PDBsum entry 3cly

Transferase

PDB id: 3cly

Contents

Protein chain

291 a.a. *

Ligands

ACP

Metals

_MG ×2

Waters ×107

* Residue conservation analysis

PDB id:

3cly

Name:

Transferase

Title:

Crystal structure of fgf receptor 2 (fgfr2) kinase domains trapped in trans-phosphorylation reaction

Structure:

Fibroblast growth factor receptor 2. Chain: a. Fragment: protein kinase domain. Synonym: fgfr-2, keratinocyte growth factor receptor 2, cd332 antigen. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: fgfr2, bek, kgfr, ksam. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.217 R-free: 0.247

Authors:

H.Chen,M.Mohammadi

Key ref:

H.Chen et al. (2008). A crystallographic snapshot of tyrosine trans-phosphorylation in action. Proc Natl Acad Sci U S A, 105, 19660-19665. PubMed id: 19060208 DOI: 10.1073/pnas.0807752105

Date:

20-Mar-08 Release date: 03-Feb-09

Protein chain

P21802  (FGFR2_HUMAN) -  Fibroblast growth factor receptor 2 from Homo sapiens

Seq: 821 a.a.

Struc: 291 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.7.10.1 - receptor protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] (Bound ligand (Het Group name = ACP) matches with 81.25% similarity) + ADP + H(+)

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

Added reference

DOI no: 10.1073/pnas.0807752105

Proc Natl Acad Sci U S A 105:19660-19665 (2008)

PubMed id: 19060208

A crystallographic snapshot of tyrosine trans-phosphorylation in action.

H.Chen, C.F.Xu, J.Ma, A.V.Eliseenkova, W.Li, P.M.Pollock, N.Pitteloud, W.T.Miller, T.A.Neubert, M.Mohammadi.

ABSTRACT

Tyrosine trans-phosphorylation is a key event in receptor tyrosine kinase signaling, yet, the structural basis for this process has eluded definition. Here, we present the crystal structure of the FGF receptor 2 kinases caught in the act of trans-phosphorylation of Y769, the major C-terminal phosphorylation site. The structure reveals that enzyme- and substrate-acting kinases engage each other through elaborate and specific interactions not only in the immediate vicinity of Y769 and the enzyme active site, but also in regions that are as much of 18 A away from D626, the catalytic base in the enzyme active site. These interactions lead to an unprecedented level of specificity and precision during the trans-phosphorylation on Y769. Time-resolved mass spectrometry analysis supports the observed mechanism of trans-phosphorylation. Our data provide a molecular framework for understanding the mechanism of action of Kallmann syndrome mutations and the order of trans-phosphorylation reactions in FGFRs. We propose that the salient mechanistic features of Y769 trans-phosphorylation are applicable to trans-phosphorylation of the equivalent major phosphorylation sites in many other RTKs.

Selected figure(s)

Figure 1.
Crystallographic snapshot of the trans-phosphorylation reaction at Y769, a major phosphorylation site in FGFR2K. (A) The substrate-acting kinase (in yellow) interacts with both N- and C-lobe of the enzyme-acting kinase (in green) during the trans-phosphorylation on Y769. (B) The tyrosine of the peptide substrate in the kinase-peptide structure (in blue) occupies a similar position as the Y769 in the substrate-acting kinase. (C) The trans-phosphorylation reaction on Y769 phosphorylation site. The near parallel arrangement of the αI helix from the substrate-acting kinase and the αG helix from the enzyme-acting kinase is denoted by the two arrows. The extra ordered residues at the C-tail of the trans-phosphorylating kinases structure compared with the kinase-peptide structure are highlighted in magenta. (D) The interaction between the C-lobe of the substrate-acting kinase and the N-lobe of the enzyme-acting kinase. Selected residues are show in stick diagrams. Atom colorings are as follows: red, oxygens; blue, nitrogens; yellow, phosphorus; carbons are colored according to the kinase molecule to which they belong. Hydrogen bonds are shown as black dashed lines. The ATP analogue (in cyan) is shown in stick representation, and its molecular surface is also shown as a solid semitransparent surface. Mg^2+ ions are in pink.

Figure 2.
Structural basis for the trans-phosphorylation on Y769 of FGFR2K. (A) Detailed view of the interactions between the substrate-acting kinase and the enzyme-acting kinase in the vicinity of active site. (B) In the kinase-peptide structure, the peptide substrate makes limited contacts with the enzyme. (C) Detailed view of the hydrophobic interactions between the L770 (P+1) and L772 (P+3) residues of the substrate-acting kinase and the residues from the A-loop and the αG and αEF helices of the enzyme-acting kinase. (D) Detailed view of the interaction between the C-lobe of the substrate-acting kinase and the nucleotide-binding loop of the enzyme-acting kinase. Yellow, substrate-acting kinase; green, enzyme-acting kinase; blue, kinase in the kinase-peptide structure; wheat, peptide substrate. Atom colorings are as in Fig. 1. Hydrogen bonds, the ATP analogue and Mg^2+ ions are rendered as in Fig. 1. Hydrophobic interactions are rendered as solid semitransparent surfaces.

Figures were selected by an automated process.