2ddr
From Proteopedia
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|PDB= 2ddr |SIZE=350|CAPTION= <scene name='initialview01'>2ddr</scene>, resolution 1.40Å | |PDB= 2ddr |SIZE=350|CAPTION= <scene name='initialview01'>2ddr</scene>, resolution 1.40Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <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> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2dds|2DDS]], [[2ddt|2DDT]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ddr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddr OCA], [http://www.ebi.ac.uk/pdbsum/2ddr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ddr RCSB]</span> | ||
}} | }} | ||
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[[Category: Takahashi, M.]] | [[Category: Takahashi, M.]] | ||
[[Category: Tsuge, H.]] | [[Category: Tsuge, H.]] | ||
| - | [[Category: CA]] | ||
[[Category: dnase i like folding]] | [[Category: dnase i like folding]] | ||
[[Category: riken structural genomics/proteomics initiative]] | [[Category: riken structural genomics/proteomics initiative]] | ||
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[[Category: structural genomic]] | [[Category: structural genomic]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:33:25 2008'' |
Revision as of 23:33, 30 March 2008
| |||||||
| , resolution 1.40Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Sphingomyelin phosphodiesterase, with EC number 3.1.4.12 | ||||||
| Related: | 2DDS, 2DDT
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion
Overview
Sphingomyelinase (SMase) from Bacillus cereus (Bc-SMase) hydrolyzes sphingomyelin to phosphocholine and ceramide in a divalent metal ion-dependent manner. Bc-SMase is a homologue of mammalian neutral SMase (nSMase) and mimics the actions of the endogenous mammalian nSMase in causing differentiation, development, aging, and apoptosis. Thus Bc-SMase may be a good model for the poorly characterized mammalian nSMase. The metal ion activation of sphingomyelinase activity of Bc-SMase was in the order Co2+ > or = Mn2+ > or = Mg2+ >> Ca2+ > or = Sr2+. The first crystal structures of Bc-SMase bound to Co2+, Mg2+, or Ca2+ were determined. The water-bridged double divalent metal ions at the center of the cleft in both the Co2+- and Mg2+-bound forms were concluded to be the catalytic architecture required for sphingomyelinase activity. In contrast, the architecture of Ca2+ binding at the site showed only one binding site. A further single metal-binding site exists at one side edge of the cleft. Based on the highly conserved nature of the residues of the binding sites, the crystal structure of Bc-SMase with bound Mg2+ or Co2+ may provide a common structural framework applicable to phosphohydrolases belonging to the DNase I-like folding superfamily. In addition, the structural features and site-directed mutagenesis suggest that the specific beta-hairpin with the aromatic amino acid residues participates in binding to the membrane-bound sphingomyelin substrate.
About this Structure
2DDR is a Single protein structure of sequence from Bacillus cereus. Full crystallographic information is available from OCA.
Reference
Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus., Ago H, Oda M, Takahashi M, Tsuge H, Ochi S, Katunuma N, Miyano M, Sakurai J, J Biol Chem. 2006 Jun 9;281(23):16157-67. Epub 2006 Apr 4. PMID:16595670
Page seeded by OCA on Mon Mar 31 02:33:25 2008
Categories: Bacillus cereus | Single protein | Sphingomyelin phosphodiesterase | Ago, H. | Katunuma, N. | Miyano, M. | Ochi, S. | Oda, M. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Sakurai, J. | Takahashi, M. | Tsuge, H. | Dnase i like folding | Riken structural genomics/proteomics initiative | Rsgi | Structural genomic
