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(-) Description

Title :  STRUCTURE OF THE 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 :  2.34
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
    Chains: A
    EC Number: 4.6.1.13
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 426430
    Strain: NEWMAN
    Synonym: PHOSPHATIDYLINOSITOL 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, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:37 , LYS A:38 , ASP A:39 , LYS A:42 , HIS A:86 , HOH A:618BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWARESER A:257 , HIS A:258 , TYR A:290BINDING SITE FOR RESIDUE IPA A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V18)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V18)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V18)

(-) 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 3V18)

(-) 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:304
 aligned with PLC_STAAE | P45723 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:304
                                                                                                                                                                                                                                                                                                                                      312   
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311|   
            PLC_STAAE    12 DSLSKSPENWMSKLDDGKHLTEINIPGSHDSGSFTLKDPVKSVWAKTQDKDYLTQMKSGVRFFDIRGRASADNMISVHHGMVYLHHELGKFLDDAKYYLSAYPNETIVMSMKKDYDSDSKVTKTFEEIFREYYYNNPQYQNLFYTGSNANPTLKETKGKIVLFNRMGGTYIKSGYGADTSGIQWADNATFETKINNGSLNLKVQDEYKDYYDKKVEAVKNLLAKAKTDSNKDNVYVNFLSVASGGSAFNSTYNYASHINPEIAKTIKANGKARTGWLIVDYAGYTWPGYDDIVSEIIDSNK---   -
               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.......................eeeeee....eeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhhh......eeee...........hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PIPLC_X_DOMAIN  PDB: A:16-166 UniProt: 26-176                                                                                                          ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v18 A   2 DSLSKSPENWMSKLDDGKHLTEINIPGSHDSGSFTLKDPVKSVWAKTQDKDYLTQMKSGVRFFDIRGRASADNMISVHHGMVYLHHELGKFLDDAKYYLSAYPNETIVMSMKKDYDSDSKVTKTFEEIFREYYYNNPQYQNLFYTGSNANPTLKETKGKIVLFNRMGGTYIKSGYGADTSGIQWADNATFETKINNGSLNLKVQDEYKDYYDKKVEAVKNLLAKAKTDSNKDNVYVNFLSVASGGSAFNSTYNYASHINPEIAKTIKANGKARTGWLIVDYAGYTWPGYDDIVSEIIDSNKLEH 305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   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 3V18)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V18)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V18)

(-) 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 | P45723: 3v16 3v1h 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