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5jg8

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Revision as of 07:47, 10 June 2020

Crystal structure of human acid sphingomyelinase

Structural highlights

5jg8 is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Gene:	SMPD1, ASM (HUMAN)
Activity:	Sphingomyelin phosphodiesterase, with EC number 3.1.4.12
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[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

[ASM_HUMAN] Converts sphingomyelin to ceramide (PubMed:1840600, PubMed:18815062). Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol.^[1] ^[2] Isoform 2 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.^[3] Isoform 3 lacks residues that bind the cofactor Zn(2+) and has no enzyme activity.^[4]

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^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schuchman EH, Suchi M, Takahashi T, Sandhoff K, Desnick RJ. Human acid sphingomyelinase. Isolation, nucleotide sequence and expression of the full-length and alternatively spliced cDNAs. J Biol Chem. 1991 May 5;266(13):8531-9. PMID:1840600
↑ Jones I, He X, Katouzian F, Darroch PI, Schuchman EH. Characterization of common SMPD1 mutations causing types A and B Niemann-Pick disease and generation of mutation-specific mouse models. Mol Genet Metab. 2008 Nov;95(3):152-62. doi: 10.1016/j.ymgme.2008.08.004. Epub, 2008 Sep 23. PMID:18815062 doi:http://dx.doi.org/10.1016/j.ymgme.2008.08.004
↑ Schuchman EH, Suchi M, Takahashi T, Sandhoff K, Desnick RJ. Human acid sphingomyelinase. Isolation, nucleotide sequence and expression of the full-length and alternatively spliced cDNAs. J Biol Chem. 1991 May 5;266(13):8531-9. PMID:1840600
↑ Schuchman EH, Suchi M, Takahashi T, Sandhoff K, Desnick RJ. Human acid sphingomyelinase. Isolation, nucleotide sequence and expression of the full-length and alternatively spliced cDNAs. J Biol Chem. 1991 May 5;266(13):8531-9. PMID:1840600
↑ Xiong ZJ, Huang J, Poda G, Pomes R, Prive GG. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis. J Mol Biol. 2016 Jun 24. pii: S0022-2836(16)30220-0. doi:, 10.1016/j.jmb.2016.06.012. PMID:27349982 doi:http://dx.doi.org/10.1016/j.jmb.2016.06.012

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5jg8"

@@ Line 1: / Line 1: @@
 ==Crystal structure of human acid sphingomyelinase==
-<StructureSection load='5jg8' size='340' side='right' caption='[[5jg8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='5jg8' size='340' side='right'caption='[[5jg8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == 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='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>
 == Disease ==
@@ Line 28: / Line 29: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Sphingomyelin phosphodiesterase]]
 [[Category: Prive, G G]]

5jg8

From Proteopedia

Revision as of 07:47, 10 June 2020

Crystal structure of human acid sphingomyelinase

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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