Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE W47A/W242A MUTANT OF BACTERIAL PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
 
Authors :  C. Shao, X. Shi, H. Wehbi, C. Zambonelli, J. F. Head, B. A. Seaton, M. F. Roberts
Date :  01 Feb 07  (Deposition) - 13 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphatidylinositol-Specific Phospholipase C, Pi-Plc, Dimer, Interfacially Impaired, Membrane Binding, Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Shao, X. Shi, H. Wehbi, C. Zambonelli, J. F. Head, B. A. Seaton, M. F. Roberts
Dimer Structure Of An Interfacially Impaired Phosphatidylinositol-Specific Phospholipase C.
J. Biol. Chem. V. 282 9228 2007
PubMed-ID: 17213187  |  Reference-DOI: 10.1074/JBC.M610918200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1-PHOSPHATIDYLINOSITOL PHOSPHODIESTERASE
    Chains: A, B
    EC Number: 4.6.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS THURINGIENSIS
    Organism Taxid: 1428
    Synonym: PHOSPHATIDYLINOSITOL DIACYLGLYCEROL-LYASE, PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C, PI-PLC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2OR2)

(-) Sites  (0, 0)

(no "Site" information available for 2OR2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OR2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:281 -Pro A:282
2Ser B:281 -Pro B:282

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OR2)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIPLC_X_DOMAINPS50007 Phosphatidylinositol-specific phospholipase X-box domain profile.PLC_BACTU51-194
 		  2A:20-163
B:20-163

(-) Exons   (0, 0)

(no "Exon" information available for 2OR2)

(-) 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:296
 aligned with PLC_BACTU | P08954 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:296
                                    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       321      
            PLC_BACTU    32 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 327
               SCOP domains d2or2a_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2or2A00 A:1-296 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..................eeee.hhhhhhhhhhhhh........hhhhhhhh...eeeeeeee.....eeeee..eeeeeehhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhh.............hhhhhh..eeeeee...................eeeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------PIPLC_X_DOMAIN  PDB: A:20-163 UniProt: 51-194                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2or2 A   1 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVAGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAANSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 296
                                    10        20        30        40        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      


Chain B from PDB  Type:PROTEIN  Length:296
 aligned with PLC_BACTU | P08954 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:296
                                    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       321      
            PLC_BACTU    32 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 327
               SCOP domains d2or2b_ B: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2or2B00 B:1-296 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -------------------------PI-PLC-X-2or2B01 B:26-164                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------PI-PLC-X-2or2B02 B:26-164                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhh............hhhhh.eeee.hhhhhhh.hhhhh........hhhhhhhh...eeeeeeee.....eeeee..eeeeeehhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhh.............hhhhhh..eeeeee...................eeeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------PIPLC_X_DOMAIN  PDB: B:20-163 UniProt: 51-194                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2or2 B   1 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVAGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAANSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 296
                                    10        20        30        40        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
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLC (20)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PLC_BACTU | P08954)
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.
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2or2)
 
  Sites
(no "Sites" information available for 2or2)
 
  Cis Peptide Bonds
    Ser A:281 - Pro A:282   [ RasMol ]  
    Ser B:281 - Pro B:282   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2or2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PLC_BACTU | P08954
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.6.1.13
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PLC_BACTU | P08954
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PLC_BACTU | P08954: 1t6m 3ea1 3ea2 3ea3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OR2)