Summary for 7CNE
| Entry DOI | 10.2210/pdb7cne/pdb |
| Descriptor | Sphingomyelinase C, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, SUCCINIC ACID, ... (4 entities in total) |
| Functional Keywords | sphingomyelinase c, streptomyces griseocarneus, metal-binding site, hydrolase |
| Biological source | Streptomyces griseocarneus |
| Total number of polymer chains | 1 |
| Total formula weight | 32572.72 |
| Authors | Murayama, K.,Fujisawa, I.,Sugimori, D. (deposition date: 2020-07-31, release date: 2020-10-28, Last modification date: 2024-11-13) |
| Primary citation | 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., 131:8-12, 2021 Cited by PubMed Abstract: 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 Å 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 ion-coordinating water molecule may be responsible for the higher optimal pH of Sg-SMC compared to that of other SMCs. PubMed: 33023861DOI: 10.1016/j.jbiosc.2020.09.005 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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