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(-) Description

Title :  CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUS WITH CALCIUM ION
 
Authors :  H. Ago, M. Oda, M. Takahashi, H. Tsuge, S. Ochi, N. Katunuma, M. Miyano, J. Sakurai, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 Feb 06  (Deposition) - 02 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Dnase I Like Folding, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ago, M. Oda, M. Takahashi, H. Tsuge, S. Ochi, N. Katunuma, M. Miyano, J. Sakurai
Structural Basis Of The Sphingomyelin Phosphodiesterase Activity In Neutral Sphingomyelinase From Bacillus Cereus.
J. Biol. Chem. V. 281 16157 2006
PubMed-ID: 16595670  |  Reference-DOI: 10.1074/JBC.M601089200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPHINGOMYELIN PHOSPHODIESTERASE
    Chains: A, B, C, D
    EC Number: 3.1.4.12
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PHY300PLK
    Expression System Strain: ISW1214
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Strain: IAM 1029
    Synonym: SPHINGOMYELINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:55 , ASN A:57 , GLU A:99 , ASP A:100 , HOH A:1331 , HOH A:1345BINDING SITE FOR RESIDUE CA A 1324
2AC2SOFTWAREGLU A:53 , HOH A:1333 , HOH A:1380 , HOH A:1387 , HOH A:1479 , HOH A:1492BINDING SITE FOR RESIDUE CA A 1325
3AC3SOFTWAREPHE B:55 , ASN B:57 , GLU B:99 , ASP B:100 , HOH B:1335 , HOH B:1357BINDING SITE FOR RESIDUE CA B 1326
4AC4SOFTWAREGLU B:53 , HOH B:1343 , HOH B:1403 , HOH B:1441 , HOH B:1482 , HOH B:1493BINDING SITE FOR RESIDUE CA B 1327
5AC5SOFTWAREPHE C:55 , ASN C:57 , GLU C:99 , ASP C:100 , HOH C:1332 , HOH C:1337BINDING SITE FOR RESIDUE CA C 1328
6AC6SOFTWAREGLU C:53 , HOH C:1341 , HOH C:1390 , HOH C:1397 , HOH C:1464BINDING SITE FOR RESIDUE CA C 1329
7AC7SOFTWAREPHE D:55 , ASN D:57 , GLU D:99 , ASP D:100 , HOH D:1338 , HOH D:1348BINDING SITE FOR RESIDUE CA D 1330
8AC8SOFTWAREGLU D:53 , HOH D:1346 , HOH D:1397 , HOH D:1427 , HOH D:1460BINDING SITE FOR RESIDUE CA D 1331

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:123 -C:159
2D:123 -D:159

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DDR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DDR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DDR)

(-) Exons   (0, 0)

(no "Exon" information available for 2DDR)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:288
 aligned with PHL2_BACCE | P11889 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:299
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323         
           PHL2_BACCE    34 NDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDDYPVEATISM 332
               SCOP domains d2ddra1 A:7-305 Sphingomyelin phosphodiesterase C                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.........hhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhh....ee.............eeee............eeee...eeeeeeee.....----....eeeeeeeee..eeeeeeeee....-------hhhhhhhhhhhhhhhhhhhhh......eeeeee.............hhhhhhhhhhh....eeee.........hhhhhhhh........eeeee........eeeeee.......eeeee..eeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ddr A   7 NDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGC----LSNKGFVYTKIKKNDRFVHVIGTHLQAE-------SPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM 305
                                    16        26        36        46        56        66        76        86        96       106       116      |  - |     136       146        |-      |166       176       186       196       206       216       226       236       246       256       266       276       286       296         
                                                                                                                                              123  128                        155     163                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with PHL2_BACCE | P11889 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:299
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323         
           PHL2_BACCE    34 NDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDDYPVEATISM 332
               SCOP domains d2ddrb_ B: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.........hhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhh....ee.............eeee............eeee...eeeeeeee.....---.....eeeeeeeee..eeeeeeeee....-------hhhhhhhhhhhhhhhhhhhhh......eeeeee.............hhhhhhhhhhh....eeee.........hhhhhhhh........eeeee........eeeeee.......eeeee..eeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ddr B   7 NDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGC---NLSNKGFVYTKIKKNDRFVHVIGTHLQAE-------SPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM 305
                                    16        26        36        46        56        66        76        86        96       106       116      |  -|      136       146        |-      |166       176       186       196       206       216       226       236       246       256       266       276       286       296         
                                                                                                                                              123 127                         155     163                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:298
 aligned with PHL2_BACCE | P11889 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:298
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324        
           PHL2_BACCE    35 DTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDDYPVEATISM 332
               SCOP domains d2ddrc_ C: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.........hhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhh....ee.............eeee............eeee...eeeeeeee.............eeeeeeeee..eeeeeeeee....hhhhh..hhhhhhhhhhhhhhhhhhhhh......eeeeee.............hhhhhhhhhhh....eeee.........hhhhhhhh........eeeee........eeeeee.......eeeee..eeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ddr C   8 DTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM 305
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297        


Chain D from PDB  Type:PROTEIN  Length:298
 aligned with PHL2_BACCE | P11889 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:298
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324        
           PHL2_BACCE    35 DTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDDYPVEATISM 332
               SCOP domains d2ddrd_ D: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.........hhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhh....ee.............eeee............eeee...eeeeeeee.............eeeeeeeee..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhh.......eeeeee.............hhhhhhhhhhh....eeee.........hhhhhhhh........eeeee........eeeeee.......eeeee..eeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ddr D   8 DTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM 305
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DDR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DDR)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PHL2_BACCE | P11889)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    GO:0004767    sphingomyelin phosphodiesterase activity    Catalysis of the reaction: H(2)O + sphingomyelin = ceramide + choline phosphate + H(+).
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PHL2_BACCE | P11889: 2dds 2ddt 2uyr

(-) Related Entries Specified in the PDB File

2dds
2ddt RELATED ID: AR_001000745.1 RELATED DB: TARGETDB