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(-) Description

Title :  CRYSTAL STRUCTURE OF SMCL
 
Authors :  A. E. A. Openshaw, P. R. Race, H. J. Monzo, J. A. Vasquez-Boland, M. J. Ban
Date :  06 Jun 05  (Deposition) - 16 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Dnase1-Like Fold, Beta-Hairpin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. E. A. Openshaw, P. R. Race, H. J. Monzo, J. A. Vasquez-Boland, M. J. Banfield
Crystal Structure Of Smcl, A Bacterial Neutral Sphingomyelinase C From Listeria.
J. Biol. Chem. V. 280 35011 2005
PubMed-ID: 16093240  |  Reference-DOI: 10.1074/JBC.M506800200

(-) Compounds

Molecule 1 - SPHINGOMYELINASE-C
    Chains: A
    EC Number: 3.1.4.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET27B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMCL
    Organism Scientific: LISTERIA IVANOVII
    Organism Taxid: 1638
    Synonym: SMCL

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:88 , HIS A:325 , HOH A:524 , HOH A:547 , HOH A:565 , HOH A:577 , HOH A:599BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWAREASN A:62 , SER A:194 , THR A:197 , SER A:312 , TYR A:319BINDING SITE FOR RESIDUE GOL A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZWX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:41 -Pro A:42

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZWX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZWX)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZWX)

(-) 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 PHLC_LISIV | Q9RLV9 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:293
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
           PHLC_LISIV    41 YPGNFKITSHNVYLFSRNIYPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSASHRLLNNLREMYPHQTPVIGRSKHGWDKTEGNYSNFALEDGGVAVVSQWPIVEKSQHIFQRGGGADRLSNKGFAYVKIMKNGKPYHIIGTHTPADDSLISKDTSRAIRAEQMQEIQTFIAKKNIPKDEIIFIGGDLNVNYGTDEYHDMFKLLNVSSPANFNGQMATWDPTTNSMLKESYPKAAPEYLDYIFVENGHARPHSWHNKVLHTKSPQWSVKSWFKTYTYQDFSDHYPVVGFTD 333
               SCOP domains d1zwxa1 A:41-333 Sphingomyelin phosphodiesterase C                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Exo_endo_phos-1zwxA01 A:44-325                                                                                                                                                                                                                                                            -------- Pfam domains
         Sec.struct. author .....eeeeeeeee.........hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh.....ee............eee.-----.......eeee...eeeeeeee....hhhhhhh..eeeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhh..................hhhhhhhh........eeeee.........eeeee.......eeeee..eeeee........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zwx A  41 YPGNFKITSHNVYLFSRNIYPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSASHRLLNNLREMYPHQTPVIGRSKHGWDKTEG-----ALEDGGVAVVSQWPIVEKSQHIFQRGGGADRLSNKGFAYVKIMKNGKPYHIIGTHTQADDSLISKDTSRAIRAEQMQEIQTFIAKKNIPKDEIIFIGGDLNVNYGTDEYHDMLKLLNVSSPANFNGQMATWDPTTNSMLKESYPKAAPEYLDYIFVENGHARPHSWHNKVLHTKSPQWSVKSWFKTYTYQDFSDHYPVVGFTD 333
                                    50        60        70        80        90       100       110       120    |    -|      140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
                                                                                                              125   131
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZWX)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (PHLC_LISIV | Q9RLV9)
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.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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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  1zwx
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 Related Entries

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