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(-) Description

Title :  STRUCTURE OF THE H258Y MUTANT OF PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM STAPHYLOCOCCUS AUREUS
 
Authors :  R. I. Goldstein, J. Cheng, B. Stec, M. F. Roberts
Date :  09 Dec 11  (Deposition) - 04 Apr 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Pi-Cation, Tim Barrel, Phospholipase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Goldstein, J. Cheng, B. Stec, M. F. Roberts
Structure Of The S. Aureus Pi-Specific Phospholipase C Reveals Modulation Of Active Site Access By A Titratable Pi-Cation Latched Loop
Biochemistry V. 51 2579 2012
PubMed-ID: 22390775  |  Reference-DOI: 10.1021/BI300057Q

(-) Compounds

Molecule 1 - 1-PHOSPHATIDYLINOSITOL PHOSPHODIESTERASE
    ChainsA
    EC Number4.6.1.13
    MutationYES
    Organism ScientificSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid426430
    StrainNEWMAN
    SynonymPHOSPHATIDYLINOSITOL DIACYLGLYCEROL-LYASE, PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C, PI-PLC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2INS1Ligand/Ion1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:30 , ARG A:67 , LYS A:113 , ARG A:166 , TRP A:185 , ASP A:206 , TYR A:208 , HOH A:502 , HOH A:624 , HOH A:693BINDING SITE FOR RESIDUE INS A 401
2AC2SOFTWARELYS A:113 , ARG A:166 , TRP A:185 , HOH A:505BINDING SITE FOR RESIDUE ACT A 402
3AC3SOFTWARELEU A:37 , LYS A:38 , ASP A:39 , LYS A:42 , HIS A:86 , TYR A:290BINDING SITE FOR RESIDUE ACT A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V1H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V1H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V1H)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIPLC_X_DOMAINPS50007 Phosphatidylinositol-specific phospholipase X-box domain profile.PLC_STAAE26-176  1A:16-166

(-) Exons   (0, 0)

(no "Exon" information available for 3V1H)

(-) 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:306
 aligned with PLC_STAAE | P45723 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:306
                                                                                                                                                                                                                                                                                                                                     312      
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312      
            PLC_STAAE    13 SLSKSPENWMSKLDDGKHLTEINIPGSHDSGSFTLKDPVKSVWAKTQDKDYLTQMKSGVRFFDIRGRASADNMISVHHGMVYLHHELGKFLDDAKYYLSAYPNETIVMSMKKDYDSDSKVTKTFEEIFREYYYNNPQYQNLFYTGSNANPTLKETKGKIVLFNRMGGTYIKSGYGADTSGIQWADNATFETKINNGSLNLKVQDEYKDYYDKKVEAVKNLLAKAKTDSNKDNVYVNFLSVASGGSAFNSTYNYASHINPEIAKTIKANGKARTGWLIVDYAGYTWPGYDDIVSEIIDSNK------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhh.eeee.hhhhhhh.hhhhhhhhh....hhhhhhhh...eeeeeeeeee..eeeeee..eeeeeehhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhh..hhhhh...........hhhhhh..eeeeee......................eeeeeee....eeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhhh......eeee...........hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------PIPLC_X_DOMAIN  PDB: A:16-166 UniProt: 26-176                                                                                                          ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v1h A   3 SLSKSPENWMSKLDDGKHLTEINIPGSHDSGSFTLKDPVKSVWAKTQDKDYLTQMKSGVRFFDIRGRASADNMISVHHGMVYLHHELGKFLDDAKYYLSAYPNETIVMSMKKDYDSDSKVTKTFEEIFREYYYNNPQYQNLFYTGSNANPTLKETKGKIVLFNRMGGTYIKSGYGADTSGIQWADNATFETKINNGSLNLKVQDEYKDYYDKKVEAVKNLLAKAKTDSNKDNVYVNFLSVASGGSAFNSTYNYASYINPEIAKTIKANGKARTGWLIVDYAGYTWPGYDDIVSEIIDSNKLEHHHH 308
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302      

   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  (0, 0)

(no "SCOP Domain" information available for 3V1H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V1H)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLC_STAAE | P45723)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004436    phosphatidylinositol diacylglycerol-lyase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol = D-myo-inositol 1,2-cyclic phosphate + diacylglycerol.
    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:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    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.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        PLC_STAAE | P457233v16 3v18 4f2b 4f2t 4f2u 4i8y 4i90 4i9j 4i9m 4i9t 4rv3 4s3g

(-) Related Entries Specified in the PDB File

3v16 PI-PLC FROM S.AUREUS WITH PI-CATION LATCH CLOSED
3v18 PI-PLC FROM S.AUREUS WITH PI-CATION LATCH OPEN