5i8r - Revision history

OCA at 08:26, 23 August 2023

OCA — Wed, 23 Aug 2023 08:26:54 GMT

←Older revision		Revision as of 08:26, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='5i8r' size='340' side='right'caption='[[5i8r]], [[Resolution\|resolution]] 3.65Å' scene=''>		<StructureSection load='5i8r' size='340' side='right'caption='[[5i8r]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i8r]] is a 3 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=5I8R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5I8R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i8r]] is a 3 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=5I8R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I8R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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]] 3.646Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i81\|5i81]], [[5i85\|5i85]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5i8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8r OCA], [https://pdbe.org/5i8r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i8r RCSB], [https://www.ebi.ac.uk/pdbsum/5i8r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8r ProSAT]</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~~://proteopedia.org/fgij/fg.htm?mol=5i8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8r OCA], [~~http~~://pdbe.org/5i8r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i8r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i8r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8r 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: Wei RR]]
-	[[Category: Wei~~, R R~~]]	+	[[Category: Zhou YF]]
-	[[Category: Zhou~~, Y F]]~~	+
-	~~[[Category: Acid sphingomyelinase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Olipudase alfa]]~~	+
-	~~[[Category: Zinc~~]]	+

OCA at 07:08, 3 June 2020

OCA — Wed, 03 Jun 2020 07:08:59 GMT

←Older revision		Revision as of 07:08, 3 June 2020
Line 1:		Line 1:

	==aSMase with zinc==		==aSMase with zinc==
-	<StructureSection load='5i8r' size='340' side='right' caption='[[5i8r]], [[Resolution\|resolution]] 3.65Å' scene=''>	+	<StructureSection load='5i8r' size='340' side='right'caption='[[5i8r]], [[Resolution\|resolution]] 3.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i8r]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8R OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I8R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i8r]] is a 3 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=5I8R OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I8R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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=BMA:BETA-D-MANNOSE'>BMA</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i81\|5i81]], [[5i85\|5i85]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i81\|5i81]], [[5i85\|5i85]]</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=5i8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8r OCA], [http://pdbe.org/5i8r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8r RCSB], [http://www.ebi.ac.uk/pdbsum/5i8r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8r 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=5i8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8r OCA], [http://pdbe.org/5i8r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8r RCSB], [http://www.ebi.ac.uk/pdbsum/5i8r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8r ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 23:
	</div>		</div>
	<div class="pdbe-citations 5i8r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i8r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sphingomyelinase\|Sphingomyelinase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Sphingomyelin phosphodiesterase]]		[[Category: Sphingomyelin phosphodiesterase]]
	[[Category: Wei, R R]]		[[Category: Wei, R R]]

OCA at 03:37, 10 December 2016

OCA — Sat, 10 Dec 2016 03:37:46 GMT

←Older revision		Revision as of 03:37, 10 December 2016
Line 13:		Line 13:
	== 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) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann-Pick disease types A and B. Olipudase alfa, a recombinant form of human ASM, is being developed as enzyme replacement therapy to treat the non-neurological manifestations of ASMD. Here we present the human ASM holoenzyme and product bound structures encompassing all of the functional domains. The catalytic domain has a metallophosphatase fold, and two zinc ions and one reaction product phosphocholine are identified in a histidine-rich active site. The structures reveal the underlying catalytic mechanism, in which two zinc ions activate a water molecule for nucleophilic attack of the phosphodiester bond. Docking of sphingomyelin provides a model that allows insight into the selectivity of the enzyme and how the ASM domains collaborate to complete hydrolysis. Mapping of known mutations provides a basic understanding on correlations between enzyme dysfunction and phenotypes observed in ASMD patients.
		+
		+	Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.,Zhou YF, Metcalf MC, Garman SC, Edmunds T, Qiu H, Wei RR Nat Commun. 2016 Oct 11;7:13082. doi: 10.1038/ncomms13082. PMID:27725636<ref>PMID:27725636</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5i8r" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:07, 10 September 2016

OCA — Sat, 10 Sep 2016 21:07:56 GMT

←Older revision		Revision as of 21:07, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i8r is ~~ON HOLD~~	+	==aSMase with zinc==
-		+	<StructureSection load='5i8r' size='340' side='right' caption='[[5i8r]], [[Resolution\|resolution]] 3.65Å' scene=''>
-	~~Authors~~: ~~Zhou~~, Y.F., ~~Wei~~, R.R.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5i8r]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I8R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I8R FirstGlance]. <br>
-	~~Description~~: ~~aSMase with zinc~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i81\|5i81]], [[5i85\|5i85]]</td></tr>
-	[[Category: Wei, R.R]]	+	<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>
-	[[Category: Zhou, Y.F]]	+	<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=5i8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i8r OCA], [http://pdbe.org/5i8r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i8r RCSB], [http://www.ebi.ac.uk/pdbsum/5i8r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i8r 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: Wei, R R]]
		+	[[Category: Zhou, Y F]]
		+	[[Category: Acid sphingomyelinase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Olipudase alfa]]
		+	[[Category: Zinc]]

OCA: Protected "5i8r" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2016 13:32:00 GMT

Protected "5i8r" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:32, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5i8r is ON HOLD Authors: Zhou, Y.F., Wei, R.R. Description: aSMase with zinc Category: Unreleased Structures Category: Wei, R.R [[Category:...

OCA — Wed, 02 Mar 2016 13:31:58 GMT

New page: '''Unreleased structure''' The entry 5i8r is ON HOLD Authors: Zhou, Y.F., Wei, R.R. Description: aSMase with zinc Category: Unreleased Structures Category: Wei, R.R [[Category:...

New page

'''Unreleased structure'''

The entry 5i8r is ON HOLD

Authors: Zhou, Y.F., Wei, R.R.

Description: aSMase with zinc
[[Category: Unreleased Structures]]
[[Category: Wei, R.R]]
[[Category: Zhou, Y.F]]