5ebb: Difference between revisions
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==Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+== | |||
<StructureSection load='5ebb' size='340' side='right'caption='[[5ebb]], [[Resolution|resolution]] 2.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ebb]] 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=5EBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EBB FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5ebb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ebb OCA], [https://pdbe.org/5ebb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ebb RCSB], [https://www.ebi.ac.uk/pdbsum/5ebb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ebb ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ASM3A_HUMAN ASM3A_HUMAN] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Human sphingomyelinase phosphodiesterase like 3a (SMPDL3a) is a secreted enzyme that shares a conserved catalytic domain with human acid sphingomyelinase (aSMase), the enzyme carrying mutations causative of Niemann Pick disease. We have solved the structure of SMPDL3a revealing a calcineurin like fold. A dimetal site, glycosylation pattern and a disulphide bond network are likely to be conserved also in human aSMase. We show that the binuclear site of SMPDL3a is occupied by two Zn2+ ions and that excess of Zn2+ leads to inhibition of enzyme activity through binding to additional sites. As an extension of recent biochemical work we uncovered that SMPDL3a catalyses the hydrolysis of several modified nucleotides that include CDP-choline, CDP-ethanolamine and ADP-ribose, but not the aSMase substrate, sphingomyelin. We subsequently determined the structure of SMPDL3a in complex with the product 5'-cytidine monophosphate (CMP), a structure that is consistent with several distinct coordination modes of the substrate/product in the active site during the reaction cycle. Based on the structure of CMP complexes, we propose a phosphoryl transfer mechanism for SMPDL3a. Finally, a homology model of human aSMase was constructed to allow for the mapping of selected Niemann Pick disease mutations on a three-dimensional framework to guide further characterisation of their effects on aSMase function. This article is protected by copyright. All rights reserved. | |||
The structure and catalytic mechanism of Human Sphingomyelin Phosphodiesterase like 3a - an acid sphingomyelinase homolog with a novel nucleotide hydrolase activity.,Lim SM, Yeung K, Tresaugues L, Ling TH, Nordlund P FEBS J. 2016 Jan 18. doi: 10.1111/febs.13655. PMID:26783088<ref>PMID:26783088</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5ebb" style="background-color:#fffaf0;"></div> | ||
[[Category: Lim | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Sphingomyelinase|Sphingomyelinase]] | ||
[[Category: | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: Lim SM]] | |||
[[Category: Nordlund P]] | |||
[[Category: Teo HL]] | |||
[[Category: Tresaugues L]] | |||
[[Category: Yeung K]] | |||
Latest revision as of 09:20, 5 July 2023
Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+
Structural highlights
FunctionPublication Abstract from PubMedHuman sphingomyelinase phosphodiesterase like 3a (SMPDL3a) is a secreted enzyme that shares a conserved catalytic domain with human acid sphingomyelinase (aSMase), the enzyme carrying mutations causative of Niemann Pick disease. We have solved the structure of SMPDL3a revealing a calcineurin like fold. A dimetal site, glycosylation pattern and a disulphide bond network are likely to be conserved also in human aSMase. We show that the binuclear site of SMPDL3a is occupied by two Zn2+ ions and that excess of Zn2+ leads to inhibition of enzyme activity through binding to additional sites. As an extension of recent biochemical work we uncovered that SMPDL3a catalyses the hydrolysis of several modified nucleotides that include CDP-choline, CDP-ethanolamine and ADP-ribose, but not the aSMase substrate, sphingomyelin. We subsequently determined the structure of SMPDL3a in complex with the product 5'-cytidine monophosphate (CMP), a structure that is consistent with several distinct coordination modes of the substrate/product in the active site during the reaction cycle. Based on the structure of CMP complexes, we propose a phosphoryl transfer mechanism for SMPDL3a. Finally, a homology model of human aSMase was constructed to allow for the mapping of selected Niemann Pick disease mutations on a three-dimensional framework to guide further characterisation of their effects on aSMase function. This article is protected by copyright. All rights reserved. The structure and catalytic mechanism of Human Sphingomyelin Phosphodiesterase like 3a - an acid sphingomyelinase homolog with a novel nucleotide hydrolase activity.,Lim SM, Yeung K, Tresaugues L, Ling TH, Nordlund P FEBS J. 2016 Jan 18. doi: 10.1111/febs.13655. PMID:26783088[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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