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| | <StructureSection load='7cne' size='340' side='right'caption='[[7cne]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='7cne' size='340' side='right'caption='[[7cne]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7cne]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_griseocarneus"_benedict_et_al._1950 "streptomyces griseocarneus" benedict et al. 1950]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wcx 3wcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CNE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7cne]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseocarneus Streptomyces griseocarneus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wcx 3wcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">smc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=51201 "Streptomyces griseocarneus" Benedict et al. 1950])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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=7cne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cne OCA], [https://pdbe.org/7cne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cne RCSB], [https://www.ebi.ac.uk/pdbsum/7cne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cne 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=7cne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cne OCA], [http://pdbe.org/7cne PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cne RCSB], [http://www.ebi.ac.uk/pdbsum/7cne PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cne ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A6P7M9_9ACTN A6P7M9_9ACTN] |
| | <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: Streptomyces griseocarneus benedict et al. 1950]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Sphingomyelin phosphodiesterase]] | |
| - | [[Category: Fujisawa, I]] | |
| - | [[Category: Murayama, K]] | |
| - | [[Category: Sugimori, D]] | |
| - | [[Category: Hydrolase]] | |
| - | [[Category: Metal-binding site]] | |
| - | [[Category: Sphingomyelinase c]] | |
| | [[Category: Streptomyces griseocarneus]] | | [[Category: Streptomyces griseocarneus]] |
| | + | [[Category: Fujisawa I]] |
| | + | [[Category: Murayama K]] |
| | + | [[Category: Sugimori D]] |
| Structural highlights
Function
A6P7M9_9ACTN
Publication Abstract from PubMed
Sphingomyelinase C (SMC) hydrolyzes sphingomyelin to ceramide and phosphocholine. Prokaryotic SMCs share sequence homology with mammalian SMCs that have enzymatic pH optima at neutral pH. SMC from the nonpathogenic prokaryote Streptomyces griseocarneus shows notable enzymatic features such as higher optimum pH and thermostability than other prokaryotic SMCs. Determination of the three-dimensional structure of S. griseocarneus-SMC (Sg-SMC) and comparison with other SMC structures represents a promising strategy to elucidate the unique enzymatic features of Sg-SMC on a structural basis. Therefore, we determined the crystal structure of Sg-SMC at 2.0 A resolution by X-ray crystallography. Comparison of the Sg-SMC structure with three other structurally known SMCs from Listeria ivanovii, Bacillus cereus, and Staphylococcus aureus indicated that Sg-SMC is more diverse in sequence and that structural differences in the main chain between these SMCs are primarily located on the molecular surface distant from the active site. Comparison of the surface area of the four SMCs revealed that Sg-SMC has the most compact structure, which may contribute to the enhanced thermostability of Sg-SMC. Regarding the hydrogen bond network in the active site of Sg-SMC, a basic amino acid, Arg278, is involved, whereas the corresponding residue in other SMCs (Ser or Asn) does not form hydrogen bonds with metal-coordinating water molecules. Hydrogen bond formation between Arg278 and a Mg(2+) ion-coordinating water molecule may be responsible for the higher optimal pH of Sg-SMC compared to that of other SMCs.
Structural basis for the high thermal stability and optimum pH of sphingomyelinase C from Streptomyces griseocarneus.,Fujisawa I, Hamana H, Tomita Y, Matsumoto Y, Murayama K, Sugimori D J Biosci Bioeng. 2020 Oct 3. pii: S1389-1723(20)30354-6. doi:, 10.1016/j.jbiosc.2020.09.005. PMID:33023861[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Fujisawa I, Hamana H, Tomita Y, Matsumoto Y, Murayama K, Sugimori D. Structural basis for the high thermal stability and optimum pH of sphingomyelinase C from Streptomyces griseocarneus. J Biosci Bioeng. 2020 Oct 3. pii: S1389-1723(20)30354-6. doi:, 10.1016/j.jbiosc.2020.09.005. PMID:33023861 doi:http://dx.doi.org/10.1016/j.jbiosc.2020.09.005
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