PDBsum entry 3hhm

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protein ligands Protein-protein interface(s) links
Transferase/oncoprotein PDB id
Protein chains
1032 a.a. *
247 a.a. *
Waters ×115
* Residue conservation analysis
PDB id:
Name: Transferase/oncoprotein
Title: Crystal structure of p110alpha h1047r mutant in complex with nish2 of p85alpha and the drug wortmannin
Structure: Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform. Chain: a. Synonym: pi3-kinase p110 subunit alpha, ptdins-3-kinase p110, pi3k. Engineered: yes. Mutation: yes. Nish2 p85alpha. Chain: b.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pik3ca. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: pi3kr1.
2.80Å     R-factor:   0.239     R-free:   0.307
Authors: L.M.Amzel,B.Vogelstein,S.B.Gabelli,D.Mandelker
Key ref:
D.Mandelker et al. (2009). A frequent kinase domain mutation that changes the interaction between PI3Kalpha and the membrane. Proc Natl Acad Sci U S A, 106, 16996-17001. PubMed id: 19805105 DOI: 10.1073/pnas.0908444106
15-May-09     Release date:   29-Sep-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P42336  (PK3CA_HUMAN) -  Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
1068 a.a.
1032 a.a.*
Protein chain
Pfam   ArchSchema ?
P27986  (P85A_HUMAN) -  Phosphatidylinositol 3-kinase regulatory subunit alpha
724 a.a.
247 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chain A: E.C.  - Phosphatidylinositol-4,5-bisphosphate 3-kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

1-Phosphatidyl-myo-inositol Metabolism
      Reaction: ATP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate = ADP + 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
+ 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
+ 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
   Enzyme class 3: Chain A: E.C.  - Non-specific serine/threonine protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
+ protein
+ phosphoprotein
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   5 terms 
  Biological process     phosphatidylinositol-3-phosphate biosynthetic process   35 terms 
  Biochemical function     nucleotide binding     15 terms  


DOI no: 10.1073/pnas.0908444106 Proc Natl Acad Sci U S A 106:16996-17001 (2009)
PubMed id: 19805105  
A frequent kinase domain mutation that changes the interaction between PI3Kalpha and the membrane.
D.Mandelker, S.B.Gabelli, O.Schmidt-Kittler, J.Zhu, I.Cheong, C.H.Huang, K.W.Kinzler, B.Vogelstein, L.M.Amzel.
Mutations in oncogenes often promote tumorigenesis by changing the conformation of the encoded proteins, thereby altering enzymatic activity. The PIK3CA oncogene, which encodes p110alpha, the catalytic subunit of phosphatidylinositol 3-kinase alpha (PI3Kalpha), is one of the two most frequently mutated oncogenes in human cancers. We report the structure of the most common mutant of p110alpha in complex with two interacting domains of its regulatory partner (p85alpha), both free and bound to an inhibitor (wortmannin). The N-terminal SH2 (nSH2) domain of p85alpha is shown to form a scaffold for the entire enzyme complex, strategically positioned to communicate extrinsic signals from phosphopeptides to three distinct regions of p110alpha. Moreover, we found that Arg-1047 points toward the cell membrane, perpendicular to the orientation of His-1047 in the WT enzyme. Surprisingly, two loops of the kinase domain that contact the cell membrane shift conformation in the oncogenic mutant. Biochemical assays revealed that the enzymatic activity of the p110alpha His1047Arg mutant is differentially regulated by lipid membrane composition. These structural and biochemical data suggest a previously undescribed mechanism for mutational activation of a kinase that involves perturbation of its interaction with the cellular membrane.
  Selected figure(s)  
Figure 2.
The nSH2 domain of p85α forms a scaffold for the PI3Kα enzyme. (A) p85α nSH2 acts as a scaffold and interacts with the p85α iSH2 domain as well as the p110α kinase, helical, and C2 domains. (B) The nSH2 αA helix fits into a crevice between the C2 and kinase domains. (C) nSH2 interactions with the p110α C2 domain. (D) Residue-residue interactions between nSH2 and the helical and kinase domains.
Figure 3.
Interactions between p110α and p85 nSH2. (A) Ribbon diagram of nSH2, helical, and kinase domains determined from the structure reported in this work. (B) The same ribbon diagram as in A but showing the position of the PDGFR phosphopeptide (gray) modeled as in PDB ID code 2IUI, at the interface between nSH2 and the helical domain. The loop of the helical domain occupies nearly the same position as the phosphopeptide, so their occurrence is mutually exclusive. (C) The phosphopeptide is predicted to disrupt the interaction between the positively charged nSH2 surface (shaded blue) and the negatively charged helical domain residues. The phosphopeptide is shown in gray, with its phosphotyrosine in stick and ball representation and the phosphate shaded red. The boxed region shows that the side chain of Glu-542 occupies the space usually occupied by the phosphate of the peptide's phosphotyrosine residue.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22729222 M.J.Lindhurst, V.E.Parker, F.Payne, J.C.Sapp, S.Rudge, J.Harris, A.M.Witkowski, Q.Zhang, M.P.Groeneveld, C.E.Scott, A.Daly, S.M.Huson, L.L.Tosi, M.L.Cunningham, T.N.Darling, J.Geer, Z.Gucev, V.R.Sutton, C.Tziotzios, A.K.Dixon, T.Helliwell, S.O'Rahilly, D.B.Savage, M.J.Wakelam, I.Barroso, L.G.Biesecker, and R.K.Semple (2012).
Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA.
  Nat Genet, 44, 928-933.  
21035489 S.B.Gabelli, K.C.Duong-Ly, E.T.Brower, and L.M.Amzel (2011).
Capitalizing on tumor genotyping: towards the design of mutation specific inhibitors of phosphoinsitide-3-kinase.
  Adv Enzyme Regul, 51, 273-279.  
21362552 X.Zhang, O.Vadas, O.Perisic, K.E.Anderson, J.Clark, P.T.Hawkins, L.R.Stephens, and R.L.Williams (2011).
Structure of lipid kinase p110β/p85β elucidates an unusual SH2-domain-mediated inhibitory mechanism.
  Mol Cell, 41, 567-578.
PDB code: 2y3a
20081827 A.Berndt, S.Miller, O.Williams, D.D.Le, B.T.Houseman, J.I.Pacold, F.Gorrec, W.C.Hon, Y.Liu, C.Rommel, P.Gaillard, T.Rückle, M.K.Schwarz, K.M.Shokat, J.P.Shaw, and R.L.Williams (2010).
The p110 delta structure: mechanisms for selectivity and potency of new PI(3)K inhibitors.
  Nat Chem Biol, 6, 117-124.
PDB codes: 2wxe 2wxf 2wxg 2wxh 2wxi 2wxj 2wxk 2wxl 2wxm 2wxn 2wxo 2wxp 2wxq 2wxr 2x38
20133840 B.G.Hale, P.S.Kerry, D.Jackson, B.L.Precious, A.Gray, M.J.Killip, R.E.Randall, and R.J.Russell (2010).
Structural insights into phosphoinositide 3-kinase activation by the influenza A virus NS1 protein.
  Proc Natl Acad Sci U S A, 107, 1954-1959.
PDB code: 3l4q
20379207 B.Vanhaesebroeck, J.Guillermet-Guibert, M.Graupera, and B.Bilanges (2010).
The emerging mechanisms of isoform-specific PI3K signalling.
  Nat Rev Mol Cell Biol, 11, 329-341.  
20071333 G.Patino-Lopez, L.Aravind, X.Dong, M.J.Kruhlak, E.M.Ostap, and S.Shaw (2010).
Myosin 1G is an abundant class I myosin in lymphocytes whose localization at the plasma membrane depends on its ancient divergent pleckstrin homology (PH) domain (Myo1PH).
  J Biol Chem, 285, 8675-8686.  
21030680 H.A.Dbouk, H.Pang, A.Fiser, and J.M.Backer (2010).
A biochemical mechanism for the oncogenic potential of the p110beta catalytic subunit of phosphoinositide 3-kinase.
  Proc Natl Acad Sci U S A, 107, 19897-19902.  
  20009532 L.Zhao, and P.K.Vogt (2010).
Hot-spot mutations in p110alpha of phosphatidylinositol 3-kinase (pI3K): differential interactions with the regulatory subunit p85 and with RAS.
  Cell Cycle, 9, 596-600.  
20713702 M.Sun, P.Hillmann, B.T.Hofmann, J.R.Hart, and P.K.Vogt (2010).
Cancer-derived mutations in the regulatory subunit p85alpha of phosphoinositide 3-kinase function through the catalytic subunit p110alpha.
  Proc Natl Acad Sci U S A, 107, 15547-15552.  
20176047 N.T.Ihle, and G.Powis (2010).
Inhibitors of phosphatidylinositol-3-kinase in cancer therapy.
  Mol Aspects Med, 31, 135-144.  
  21179398 O.Schmidt-Kittler, J.Zhu, J.Yang, G.Liu, W.Hendricks, C.Lengauer, S.B.Gabelli, K.W.Kinzler, B.Vogelstein, D.L.Huso, and S.Zhou (2010).
PI3Kα inhibitors that inhibit metastasis.
  Oncotarget, 1, 339-348.  
20799872 S.Carvalho, and F.Schmitt (2010).
Potential role of PI3K inhibitors in the treatment of breast cancer.
  Future Oncol, 6, 1251-1263.  
20689039 Z.Sun, Z.Li, and Y.Zhang (2010).
Adult testicular dysgenesis of Inhba conditional knockout mice may also be caused by disruption of cross-talk between Leydig cells and germ cells.
  Proc Natl Acad Sci U S A, 107, E135; author reply E136.  
  19902965 T.W.Sturgill, and M.N.Hall (2009).
Activating mutations in TOR are in similar structures as oncogenic mutations in PI3KCalpha.
  ACS Chem Biol, 4, 999.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.