2ddr
From Proteopedia
(New page: 200px<br /><applet load="2ddr" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ddr, resolution 1.40Å" /> '''Crystal structure of...) |
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| - | [[Image:2ddr.gif|left|200px]]<br /><applet load="2ddr" size=" | + | [[Image:2ddr.gif|left|200px]]<br /><applet load="2ddr" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2ddr, resolution 1.40Å" /> | caption="2ddr, resolution 1.40Å" /> | ||
'''Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion'''<br /> | '''Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Sphingomyelinase (SMase) from Bacillus cereus (Bc-SMase) hydrolyzes | + | 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== | ==About this Structure== | ||
| - | 2DDR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http:// | + | 2DDR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDR OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Ochi, S.]] | [[Category: Ochi, S.]] | ||
[[Category: Oda, M.]] | [[Category: Oda, M.]] | ||
| - | [[Category: RSGI, RIKEN | + | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] |
[[Category: Sakurai, J.]] | [[Category: Sakurai, J.]] | ||
[[Category: Takahashi, M.]] | [[Category: Takahashi, M.]] | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:57:48 2008'' |
Revision as of 14:57, 21 February 2008
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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 with as ligand. Active as Sphingomyelin phosphodiesterase, with EC number 3.1.4.12 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 Thu Feb 21 16:57:48 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. | CA | Dnase i like folding | Riken structural genomics/proteomics initiative | Rsgi | Structural genomics
