PDBsum entry 3hiz

Transferase/oncoprotein

PDB id: 3hiz

Contents

Protein chains

1024 a.a. *

234 a.a. *

* Residue conservation analysis

PDB id:

3hiz

Name:

Transferase/oncoprotein

Title:

Crystal structure of p110alpha h1047r mutant in complex with nish2 of p85alpha

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. Phosphatidylinositol 3-kinase regulatory subunit alpha. Chain: b. Fragment: unp residues 322-694.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pik3ca. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7101. Gene: grb1, pi3kr1, pik3r1.

Resolution:

3.30Å R-factor: 0.263 R-free: 0.333

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

Date:

20-May-09 Release date: 29-Sep-09

Protein chain

P42336  (PK3CA_HUMAN) -  Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform from Homo sapiens

Seq: 1068 a.a.

Struc: 1024 a.a.*

Protein chain

P27986  (P85A_HUMAN) -  Phosphatidylinositol 3-kinase regulatory subunit alpha from Homo sapiens

Seq: 724 a.a.

Struc: 234 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺
• Enzyme class 3: Chain A: E.C.2.7.1.137 - phosphatidylinositol 3-kinase.

Pathway:

• Reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + ATP = a 1,2-diacyl- sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + ADP + H⁺
• Enzyme class 4: Chain A: E.C.2.7.1.153 - phosphatidylinositol-4,5-bisphosphate 3-kinase.

Pathway:

• Reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) + ATP = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3,4,5- trisphosphate) + ADP + H⁺

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

reference

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.

ABSTRACT

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.