The Ligand Specificity of Yeast Rad53 FHA Domains at the +3 Position Is Determined by Nonconserved Residues^,

Abstract

On the basis of the results from our laboratory and others, we recently suggested that the ligand specificity of forkhead-associated (FHA) domains is controlled by variations in three major factors: (i) residues interacting with pThr, (ii) residues recognizing the +1 to +3 residues from pThr, and (iii) an extended binding surface. While the first factor has been well established by several solution and crystal structures of FHA-phosphopeptide complexes, the structural bases of the second and third factors are not well understood and are likely to vary greatly between different FHA domains. In this work, we proposed and tested the hypothesis that nonconserved residues G133 and G135 of FHA1 and I681 and D683 of FHA2, located outside of the core FHA region of yeast Rad53 FHA domains, contribute to the specific recognition of the +3 position of different phosphopeptides. By rational mutagenesis of these residues, the specificity of FHA1 has been changed from predominantly pTXXD to be equally acceptable for pTXXD, pTXXL, and pYXL, which are similar to the specificities of the FHA2 domain of Rad53. Conversely, the +3 position specificity of FHA2 has been engineered to be more like FHA1 with the I681A mutation. These results were based on library screening as well as binding analyses of specific phosphopeptides. Furthermore, results of structural analyses by NMR indicate that some of these residues are also important for the structural integrity of the loops.Recently, a phosphorylation-dependent recognition domain, known as the forkhead-associated (FHA) 1 domain, has been shown to mediate protein-protein interactions in many cellular processes of different species (1-4). Although the FHA domain has been found in more than 200 different proteins, the tertiary structure has only been obtained for yeast Rad53 (which consists of two FHA domains, FHA1 at the N-terminus and FHA2 at the C-terminus), human Chk2, human Chfr, human Ki67, and plant kinase-associated protein phosphatase (KAPP) (5-11). While the level of sequence homology of FHA domains is relatively low (∼20%), the tertiary structures reveal a remarkably similar folding, consisting of -strands linked by several loops to form two large twisted antiparallel -sheets folded into a -sandwich. The biological functions of FHA domains are very diverse. Therefore, the structure-function relationship of FHA domains and the structural basis of interactions between FHA domains and their binding proteins have been subjects of extensive research in many laboratories. The biological binding protein and the actual binding site have been unequivocally identified in only very few cases (12-16). Nevertheless, a wealth of information about the ligand specificity of FHA domains has been obtained by use of short phosphopeptides and phosphopeptide libraries consisting of 6-15 residues (5-7, 9, 17-20). These studies with short phosphopeptides showed that, while the Rad53 FHA1 domain specifically recognizes the phosphothreonine peptides containing Asp at the +3 position (pTXXD),...

PhosphoThr Peptide Binding Globally Rigidifies Much of the FHA Domain from Arabidopsis Receptor Kinase-Associated Protein Phosphatase,

“…The pT+3 position of peptide ligands is the most important determinant of their affinity for FHA domains (3,79). The non-conserved residues that divergent FHA domains place around the pT+3 site appear to be important for affinity (77). These residues of KI-FHA of KAPP, namely Gly227, Leu249, Gly284, and Thr285 are rigid (Figure 4,Figure 5), consistent with the theme of high rigidity of residues conferring affinity (12,78).…”

Chlamydophila pneumoniae PknD Exhibits Dual Amino Acid Specificity and Phosphorylates Cpn0712, a Putative Type III Secretion YscD Homolog

“…The GST-FHA-2 point mutants were phosphorylated by GST-PknD KD to the same level as GST-FHA-2 (data not shown), suggesting that FHA-2 conserved amino acids S441 and N464 play only a minor role, if any, in mediating the interaction with PknD. Alternatively, other conserved or nonconserved amino acids within the FHA-2 domain may be important in mediating interactions with PknD; it has recently been demonstrated that the ligand specificity of the FHA domains of Rad53 is determined by nonconserved amino acid residues (35). Despite our inability to indicate a role for FHA-2 S441 or N464 in binding to PknD, our results clearly show that Cpn0712 is indeed a substrate of PknD.…”

A Novel Non-canonical Forkhead-associated (FHA) Domain-binding Interface Mediates the Interaction between Rad53 and Dbf4 Proteins

“…The protein was purified as described above and stored in 10 mM sodium phosphate buffer (pH 6.5), 1 mM EDTA, and 5 mM DTT. All experiments with labeled FHA1 were conducted at 293 K as described previously (25). Experiments including both 15N FHA1 and HBRCT (or BRCT) were also performed in 10 mM sodium phosphate buffer (pH 6.5), 1 mM EDTA, and 5 mM DTT.…”