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Title :   CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUS WITH MAGNESIUM ION

Authors :   H. Ago, M. Oda, H. Tsuge, 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 :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (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)

Molecule 1 - SPHINGOMYELIN PHOSPHODIESTERASE
	Chains	:	A, B
	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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:53 , HOH B:328 , HOH B:334 , HOH B:351 , HOH B:353 , HOH B:386	BINDING SITE FOR RESIDUE MG B 308
2	AC2	SOFTWARE	PHE B:55 , ASN B:57 , GLU B:99 , ASP B:100 , HOH B:383 , HOH B:400	BINDING SITE FOR RESIDUE MG B 309
3	AC3	SOFTWARE	GLU A:53 , HOH A:322 , HOH A:326 , HOH A:352 , HOH A:367 , HOH A:384	BINDING SITE FOR RESIDUE MG A 310
4	AC4	SOFTWARE	PHE A:55 , ASN A:57 , GLU A:99 , ASP A:100 , HOH A:330 , HOH A:372	BINDING SITE FOR RESIDUE MG A 311
5	AC5	SOFTWARE	ALA A:40 , ASP A:41 , TYR A:42 , LYS A:275 , TYR A:293 , HOH A:597	BINDING SITE FOR RESIDUE SO4 A 312
6	AC6	SOFTWARE	ASP B:41 , TYR B:42 , LYS B:275 , TYR B:293 , HOH B:813	BINDING SITE FOR RESIDUE SO4 B 313
7	AC7	SOFTWARE	TYR A:25 , PRO A:26 , ASN A:27 , TRP A:28 , TYR A:242 , VAL A:281 , SER A:283 , TRP A:284 , TYR A:288 , TYR A:290	BINDING SITE FOR RESIDUE MES A 313
8	AC8	SOFTWARE	TYR B:25 , PRO B:26 , ASN B:27 , TRP B:28 , TYR B:242 , VAL B:281 , SER B:283 , TRP B:284 , TYR B:288 , TYR B:290 , HOH B:707	BINDING SITE FOR RESIDUE MES B 307

(no "SS Bond" information available for 2DDT)

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

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

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

(no "Exon" information available for 2DDT)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:288
 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 d2ddta_ A: 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
                 2ddt A   8 DTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGC---NLSNKGFVYTKIKKNDRFVHVIGTHLQAE-------SPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM 305
                                    17        27        37        47        57        67        77        87        97       107       117     | 127       137       147       | -     | 167       177       187       197       207       217       227       237       247       257       267       277       287       297        
                                                                                                                                             123 127                         155     163

Chain B from PDB  Type:PROTEIN  Length:287
 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 d2ddtb_ 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....-------hhhhhhhhhhhhhhhhhhhh.......eeeeee.............hhhhhhhhhh.....eeee.........hhhhhhhh........eeeee........eeeeee.......eeeee..eeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ddt B   8 DTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGC----LSNKGFVYTKIKKNDRFVHVIGTHLQAE-------SPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM 305
                                    17        27        37        47        57        67        77        87        97       107       117     |   -|      137       147       | -     | 167       177       187       197       207       217       227       237       247       257       267       277       287       297        
                                                                                                                                             123  128                        155     163

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: DNase I-like (70)

Superfamily: DNase I-like (70)

Family: Sphingomyelin phosphodiesterase-like (6)

Protein domain: automated matches (4)

Bacillus cereus [TaxId: 1396] (4)

1a	d2ddta_	A:
1b	d2ddtb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	PHL2_BACCE \| P11889	:	2ddr 2dds 2uyr

2ddr
2dds	RELATED ID: AR_001000745.3 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

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