ref>PMID:1840600</ref> <ref>PMID:18815062</ref> Isoform 2 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref> Isoform 3 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.<ref>PMID:1840600</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Sphingomyelin phosphodiesterase]]
		+	[[Category: Prive, G G]]
		+	[[Category: Xiong, Z J]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lysosomal hydrolase]]
		+	[[Category: Neimann-pick disease]]
		+	[[Category: Saposin]]
		+	[[Category: Sphingolipid]]

OCA at 15:23, 15 May 2016

OCA — Sun, 15 May 2016 15:23:05 GMT

←Older revision		Revision as of 15:23, 15 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jg8 is ON HOLD	+	The entry 5jg8 is ON HOLD until Paper Publication

-	Authors: ~~XIONG, Z.J., Prive, G.G.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Prive, G.G]]
-	[[Category: Xiong, Z.J]]

OCA: Protected "5jg8" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 02:00:27 GMT

Protected "5jg8" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:00, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jg8 is ON HOLD Authors: XIONG, Z.J., Prive, G.G. Description: Category: Unreleased Structures Category: Prive, G.G [[Category: Xiong, Z.J...

OCA — Wed, 11 May 2016 02:00:25 GMT

New page: '''Unreleased structure''' The entry 5jg8 is ON HOLD Authors: XIONG, Z.J., Prive, G.G. Description: Category: Unreleased Structures Category: Prive, G.G [[Category: Xiong, Z.J...

New page

'''Unreleased structure'''

The entry 5jg8 is ON HOLD

Authors: XIONG, Z.J., Prive, G.G.

Description:
[[Category: Unreleased Structures]]
[[Category: Prive, G.G]]
[[Category: Xiong, Z.J]]