PDBsum entry 3dqw

Transferase

PDB id: 3dqw

Contents

Protein chains

279 a.a. *

Ligands

AGS ×4

Metals

_MG ×4

Waters ×628

* Residue conservation analysis

PDB id:

3dqw

Name:

Transferase

Title:

C-src kinase domain thr338ile mutant in complex with atpgs

Structure:

Proto-oncogene tyrosine-protein kinase src. Chain: a, b, c, d. Fragment: chicken c-src kinase domain 251-533. Synonym: pp60c-src, p60-src, c-src. Engineered: yes. Mutation: yes

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Gene: src. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.02Å R-factor: 0.207 R-free: 0.246

Authors:

M.Azam,M.A.Seeliger,N.Gray,J.Kuriyan,G.Q.Daley

Key ref:

M.Azam et al. (2008). Activation of tyrosine kinases by mutation of the gatekeeper threonine. Nat Struct Biol, 15, 1109-1118. PubMed id: 18794843 DOI: 10.1038/nsmb.1486

Date:

09-Jul-08 Release date: 23-Sep-08

Protein chains

P00523  (SRC_CHICK) -  Proto-oncogene tyrosine-protein kinase Src from Gallus gallus

Seq: 533 a.a.

Struc: 279 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.7.10.2 - non-specific protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

L-tyrosyl-[protein] (Bound ligand (Het Group name = AGS) matches with 93.75% similarity) + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1038/nsmb.1486

Nat Struct Biol 15:1109-1118 (2008)

PubMed id: 18794843

Activation of tyrosine kinases by mutation of the gatekeeper threonine.

M.Azam, M.A.Seeliger, N.S.Gray, J.Kuriyan, G.Q.Daley.

ABSTRACT

Protein kinases targeted by small-molecule inhibitors develop resistance through mutation of the 'gatekeeper' threonine residue of the active site. Here we show that the gatekeeper mutation in the cellular forms of c-ABL, c-SRC, platelet-derived growth factor receptor-alpha and -beta, and epidermal growth factor receptor activates the kinase and promotes malignant transformation of BaF3 cells. Structural analysis reveals that a network of hydrophobic interactions-the hydrophobic spine-characteristic of the active kinase conformation is stabilized by the gatekeeper substitution. Substitution of glycine for the residues constituting the spine disrupts the hydrophobic connectivity and inactivates the kinase. Furthermore, a small-molecule inhibitor that maximizes complementarity with the dismantled spine (compound 14) inhibits the gatekeeper mutation of BCR-ABL-T315I. These results demonstrate that mutation of the gatekeeper threonine is a common mechanism of activation for tyrosine kinases and provide structural insights to guide the development of next-generation inhibitors.

Selected figure(s)

Figure 4.
(a) The surface projections of the hydrophobic spine that assembled during ABL kinase activation in ABL-ADP conformation (shown in blue; PDB 2G2I). The gatekeeper residue, Thr334, is shown as an orange surface. (b) The surface projections of the dismantled hydrophobic spine in the inactive kinase conformation of ABL–imatinib (PDB 1OPJ). Imatinib binds to the inactive kinase which is stabilized by the DFG-out conformation caused by dismantling of the hydrophobic spine.

Figure 5.
(a) Crystal structure of chicken c-SRC-T338I bound to ATP S. SRC-T338I is homologous to T334I in human c-SRC. Chicken SRC residues are numbered according to the human c-SRC kinase numbering. The residues Leu328, Met317, Phe408 and His387, which constitute the hydrophobic spine, are shown in blue. The gatekeeper isoleucine residue is shown in orange. The activation loop is shown in red. (b) The inactive conformation of chicken c-SRC (PDB 2SRC), colored as in a. (c) Active site of Lck kinase (PDB 1QPC) in the active state bound with AMP-PNP shown in yellow. Gatekeeper residue Thr316 and the catalytic Lys273 are shown as green surfaces. The water molecules sandwiched between the residues Thr316 and Lys273 are shown as red circles. The interactions of lysine with ANP and the catalytic Glu288 are shown; bond distances are presented in angstroms. (d) Active site of SRC-T341I kinase domain (PDB 3DQW) bound with ATP S shown in yellow. The surfaces of the side chains for residues Ile341 and Lys298 are shown in green. Interactions of Lys298 with Glu310 and ATP S are mapped and the bond distances are indicated in angstroms. (e) Active site of insulin receptor kinase (IRK; PDB entry 1GAG) bound with ANP shown in yellow. The surfaces of the side chains for residues Met1076 and Lys1030 are shown in green. Interactions of catalytic Lys1030 with Glu1047 and ANP are mapped, and the bond distances are indicated in angstroms.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 1109-1118) copyright 2008.

Figures were selected by an automated process.