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(-) Description

Title :  STRUCTURE DETERMINANTS OF PHOSPHOINOSITIDE 3-KINASE INHIBITION BY WORTMANNIN, LY294002, QUERCETIN, MYRICETIN AND STAUROSPORINE
 
Authors :  E. H. Walker, M. E. Pacold, O. Perisic, L. Stephens, P. T. Hawkins, M. P. Wymann, R. L. Williams
Date :  03 Oct 00  (Deposition) - 17 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphoinositide 3-Kinase Gamma, Secondary Messenger Generation, Pi3K, Pi 3K, Quercetin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. H. Walker, M. E. Pacold, O. Perisic, L. Stephens, P. T. Hawkins, M. P. Whymann, R. L. Williams
Structural Determinations Of Phosphoinositide 3-Kinase Inhibition By Wortmannin, Ly294002, Quercetin, Myricetin And Staurosporine
Mol. Cell V. 6 909 2000
PubMed-ID: 11090628  |  Reference-DOI: 10.1016/S1097-2765(05)00089-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT
    CellNEUTROPHIL
    ChainsA
    EC Number2.7.1.137
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System GeneP120S144C
    Expression System PlasmidPACHLT-C
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentPI3-KINASE P110 SUBUNIT GAMMA
    GeneP120S144C
    MutationYES
    Organism CommonWILD BOAR
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    Other DetailsQUERCETIN
    PlasmidPACHLT-C
    StrainSF9
    SynonymPTDINS-3-KINASE P110, PI3K

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1QUE1Ligand/Ion3,5,7,3',4'-PENTAHYDROXYFLAVONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:812 , LYS A:833 , TYR A:867 , ILE A:879 , GLU A:880 , ILE A:881 , VAL A:882 , MET A:953 , ILE A:963 , ASP A:964BINDING SITE FOR RESIDUE QUE A2095

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E8W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E8W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E8W)

(-) PROSITE Motifs  (6, 6)

Asymmetric/Biological Unit (6, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PI3K_RBDPS51546 Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile.PK3CG_PIG217-309  1A:217-309
2PI3K_C2PS51547 Phosphatidylinositol 3-kinase C2 (PI3K C2) domain profile.PK3CG_PIG357-521  1A:357-521
3PIK_HELICALPS51545 PIK helical domain profile.PK3CG_PIG541-723  1A:546-723
4PI3_4_KINASE_3PS50290 Phosphatidylinositol 3- and 4-kinases family profile.PK3CG_PIG828-1073  1A:828-1073
5PI3_4_KINASE_1PS00915 Phosphatidylinositol 3- and 4-kinases signature 1.PK3CG_PIG832-846  1A:832-846
6PI3_4_KINASE_2PS00916 Phosphatidylinositol 3- and 4-kinases signature 2.PK3CG_PIG931-951  1A:931-951

(-) Exons   (0, 0)

(no "Exon" information available for 1E8W)

(-) 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:851
 aligned with PK3CG_PIG | O02697 from UniProtKB/Swiss-Prot  Length:1102

    Alignment length:952
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092  
           PK3CG_PIG    143 PSEETLAFQRQLNALIGYDVTDVSNVHDDELEFTRRRLVTPRMAEVAGRDPKLYAMHPWVTSKPLPEYLLKKITNNCVFIVIHRSTTSQTIKVSADDTPGTILQSFFTKMAKKKSLMDIPESQNERDFVLRVCGRDEYLVGETPIKNFQWVRQCLKNGEEIHLVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRTADLTVFVEANIQYGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSGKTSAEMPSPESKGKAQLLYYVNLLLIDHRFLLRHGEYVLHMWQLSGKGEDQGSFNADKLTSRTNPDKENSMSISILLDNYCHPIALPKHRPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKDPKAYPKLFSSVKWGQQEIVAKTYQLLAKREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIDMLQKVTIDIKSLSAEKYDVSSQVISQLKQKLENLQNLNLPQSFRVPYDPGLKAGALVIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLSHWLKEKCPIEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMISETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSLHFQKFQDVCVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKSEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGI 1094
               SCOP domains d1e8wa3 A:143-321 Phoshoinositide 3-kinase (PI3K)                                                                                                                                                                d1e8wa2 A:352-524 Phoshoinositide 3-kinase (PI3K)                                                                                                                            d1e8wa1              A:525-725 Phoshoinositide 3-kinase (PI3K) helical domain                                                                                                                            d1e8wa4 A:726-1094 Phoshoinositide 3-kinase (PI3K), catalytic domain                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1e8wA01 A:144-321 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                                                                                                                            -----1e8wA02 A:357-526 C2- domain Calcium/lipid binding domain                                                                                                                 1e8wA0             3 A:527-725  [code=1.25.40.70, no name defined]                                                                                                                                     1e8wA04 A:726-883 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4                                                                          1e8wA05 A:884-1084 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain             5                                                                                                        ---------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh.hhhhhhhh........hhhhhh.....eeeeeee....eeeeeee.....hhhhhhhhh..----------------...eee...........hhhhhhhhhhhhhh....eeee....hhhhhh....------------------------------........eeeeeeeeee...........eeeeeeeee..eeeeee.........eee..eeeeeeee.hhh....eeeeeeee.----------------------.eeeeeeee..........eeeeee.....--------.hhhhhh...........eeeeee............-------------..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh......eee..eeeeee....hhhh.........eeeee............eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhhhhhh........hhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh.....hhh.eeee....eee....------------.........hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------PI3K_RBD  PDB: A:217-309 UniProt: 217-309                                                    -----------------------------------------------PI3K_C2  PDB: A:357-521 UniProt: 357-521                                                                                                                             -------------------PIK_HELICAL  PDB: A:546-723 UniProt: 541-723                                                                                                                                           --------------------------------------------------------------------------------------------------------PI3_4_KINASE_3  PDB: A:828-1073 UniProt: 828-1073                                                                                                                                                                                                     --------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PI3_4_KINASE_1 ------------------------------------------------------------------------------------PI3_4_KINASE_2       ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1e8w A  143 ASEETLAFQRQLNALIGYDVTDVSNVHDDELEFTRRRLVTPRMAEVAGRDPKLYAMHPWVTSKPLPEYLLKKITNNCVFIVIHRSTTSQTIKVSADDTPGTILQSFFTKM----------------DFVLRVCGRDEYLVGETPIKNFQWVRQCLKNGEEIHLVLDTPPDPALDEVRKE------------------------------VSLWDCDRKFRVKIRGIDIPVLPRTADLTVFVEANIQYGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCG----------------------QLLYYVNLLLIDHRFLLRHGEYVLHMWQLS--------FNADKLTSATNPDKENSMSISILLDNYCHPIALPKH-------------EMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKDPKAYPKLFSSVKWGQQEIVAKTYQLLAKREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIDMLQKVTIDIKSLSAEKYDVSSQVISQLKQKLENLQNLNLPQSFRVPYDPGLKAGALVIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLSHWLKEKCPIEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMISETGNLFHIDFG------------NKERVPFVLTPDFLFVMGTSGKKTSLHFQKFQDVCVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKSEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGI 1094
                                   152       162       172       182       192       202       212       222       232       242       252         -      |272       282       292       302       312        |-         -         -       352       362       372       382       392       402       412       422       432   |     -         -      |462       472       482     |   -    |  502       512       522       532         -   |   552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962   |     -      |982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092  
                                                                                                                                       252              269                                                 321                            352                                                                                 436                    459                          488      497                                532           546                                                                                                                                                                                                                                                                                                                                                                                                                                 966          979                                                                                                                   

   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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (5, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E8W)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PK3CG_PIG | O02697)
molecular function
    GO:0016303    1-phosphatidylinositol-3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H(+).
    GO:0035005    1-phosphatidylinositol-4-phosphate 3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4-phosphate + ATP = 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + ADP + 2 H(+).
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0046934    phosphatidylinositol-4,5-bisphosphate 3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0046854    phosphatidylinositol phosphorylation    The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
    GO:0036092    phosphatidylinositol-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005942    phosphatidylinositol 3-kinase complex    A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PK3CG_PIG | O026971e7u 1e7v 1e8x 1e90

(-) Related Entries Specified in the PDB File

1e7u STRUCTURE DETERMINANTS OF PHOSPHOINOSITIDE 3-KINASE INHIBITION BY WORTMANNIN, LY294002, QUERCETIN, MYRICETIN AND STAUROSPORINE
1e7v STRUCTURE DETERMINANTS OF PHOSPHOINOSITIDE 3-KINASE INHIBITION BY WORTMANNIN, LY294002, QUERCETIN, MYRICETIN AND STAUROSPORINE
1e8x STRUCTURAL INSIGHTS INTO PHOSHOINOSITIDE 3-KINASE ENZYMATIC MECHANISM AND SIGNALLING
1qmm STRUCTURAL INSIGHTS INTO PHOSHOINOSITIDE 3-KINASE ENZYMATIC MECHANISM AND SIGNALLING