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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS CEREUS SPHINGOMYELINASE MUTANT :N57A
 
Authors :  M. Oda, H. Tsuge, J. Sakurai
Date :  12 Apr 07  (Deposition) - 27 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  X
Keywords :  Hydrolase, N57A Metal Ion Of Side-Edge, Bacillus Cereus Sphingomyelinase, Hemolysis, Cytolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Oda, H. Tsuge, J. Sakurai
Crystal Structure Of Bacillus Cereus Sphingomyelinase Mutant : N57A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SPHINGOMYELINASE C
    Chains: X
    EC Number: 3.1.4.12
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Expression System Vector: PHY300PLK
    Mutation: YES
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Strain: IAM 1029
    Synonym: SPHINGOMYELINASE, SPHINGOMYELIN PHOSPHODIESTERASE, SMASE, SMPLC, CEREOLYSIN B
    Variant: N57A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU X:53 , HOH X:2009 , HOH X:2010 , HOH X:2083 , HOH X:2084 , HOH X:2086BINDING SITE FOR RESIDUE MG X1306

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1X:123 -X:159

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UYR)

(-) Sequences/Alignments

Asymmetric/Biological 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 X from PDB  Type:PROTEIN  Length:299
 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 d2uyrx_ X: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Exo_endo_phos-2uyrX01 X:13-295                                                                                                                                                                                                                                                             ---------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.........hhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhh....ee.............eeee............eeee...eeeeeeee....hhhhhhh..eeeeeeeee..eeeeeeeee....hhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeeee.............hhhhhhhhhhh....eeee.........hhhhhhhh........eeeee........eeeeee.......eeeee..eeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyr X   7 NDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDASASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM 305
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Exo_endo_phos] (21)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (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: 2ddr 2dds 2ddt

(-) Related Entries Specified in the PDB File

2ddr CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUSWITH CALCIUM ION
2dds CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUSWITH COBALT ION
2ddt CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUSWITH MAGNESIUM ION