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(-) Description

Title :  CRYSTAL STRUCTURE OF LOXOSCELES INTERMEDIA PHOSPHOLIPASE D ISOFORM 1 H12A MUTANT
 
Authors :  P. O. Giuseppe, A. Ullah, S. S. Veiga, M. T. Murakami, R. K. Arni
Date :  19 Apr 11  (Deposition) - 24 Aug 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Beta/Alpha-Barrel, Plc-Like Phosphodiesterase, Inactive Mutant H12A Phospholipase D, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ullah, P. O. De Giuseppe, M. T. Murakami, D. Trevisan-Silva, A. C. Wille, D. Chaves-Moreira, L. H. Gremski, R. B. Da Silveira, A. Sennf-Ribeiro, O. M. Chaim, S. S. Veiga, R. K. Arni
Crystallization And Preliminary X-Ray Diffraction Analysis Of A Class Ii Phospholipase D From Loxosceles Intermedia Venom.
Acta Crystallogr. , Sect. F V. 67 234 2011
PubMed-ID: 21301094  |  Reference-DOI: 10.1107/S1744309110050931

(-) Compounds

Molecule 1 - SPHINGOMYELIN PHOSPHODIESTERASE D LISICTOX-ALPHAIA1A
    ChainsA
    EC Number3.1.4.41
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-14B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonSPIDER
    Organism ScientificLOXOSCELES INTERMEDIA
    Organism Taxid58218
    SynonymDERMONECROTIC PROTEIN 1, LIRECDT1, SPHINGOMYELIN PHOSPHODIESTERASE D 1, SMD 1, SMASE D 1, SPHINGOMYELINASE D 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:32 , ASP A:34 , ASP A:91 , HOH A:357 , HOH A:475BINDING SITE FOR RESIDUE MG A 286
2AC2SOFTWAREASN A:200BINDING SITE FOR RESIDUE EDO A 287
3AC3SOFTWAREASN A:41 , LYS A:108 , PGE A:289BINDING SITE FOR RESIDUE PEG A 288
4AC4SOFTWAREASP A:104 , LYS A:107 , LYS A:108 , LYS A:111 , PEG A:288BINDING SITE FOR RESIDUE PGE A 289
5AC5SOFTWAREASN A:137 , LYS A:185BINDING SITE FOR RESIDUE EDO A 290
6AC6SOFTWAREASP A:39 , ASN A:39A , HOH A:387BINDING SITE FOR RESIDUE EDO A 291
7AC7SOFTWAREALA A:264 , LYS A:268BINDING SITE FOR RESIDUE PGE A 292
8AC8SOFTWARELYS A:267BINDING SITE FOR RESIDUE PEG A 293
9AC9SOFTWAREGLY A:180 , ILE A:188 , PHE A:223BINDING SITE FOR RESIDUE EDO A 294

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:51 -A:57
2A:53 -A:201

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:49 -Pro A:50
2Trp A:230 -Thr A:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RLG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RLG)

(-) Exons   (0, 0)

(no "Exon" information available for 3RLG)

(-) 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 A from PDB  Type:PROTEIN  Length:278
 aligned with A1HA_LOXIN | P0CE80 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:278
                                    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        
           A1HA_LOXIN    28 GNRRPIWIMGHMVNAIGQIDEFVNLGANSIETDVSFDDNANPEYTYHGIPCDCGRNCKKYENFNDFLKGLRSATTPGNSKYQEKLVLVVFDLKTGSLYDNQANDAGKKLAKNLLQHYWNNGNNGGRAYIVLSIPDLNHYPLIKGFKDQLTKDGHPELMDKVGHDFSGNDDIGDVGKAYKKAGITGHIWQSDGITNCLPRGLSRVNAAVANRDSANGFINKVYYWTVDKRSTTRDALDAGVDGIMTNYPDVITDVLNEAAYKKKFRVATYDENPWVTFK 305
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhh...eeeeee...........................hhhhhhhhhhhhhh...........eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh.hhhhhh.eeeee....hhhhhhhhhhhh......eeeee........hhhhhhhhhhhh.......eeeee...hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh.eee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rlg A   2 GNRRPIWIMGAMVNAIGQIDEFVNLGANSIETDVSFDDNANPEYTYHGIPCDCGRNCKKYENFNDFLKGLRSATTPGNSKYQEKLVLVVFDLKTGSLYDNQANDAGKKLAKNLLQHYWNNGNNGGRAYIVLSIPDLNHYPLIKGFKDQLTKDGHPELMDKVGHDFSGNDDIGDVGKAYKKAGITGHIWQSDGITNCLPRGLSRVNAAVANRDSANGFINKVYYWTVDKRSTTRDALDAGVDGIMTNYPDVITDVLNEAAYKKKFRVATYDDNPWVTFK 284
                                    11        21        31        40        50        60        70        80        90       100       110       120       130       140       150       160      |175       185       195       205|      216       226       236       246       256       266       276        
                                                                39A                                                                                                                             167|                             205|                                                                             
                                                                                                                                                                                                 173                              207                                                                             

   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  (0, 0)

(no "SCOP Domain" information available for 3RLG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RLG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RLG)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1HA_LOXIN | P0CE80)
molecular function
    GO:0070290    N-acylphosphatidylethanolamine-specific phospholipase D activity    Catalysis of the release of N-acylethanolamine from N-acyl-phosphatidylethanolamine (NAPE) to generate N-acylethanolamine (NAE).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004630    phospholipase D activity    Catalysis of the reaction: a phosphatidylcholine + H2O = choline + a phosphatidate.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
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:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
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
        A1HA_LOXIN | P0CE803rlh

(-) Related Entries Specified in the PDB File

3rlh