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Transferase/oncoprotein PDB-id
2rd0
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Description
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References
PROCHECK
Protein chains
997 a.a. *
139 a.a. *

* Residue conservation analysis
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PDB id: 2rd0
Name: Transferase/oncoprotein
Title: Structure of a human p110alpha/p85alpha complex

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. Phosphatidylinositol 3-kinase regulatory subunit alpha. Chain: b.

Source:
Homo sapiens. Human. Organism_taxid: 9606. Gene: pik3ca. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: pik3r1, grb1.

UniProt:
Chain A: P42336 (PK3CA_HUMAN)
Pfam   ArchSchema ?
Seq:
Struc:
Seq:
Struc:
Seq:
Struc:
Seq:
Struc:
Seq: 1068 a.a.
Struc: 997 a.a.*

Chain B: P27986 (P85A_HUMAN)
Pfam   ArchSchema ?
Seq:
Struc:
Seq:
Struc:
Seq: 724 a.a.
Struc: 139 a.a.
Key:    PfamA domain
 Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme class:
Chain A: E.C.2.7.1.153   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:
ATP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate = ADP + 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate (see diagram below)

Pathway:
1-Phosphatidyl-myo-inositol Metabolism

Resolution:
3.05Å

R-factor:
0.267

R-free:
0.323

Authors:
C.Huang,S.B.Gabelli,L.M.Amzel

Key ref:
C.H.Huang et al. (2007). The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations.. Science, 318, 1744-1748. [PubMed id: 18079394] [DOI: 10.1126/science.1150799]

Date:
20-Sep-07

Release date:
25-Dec-07
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Enzyme reaction for E.C.2.7.1.153


ATP
+
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
=
ADP
+
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

 
    Key reference    
 
 
DOI no: 10.1126/science.1150799 Science 318:1744-1748 (2007)
PubMed id: 18079394  
 
 
The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations.
C.H.Huang, D.Mandelker, O.Schmidt-Kittler, Y.Samuels, V.E.Velculescu, K.W.Kinzler, B.Vogelstein, S.B.Gabelli, L.M.Amzel.
 
  ABSTRACT  
 
PIK3CA, one of the two most frequently mutated oncogenes in human tumors, codes for p110alpha, the catalytic subunit of a phosphatidylinositol 3-kinase, isoform alpha (PI3Kalpha, p110alpha/p85). Here, we report a 3.0 angstrom resolution structure of a complex between p110alpha and a polypeptide containing the p110alpha-binding domains of p85alpha, a protein required for its enzymatic activity. The structure shows that many of the mutations occur at residues lying at the interfaces between p110alpha and p85alpha or between the kinase domain of p110alpha and other domains within the catalytic subunit. Disruptions of these interactions are likely to affect the regulation of kinase activity by p85 or the catalytic activity of the enzyme, respectively. In addition to providing new insights about the structure of PI3Kalpha, these results suggest specific mechanisms for the effect of oncogenic mutations in p110alpha and p85alpha.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Mutations in PIK3CA identified in human cancers. (A) Distribution of representative mutations within p110 . Residues mutated in cancers are shown as CPK models. The start of the cancer-associated truncation (residue 571 of p85) is shown by the red arrowhead. (B) Electron density map of Arg^38 and Arg^88 cancer mutations shown at the interface between the ABD and the kinase domains. (C) Close-up view of the interface of the C2 domain of p110 with iSH2 of p85. The stick representation of the Asn^345 mutation of C2 and the residues within iSH2 (Asp^560 and Asn^564) with which it may interact are shown. (D) Mutations in the helical domain (Glu^542, Glu^545, and Gln^546), located at the interface with nSH2 (orange surface). (E) Mutations of the kinase domain (Met^1043 and His^1047), located near the C-terminal end of the activation loop, are shown in light green. The part of the activation loop between residues 941 and 950 could not be traced (see text).
Figure 3.
Fig. 3. Model of membrane interaction. (A) Positively charged residues on the surface of iSH2 domain of p85 (red) and loops of the C2 and kinase domains of p110 (black) are proposed to contact the negatively charged phospholipid bilayer. (B) Model of p110 /niSH2 bound to Ras and its proposed orientation with respect to the lipid membrane.
 
  The above figures are reprinted by permission from the AAAs: Science (2007, 318, 1744-1748) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20081818 P.Workman, and R.L.van Montfort (2010).
PI(3) kinases: revealing the delta lady.
  Nat Chem Biol, 6, 82-83.  
  18523868 C.García-Echeverría (2009).
Protein and lipid kinase inhibitors as targeted anticancer agents of the Ras/Raf/MEK and PI3K/PKB pathways.
  Purinergic Signal, 5, 117-125.  
19293927 C.Zhang, N.Yang, C.H.Yang, H.S.Ding, C.Luo, Y.Zhang, M.J.Wu, X.W.Zhang, X.Shen, H.L.Jiang, L.H.Meng, and J.Ding (2009).
S9, a novel anticancer agent, exerts its anti-proliferative activity by interfering with both PI3K-Akt-mTOR signaling and microtubule cytoskeleton.
  PLoS ONE, 4, e4881.  
19290933 D.A.Fruman, and G.Bismuth (2009).
Fine tuning the immune response with PI3K.
  Immunol Rev, 228, 253-272.  
19805105 D.Mandelker, S.B.Gabelli, O.Schmidt-Kittler, J.Zhu, I.Cheong, C.H.Huang, K.W.Kinzler, B.Vogelstein, and L.M.Amzel (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.
PDB codes: 3hhm 3hiz
19779456 H.Lempiäinen, and T.D.Halazonetis (2009).
Emerging common themes in regulation of PIKKs and PI3Ks.
  EMBO J, 28, 3067-3073.  
19915146 H.Wu, S.C.Shekar, R.J.Flinn, M.El-Sibai, B.S.Jaiswal, K.I.Sen, V.Janakiraman, S.Seshagiri, G.J.Gerfen, M.E.Girvin, and J.M.Backer (2009).
Regulation of Class IA PI 3-kinases: C2 domain-iSH2 domain contacts inhibit p85/p110alpha and are disrupted in oncogenic p85 mutants.
  Proc Natl Acad Sci U S A, 106, 20258-20263.  
19629070 J.A.Engelman (2009).
Targeting PI3K signalling in cancer: opportunities, challenges and limitations.
  Nat Rev Cancer, 9, 550-562.  
19603024 J.Souglakos, J.Philips, R.Wang, S.Marwah, M.Silver, M.Tzardi, J.Silver, S.Ogino, S.Hooshmand, E.Kwak, E.Freed, J.A.Meyerhardt, Z.Saridaki, V.Georgoulias, D.Finkelstein, C.S.Fuchs, M.H.Kulke, and R.A.Shivdasani (2009).
Prognostic and predictive value of common mutations for treatment response and survival in patients with metastatic colorectal cancer.
  Br J Cancer, 101, 465-472.  
19234438 L.Catasus, A.Gallardo, M.Cuatrecasas, and J.Prat (2009).
Concomitant PI3K-AKT and p53 alterations in endometrial carcinomas are associated with poor prognosis.
  Mod Pathol, 22, 522-529.  
19668850 M.A.Ali, and T.Sjöblom (2009).
Molecular pathways in tumor progression: from discovery to functional understanding.
  Mol Biosyst, 5, 902-908.  
19318683 M.Niedermeier, B.T.Hennessy, Z.A.Knight, M.Henneberg, J.Hu, A.V.Kurtova, W.G.Wierda, M.J.Keating, K.M.Shokat, and J.A.Burger (2009).
Isoform-selective phosphoinositide 3'-kinase inhibitors inhibit CXCR4 signaling and overcome stromal cell-mediated drug resistance in chronic lymphocytic leukemia: a novel therapeutic approach.
  Blood, 113, 5549-5557.  
18951408 P.K.Mankoo, S.Sukumar, and R.Karchin (2009).
PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations.
  Proteins, 75, 499-508.  
19644473 P.Liu, H.Cheng, T.M.Roberts, and J.J.Zhao (2009).
Targeting the phosphoinositide 3-kinase pathway in cancer.
  Nat Rev Drug Discov, 8, 627-644.  
19564600 Y.Yu, R.Anjum, K.Kubota, J.Rush, J.Villen, and S.P.Gygi (2009).
A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry.
  Proc Natl Acad Sci U S A, 106, 11606-11611.  
18794885 C.Garcia-Echeverria, and W.R.Sellers (2008).
Drug discovery approaches targeting the PI3K/Akt pathway in cancer.
  Oncogene, 27, 5511-5526.  
18673581 E.Hodis, J.Prilusky, E.Martz, I.Silman, J.Moult, and J.L.Sussman (2008).
Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules.
  Genome Biol, 9, R121.  
18633356 L.M.Amzel, C.H.Huang, D.Mandelker, C.Lengauer, S.B.Gabelli, and B.Vogelstein (2008).
Structural comparisons of class I phosphoinositide 3-kinases.
  Nat Rev Cancer, 8, 665-669.  
19568796 L.M.Ballou, and R.Z.Lin (2008).
Rapamycin and mTOR kinase inhibitors.
  J Chem Biol, 1, 27-36.  
18268322 L.Zhao, and P.K.Vogt (2008).
Helical domain and kinase domain mutations in p110alpha of phosphatidylinositol 3-kinase induce gain of function by different mechanisms.
  Proc Natl Acad Sci U S A, 105, 2652-2657.  
18794883 L.Zhao, and P.K.Vogt (2008).
Class I PI3K in oncogenic cellular transformation.
  Oncogene, 27, 5486-5496.  
18772890 R.McLendon, A.Friedman, D.Bigner, E.G.Van Meir, D.J.Brat, G.M.Mastrogianakis, J.J.Olson, T.Mikkelsen, N.Lehman, K.Aldape, W.K.Yung, O.Bogler, J.N.Weinstein, S.VandenBerg, M.Berger, M.Prados, D.Muzny, M.Morgan, S.Scherer, A.Sabo, L.Nazareth, L.Lewis, O.Hall, Y.Zhu, Y.Ren, O.Alvi, J.Yao, A.Hawes, S.Jhangiani, G.Fowler, A.San Lucas, C.Kovar, A.Cree, H.Dinh, J.Santibanez, V.Joshi, M.L.Gonzalez-Garay, C.A.Miller, A.Milosavljevic, L.Donehower, D.A.Wheeler, R.A.Gibbs, K.Cibulskis, C.Sougnez, T.Fennell, S.Mahan, J.Wilkinson, L.Ziaugra, R.Onofrio, T.Bloom, R.Nicol, K.Ardlie, J.Baldwin, S.Gabriel, E.S.Lander, L.Ding, R.S.Fulton, M.D.McLellan, J.Wallis, D.E.Larson, X.Shi, R.Abbott, L.Fulton, K.Chen, D.C.Koboldt, M.C.Wendl, R.Meyer, Y.Tang, L.Lin, J.R.Osborne, B.H.Dunford-Shore, T.L.Miner, K.Delehaunty, C.Markovic, G.Swift, W.Courtney, C.Pohl, S.Abbott, A.Hawkins, S.Leong, C.Haipek, H.Schmidt, M.Wiechert, T.Vickery, S.Scott, D.J.Dooling, A.Chinwalla, G.M.Weinstock, E.R.Mardis, R.K.Wilson, G.Getz, W.Winckler, R.G.Verhaak, M.S.Lawrence, M.O'Kelly, J.Robinson, G.Alexe, R.Beroukhim, S.Carter, and D.Chiang (2008).
Comprehensive genomic characterization defines human glioblastoma genes and core pathways.
  Nature, 455, 1061-1068.  
18621722 T.L.Yuan, H.S.Choi, A.Matsui, C.Benes, E.Lifshits, J.Luo, J.V.Frangioni, and L.C.Cantley (2008).
Class 1A PI3K regulates vessel integrity during development and tumorigenesis.
  Proc Natl Acad Sci U S A, 105, 9739-9744.  
18794884 T.L.Yuan, and L.C.Cantley (2008).
PI3K pathway alterations in cancer: variations on a theme.
  Oncogene, 27, 5497-5510.  
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 codes are shown on the right.