PDBsum entry 1k2m

Transferase

PDB id: 1k2m

Contents

Protein chain

158 a.a. *

Ligands

GLU-ASP-ILE-PTR-TYR-LEU-ASP

* Residue conservation analysis

PDB id:

1k2m

Name:

Transferase

Title:

Solution structure of the fha2 domain of rad53 complexed with a phosphotyrosyl peptide derived from rad9

Structure:

Protein kinase spk1. Chain: a. Fragment: c-terminal fha domain (fha2). Engineered: yes. DNA repair protein rad9. Chain: p. Fragment: residues 826-832. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: spk1 or rad53. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: this phosphotyrosyl peptide was chemically synthesized.

NMR struc:

22 models

Authors:

I.-J.L.Byeon,S.Yongkiettrakul,M.-D.Tsai

Key ref:

I.J.Byeon et al. (2001). Solution structure of the yeast Rad53 FHA2 complexed with a phosphothreonine peptide pTXXL: comparison with the structures of FHA2-pYXL and FHA1-pTXXD complexes. J Mol Biol, 314, 577-588. PubMed id: 11846568 DOI: 10.1006/jmbi.2001.5141

Date:

28-Sep-01 Release date: 05-Dec-01

Protein chain

P22216  (RAD53_YEAST) -  Serine/threonine-protein kinase RAD53 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 821 a.a.

Struc: 158 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.12.1 - dual-specificity 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⁺
  3. L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

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

reference

DOI no: 10.1006/jmbi.2001.5141

J Mol Biol 314:577-588 (2001)

PubMed id: 11846568

Solution structure of the yeast Rad53 FHA2 complexed with a phosphothreonine peptide pTXXL: comparison with the structures of FHA2-pYXL and FHA1-pTXXD complexes.

I.J.Byeon, S.Yongkiettrakul, M.D.Tsai.

ABSTRACT

It was proposed previously that the FHA2 domain of the yeast protein kinase Rad53 has dual specificity toward pY and pT peptides. The consensus sequences of pY peptides for binding to FHA2, as well as the solution structures of free FHA2 and FHA2 complex with a pY peptide derived from Rad9, have been obtained previously. We now report the use of a pT library to screen for binding of pT peptides with the FHA2 domain. The results show that FHA2 binds favorably to pT peptides with Ile at the +3 position. We then searched the Rad9 sequences with a pTXXI/L motif, and tested the binding affinity of FHA2 toward ten pT peptides derived from Rad9. One of the peptides, (599)EVEL(pT)QELP(607), displayed the best binding affinity (K(d)=12.9 microM) and the greatest chemical shift changes. The structure of the FHA2 complex with this peptide was then determined by solution NMR and the structure of the complex between FHA2 and the pY peptide (826)EDI(pY)YLD(832) was further refined. Structural comparison of these two complexes indicates that the Leu residue at the +3 position in the pT peptide and that at the +2 position in the pY peptide occupy a very similar position relative to the binding site residues from FHA2. This can explain why FHA2 is able to bind both pT and pY peptides. This position change from +3 to +2 could be the consequence of the size difference between Thr and Tyr. Further insight into the structural basis of ligand specificity of FHA domains was obtained by comparing the structures of the FHA2-pTXXL complex obtained in this work and the FHA1-pTXXD complex reported in the accompanying paper.

Selected figure(s)

Figure 5.
Figure 5. Structures of (a) the FHA2-pT peptide complex and (b) the FHA2-pY peptide complex. FHA2 is shown in ribbons and the peptides are shown as sticks. The side-chains of (a) pT and (b) pY are colored magenta, and those of Leu at (a) +3 and at (b) +2 are colored green. The minimized mean structures are used.

Figure 7.
Figure 7. Diagrams showing detailed interactions between the phosphopeptide and the protein in (a) the FHA2-pT peptide complex and (b) the FHA2-pY peptide complex. Possible hydrogen bonds are defined as for Figure 6 and shown as dotted lines. Intermolecular NOEs are shown as double-pointed arrows, where thick and thin lines indicate strong and medium-sized NOEs, respectively. Highly conserved residues are colored cyan. The intramolecular hydrogen bond between Arg617 and Asp683 is also predicted and is shown with a question mark because the distance between donor and acceptor heavy atoms is somewhat larger than the definition: (a) 4.6 Å in the pT complex and (b) 4.8 Å in the pY complex.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 577-588) copyright 2001.

Figures were selected by an automated process.