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(-) Description

Title :  STRUCTURAL INSIGHTS INTO PHOSHOINOSITIDE 3-KINASE ENZYMATIC MECHANISM AND SIGNALLING
 
Authors :  E. H. Walker, O. Perisic, C. Ried, L. Stephens, R. L. Williams
Date :  03 Oct 00  (Deposition) - 26 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphoinositide 3-Kinase Gamma, Secondary Messenger Generation, Pi3K, Pi 3K (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 DetailsLUTETIUM DERIVATIVE
    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  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2LU9Ligand/IonLUTETIUM (III) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:951 , ASP A:964 , ATP A:3000BINDING SITE FOR RESIDUE LU A3001
02AC2SOFTWAREHOH A:2080 , HOH A:2171 , LU A:3003 , LU A:3004BINDING SITE FOR RESIDUE LU A3002
03AC3SOFTWAREHOH A:2011 , HOH A:2171 , LU A:3002 , LU A:3004BINDING SITE FOR RESIDUE LU A3003
04AC4SOFTWAREHOH A:2011 , HOH A:2081 , HOH A:2175 , LU A:3002 , LU A:3003BINDING SITE FOR RESIDUE LU A3004
05AC5SOFTWAREASP A:836 , ASP A:964 , HOH A:2193 , ATP A:3000BINDING SITE FOR RESIDUE LU A3005
06AC6SOFTWAREASP A:161 , ASP A:164BINDING SITE FOR RESIDUE LU A3006
07AC7SOFTWAREASP A:358 , ASP A:884 , LU A:3008 , LU A:3009BINDING SITE FOR RESIDUE LU A3007
08AC8SOFTWAREASP A:358 , LU A:3007BINDING SITE FOR RESIDUE LU A3008
09AC9SOFTWAREHOH A:2089 , LU A:3007BINDING SITE FOR RESIDUE LU A3009
10BC1SOFTWAREMET A:804 , SER A:806 , LYS A:807 , LYS A:808 , PRO A:810 , ILE A:831 , LYS A:833 , ASP A:836 , TYR A:867 , GLU A:880 , VAL A:882 , ASN A:951 , MET A:953 , ILE A:963 , ASP A:964 , HOH A:2253 , LU A:3001 , LU A:3005BINDING SITE FOR RESIDUE ATP A3000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E8X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E8X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E8X)

(-) 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 1E8X)

(-) 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:841
 aligned with PK3CG_PIG | O02697 from UniProtKB/Swiss-Prot  Length:1102

    Alignment length:951
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091 
           PK3CG_PIG    142 APSEETLAFQRQLNALIGYDVTDVSNVHDDELEFTRRRLVTPRMAEVAGRDPKLYAMHPWVTSKPLPEYLLKKITNNCVFIVIHRSTTSQTIKVSADDTPGTILQSFFTKMAKKKSLMDIPESQNERDFVLRVCGRDEYLVGETPIKNFQWVRQCLKNGEEIHLVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRTADLTVFVEANIQYGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSGKTSAEMPSPESKGKAQLLYYVNLLLIDHRFLLRHGEYVLHMWQLSGKGEDQGSFNADKLTSRTNPDKENSMSISILLDNYCHPIALPKHRPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKDPKAYPKLFSSVKWGQQEIVAKTYQLLAKREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIDMLQKVTIDIKSLSAEKYDVSSQVISQLKQKLENLQNLNLPQSFRVPYDPGLKAGALVIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLSHWLKEKCPIEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMISETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSLHFQKFQDVCVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKSEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVL 1092
               SCOP domains d1e8xa3 A:142-321 Phoshoinositide 3-kinase (PI3K)                                                                                                                                                                      d1e8xa2 A:357-522 Phoshoinositide 3-kinase (PI3K)                                                                                                                       d1e8x                a1 A:525-725 Phoshoinositide 3-kinase (PI3K) helical domain                                                                                                                         d1e8xa4 A:726-1092 Phoshoinositide 3-kinase (PI3K), catalytic domain                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --1e8xA01 A:144-321 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                                                                                                                                 1e8xA02 A:357-522 C2- domain Calcium/lipid binding domain                                                                                                               1e8xA                03 A:525-725  [code=1.25.40.70, no name defined]                                                                                                                                    1e8xA04 A:726-883 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4                                                                          1e8xA05 A:884-1084 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain                5                                                                                                     -------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh...eeeeee........eeeeeehhhhhhhhhhhhhh------------.....eeee.....ee....hhhhhhhhhhhhhh.....eeee...hhhhh.....-----------------------------------...eeeeeeeeee..........eeeeeeeeee..eeeeeee...ee...eeeeeeeeeeeee.hhh....eeeeeee.-----------------------.eeeeeeee..........eeeeee.ee...-------.hhhhhh...........eeeeee..--.....----------------.....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhh..hhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh......eee..eeeeeeeee.hhhhee.......eeeeeee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..........eeeee..eeeee....eeehhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhh.eeee....eee.....---------------.....hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh 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
                1e8x A  142 AASEETLAFQRQLNALIGYDVTDVSNVHDDELEFTRRRLVTPRMAEVAGRDPKLYAMHPWVTSKPLPEYLLKKITNNCVFIVIHRSTTSQTIKVSADDTPGTILQSFFTKMA------------NERDFVLRVCGRDEYLVGETPIKNFQWVRQCLKNGEEIHLVLDTPPDPALDEVRKE-----------------------------------CDRKFRVKIRGIDIPVLPRTADLTVFVEANIQYGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYC-----------------------QLLYYVNLLLIDHRFLLRHGEYVLHMWQLSG-------FNADKLTSATNPDKENSMSISILLDN--HPIAL----------------EMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKDPKAYPKLFSSVKWGQQEIVAKTYQLLAKREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIDMLQKVTIDIKSLSAEKYDVSSQVISQLKQKLENLQNLNLPQSFRVPYDPGLKAGALVIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLSHWLKEKCPIEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMISETGNLFHIDFGH---------------VPFVLTPDFLFVMGTSGKKTSLHFQKFQDVCVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKSEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVL 1092
                                   151       161       171       181       191       201       211       221       231       241       251 |       -    |  271       281       291       301       311       321         -         -         -     | 361       371       381       391       401       411       421       431   |     -         -       461       471       481       | -     | 501       511       521|  |   | -         -    |  551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961     |   -         - |     991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091 
                                                                                                                                         253          266                                                    321                                 357                                                                           435                     459                           489     497                      522  | 529              546                                                                                                                                                                                                                                                                                                                                                                                                                                  967             983                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                         525                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       

   Legend:   → Mismatch (orange background)
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  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 1E8X)

(-) 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 1e8w 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
1e8w STRUCTURE DETERMINANTS OF PHOSPHOINOSITIDE 3-KINASE INHIBITION BY WORTMANNIN, LY294002, QUERCETIN, MYRICETIN AND STAUROSPORINE
1qmm STRUCTURAL INSIGHTS INTO PHOSHOINOSITIDE 3-KINASE ENZYMATIC MECHANISM AND SIGNALLING