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(-) Description

Title :  X-RAY STRUCTURE OF THE R70D PI-PLC ENZYME: INSIGHT INTO THE ROLE OF CALCIUM AND SURROUNDING AMINO ACIDS ON ACTIVE SITE GEOMETRY AND CATALYSIS.
 
Authors :  D. Apiyo, L. Zhao, M. -D. Tsai, T. L. Selby
Date :  06 May 04  (Deposition) - 16 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pi-Plc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Apiyo, L. Zhao, M. -D. Tsai, T. L. Selby
X-Ray Structure Of The R69D Phosphatidylinositol-Specific Phospholipase C Enzyme: Insight Into The Role Of Calcium And Surrounding Amino Acids In Active Site Geometry And Catalysis.
Biochemistry V. 44 9980 2005
PubMed-ID: 16042375  |  Reference-DOI: 10.1021/BI047896V
(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
    Expression System Taxid: 562
    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  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:228 , ASN A:230 , HIS A:231 , HOH A:546BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREASP A:37 , ASP A:73 , HOH A:503 , HOH A:549BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREASP B:37 , ASP B:73 , HOH B:554BINDING SITE FOR RESIDUE CA B 503
4AC4SOFTWAREASP B:228 , ASN B:230BINDING SITE FOR RESIDUE CA B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T6M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:13 -Trp A:14
2Thr A:244 -Ala A:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T6M)

(-) 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:24-167
B:24-167

(-) Exons   (0, 0)

(no "Exon" information available for 1T6M)

(-) 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 d1t6ma_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1t6mA00 A:5-300 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..................eeee...hhhhh.hhhhhhhhh....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:24-167 UniProt: 51-194                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t6m A   5 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIDGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 300
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294      


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 d1t6mb_ B: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1t6mB00 B:5-300 Phosphatidylinositol (PI) phosphodiesterase                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -------------------------PI-PLC-X-1t6mB01 B:30-168                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------PI-PLC-X-1t6mB02 B:30-168                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhh............hhhhh.eeee.........hhhhhhhhh....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:24-167 UniProt: 51-194                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t6m B   5 ASSVNELENWSKWMQPIPDNIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIDGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEGSFSSTFEKNYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNESGGYNNFYWPDNETFTTTVNQNVNVTVQDKYKVNYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYYYASYINPEIANDIKQKNPTRVGWVIQDYINEKWSPLLYQEVIRANKSLI 300
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
   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.

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 Related Entries

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        PLC_BACTU | P08954: 2or2 3ea1 3ea2 3ea3

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