5udy: Difference between revisions

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<StructureSection load='5udy' size='340' side='right'caption='[[5udy]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='5udy' size='340' side='right'caption='[[5udy]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5udy]] is a 1 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=5UDY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UDY FirstGlance]. <br>
<table><tr><td colspan='2'>[[5udy]] is a 1 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=5UDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UDY FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.6&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ENPP7, UNQ3077/PRO9912 ([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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5udy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udy OCA], [https://pdbe.org/5udy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5udy RCSB], [https://www.ebi.ac.uk/pdbsum/5udy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5udy 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=5udy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5udy OCA], [http://pdbe.org/5udy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5udy RCSB], [http://www.ebi.ac.uk/pdbsum/5udy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5udy ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/ENPP7_HUMAN ENPP7_HUMAN]] Converts sphingomyelin to ceramide. Also has phospholipase C activity toward palmitoyl lyso-phosphocholine. Does not appear to have nucleotide pyrophosphatase activity.<ref>PMID:12885774</ref>
[https://www.uniprot.org/uniprot/ENPP7_HUMAN ENPP7_HUMAN] Converts sphingomyelin to ceramide. Also has phospholipase C activity toward palmitoyl lyso-phosphocholine. Does not appear to have nucleotide pyrophosphatase activity.<ref>PMID:12885774</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: Gorelik A]]
[[Category: Gorelik, A]]
[[Category: Illes K]]
[[Category: Illes, K]]
[[Category: Liu F]]
[[Category: Liu, F]]
[[Category: Nagar B]]
[[Category: Nagar, B]]
[[Category: Hydrolase]]
[[Category: Sphingomyelin]]
[[Category: Sphingomyelinase]]

Latest revision as of 13:53, 30 October 2024

Human alkaline sphingomyelinase (alk-SMase, ENPP7, NPP7)Human alkaline sphingomyelinase (alk-SMase, ENPP7, NPP7)

Structural highlights

5udy is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENPP7_HUMAN Converts sphingomyelin to ceramide. Also has phospholipase C activity toward palmitoyl lyso-phosphocholine. Does not appear to have nucleotide pyrophosphatase activity.[1]

Publication Abstract from PubMed

Absorption of dietary sphingomyelin (SM) requires its initial degradation into ceramide, a process catalyzed by the intestinal enzyme alkaline sphingomyelinase (alk-SMase, NPP7, ENPP7). Alk-SMase belongs to the nucleotide pyrophosphatase / phosphodiesterase family, the members of which hydrolyze nucleoside phosphates, phospholipids and other related molecules. NPP7 is the only paralog that can cleave SM, and its activity requires the presence of bile salts, a class of physiological anionic detergents. To elucidate the mechanism of substrate recognition, we determined the crystal structure of human alk-SMase in complex with phosphocholine, a reaction product. Although the overall fold and catalytic center is conserved relative to other NPPs, alk-SMase recognizes the choline moiety of its substrates via an NPP7-specific aromatic box composed of tyrosine residues. Mutational analysis and enzymatic activity assays identified features on the surface of the protein - a cationic patch and a unique hydrophobic loop - that are essential for accessing SM in bile salt micelles. These results shed new light on substrate specificity determinants within the NPP enzyme family.

Crystal Structure of the Human Alkaline Sphingomyelinase Provides Insights into Substrate Recognition.,Gorelik A, Liu F, Illes K, Nagar B J Biol Chem. 2017 Mar 14. pii: jbc.M116.769273. doi: 10.1074/jbc.M116.769273. PMID:28292932[2]

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

See Also

References

  1. ↑ Duan RD, Bergman T, Xu N, Wu J, Cheng Y, Duan J, Nelander S, Palmberg C, Nilsson A. Identification of human intestinal alkaline sphingomyelinase as a novel ecto-enzyme related to the nucleotide phosphodiesterase family. J Biol Chem. 2003 Oct 3;278(40):38528-36. Epub 2003 Jul 28. PMID:12885774 doi:http://dx.doi.org/10.1074/jbc.M305437200
  2. ↑ Gorelik A, Liu F, Illes K, Nagar B. Crystal Structure of the Human Alkaline Sphingomyelinase Provides Insights into Substrate Recognition. J Biol Chem. 2017 Mar 14. pii: jbc.M116.769273. doi: 10.1074/jbc.M116.769273. PMID:28292932 doi:http://dx.doi.org/10.1074/jbc.M116.769273

5udy, resolution 2.60Å

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