PDBsum entry: 1he8

Kinase/hydrolase

PDB id: 1he8

Contents

Protein chains

749 a.a. *

166 a.a. *

Ligands

GNP

Metals

_MG

Waters ×6

* Residue conservation analysis

PDB id:

1he8

Name:

Kinase/hydrolase

Title:

Ras g12v - pi 3-kinase gamma complex

Structure:

Phosphatidylinositol 3-kinase catalytic subunit, gamma isoform. Chain: a. Fragment: p110 gamma catalytic subunit. Synonym: pi3-kinase p110 subunit gamma, ptdins-3-kinase p110, pi3k. Engineered: yes. Mutation: yes. Transforming protein p21/h-ras-1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: c41(de3).

Biol. unit:

Dimer (from PQS)

Resolution:

3.0Å R-factor: 0.212 R-free: 0.280

Authors:

M.E.Pacold,S.Suire,O.Perisic,S.Lara-Gonzalez,C.T.Davis, P.T.Hawkins,E.H.Walker,L.Stephens,J.F.Eccleston, R.L.Williams

Key ref:

M.E.Pacold et al. (2000). Crystal structure and functional analysis of Ras binding to its effector phosphoinositide 3-kinase gamma. Cell, 103, 931-943. PubMed id: 11136978 DOI: 10.1016/S0092-8674(00)00196-3

Date:

20-Nov-00 Release date: 08-Jan-01

Protein chain

P48736  (PK3CG_HUMAN) -  Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform

Seq: 1102 a.a.

Struc: 749 a.a.*

Protein chain

P23175  (RASH_MSVNS) -  GTPase HRas

Seq: 189 a.a.

Struc: 166 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.7.1.153 - Phosphatidylinositol-4,5-bisphosphate 3-kinase.
• Pathway: 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

ATP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate = ADP (Bound ligand (Het Group name = GNP) matches with 78.00% similarity) + 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate

• Enzyme class 3: Chain A: E.C.2.7.11.1 - Non-specific serine/threonine protein kinase.
• Reaction: ATP + a protein = ADP + a 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 

• Cellular component: membrane (2 terms)
• Biological process: signal transduction (5 terms)
• Biochemical function: binding (8 terms)

reference

DOI no: 10.1016/S0092-8674(00)00196-3

Cell 103:931-943 (2000)

PubMed id: 11136978

Crystal structure and functional analysis of Ras binding to its effector phosphoinositide 3-kinase gamma.

M.E.Pacold, S.Suire, O.Perisic, S.Lara-Gonzalez, C.T.Davis, E.H.Walker, P.T.Hawkins, L.Stephens, J.F.Eccleston, R.L.Williams.

ABSTRACT

Ras activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. We find that PI3Kgamma is strongly and directly activated by H-Ras G12V in vivo or by GTPgammaS-loaded H-Ras in vitro. We have determined a crystal structure of a PI3Kgamma/Ras.GMPPNP complex. A critical loop in the Ras binding domain positions Ras so that it uses its switch I and switch II regions to bind PI3Kgamma. Mutagenesis shows that interactions with both regions are essential for binding PI3Kgamma. Ras also forms a direct contact with the PI3Kgamma catalytic domain. These unique Ras/PI3Kgamma interactions are likely to be shared by PI3Kalpha. The complex with Ras shows a change in the PI3K conformation that may represent an allosteric component of Ras activation.

Selected figure(s)

Figure 3.
Figure 3. Structure of a Ras·PI3Kγ Complex(A) Diagram of the PI3Kγ·Ras interface. Also shown are the residues that hold the 255–267 loop in place. The RBD is colored purple, the Ras is orange, and the catalytic domain is yellow. Putative hydrogen bonds are indicated by dashed lines, and possible salt bridges by dotted lines. PI3Kγ residues that can be mutated to eliminate or attenuate binding are colored red or blue, respectively. Ellipses indicate residues that were mutated to enhance binding. The V223K tighter binding mutant is shown hydrogen bonding to Ras Glu37.(B) A closer view of the interface between the RBD (purple) and Ras (orange). The switch I and switch II regions of Ras are colored pale and dark blue, respectively. Boxes around residue labels denote mutations that abolish binding, and ellipses indicate mutations that enhance binding. The 255–267 loop that becomes ordered on binding is colored dark green. The GMPPNP and Mg^2+ in Ras are rendered in gray.(C) Molecular surface of the Ras·PI3Kγ complex. The Ras (orange) and four domains of the PI3Kγ, comprising the RBD (purple), C2 domain (cyan), helical domain (green), and N- and C-terminal lobes of the catalytic domain (red and yellow) are shown. The N-terminal linker is rendered in white. A schematic of PI3Kγ domain organization is also shown.(D) Ribbon diagram of the Ras·PI3Kγ complex. The color scheme is the same as the previous panel. The location of the γ phosphate of the ATP·PI3Kγ structure is marked with a large gray sphere. This location roughly corresponds to the phosphoinositide headgroup binding site.

Figure 6.
Figure 6. A Putative Model of the Ras·PI3Kγ Complex at a Membrane SurfaceAll regions not visible in the structure are drawn as dashed lines. Lys973 marks the substrate binding loop. The 20 residue C-terminal tail of Ras was arbitrarily modeled to illustrate that this peptide could easily span the gap between the RBD-bound Ras and the putative membrane surface. The location of the farnesyl group is indicated schematically. Potential membrane-interacting residues at the tips of the catalytic domain loops are labeled.

The above figures are reprinted by permission from Cell Press: Cell (2000, 103, 931-943) copyright 2000.

Figures were selected by the author.