The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide‐binding sites

Abstract

From an analysis of current data on 16 protein structures with defined nucleotide-binding sites consensus motifs were determined for the peptide segments that form such nucleotide-binding sites. This was done by using the actual residues shown to contact ligands in the different protein structures, plus an additional 50 sequences for various kinases. Three peptide segments are commonly required to form the binding site for ATP or GTP. Binding motif Kinase-1 a is found in almost all sequences examined, and functions in binding the phosphates of the ligand. Variant versions, comparable to Kinase-1 a, are found in a subset of proteins and appear to be related to unique functions of those enzymes. Motif Kinase-2 contains the conserved aspartate that coordinates the metal ion on Mg-ATP. Motif Kinase-3 occurs in at least four versions, and functions in binding the purine base or the pentose. Two protein structures show ATP-binding at a separate regulatory site, formed by the motifs Regulatory-1 and Regulatory-2. Structures for adenylate kinase and guanylate kinase show three different sequence motifs that form the binding site for a nucleoside monophosphate (NMP). NMP-I and NMP-2 bind to the pentose and phosphate of the bound ligand. NMP-I is found in almost all the kinases that phosphorylate AMP, CMP, GMP, dTMP, or UMP. NMP-3a is found in kinases for AMP, GMP, and UMP, while NMP-3b binds only GMP. For the binding of NTPs, three distinct types of nucleotide-binding fold structures have been described. Each structure is associated with a particular function (e.g. transfer of the y-phosphate, or of the adenylate to an acceptor) and also with a particular spatial arrangement of the three Kinase segments evident in the linear sequence for the protein.With the rapid proliferation of DNA sequences in the last decade, the finding that a few consensus sequences might generally correspond to ATP-binding sites was immediately useful. In 1982 Walker et al. deduced from a search of available sequences for ATP-binding proteins that one, or both, of two sequence motifs appeared in nine proteins, with four proteins having both sequences [l]. Since both of these motifs occurred in porcine adenylate kinase, at positions corresponding to the proposed nucleotide-bindmg site in the crystal structure [2], the association of these sequences with actual ATP-bindmg appeared to be established. Although adenylate kinase uses ATP to phosphorylate AMP, the crystal structure then available had some ambiguity as to whether the Walker A site or the Walker B site bound ATP or AMP; the appearance of these motif sequences in other ATP-binding proteins favored the former nucleotide site. Since this original paper also found only a Walker B sequence in phosphofructokinase [l], an easy interpretation was that either

Truncation of Amino Acids 12–128 Causes Deregulation of the Phosphatase Activity of the Sensor Kinase KdpD of Escherichia coli

“…4, a Walker B motif can also be found. The most frequently published form of the Walker A motif is GXXXXGKT (39,40). The motif found in KdpD has one more X between the first and second Gs.…”

Nucleotide bindind by the synapse associated protein SAP90

“…Kinetic analysis of mammalian GKs [20] revealed that the calculated Km values (in raM) for GMP are between 6 and 18 and only 10-20-fold lower for ATP (100-200 pM). Our results on GMP binding in SAP90 (Fig.…”

“…In contrast p55 contains the entire GxxGxGK motif found in the GKs. Additional residues (aa 131, 135, 146 in yeast GK) are expected to coordinate the phosphate groups of the ATP during phosphoryl transfer, based on structural studies on adenylate kinases [20,21]. Among these aa in GK which are believed to be essential for the catalysis, only one is conserved in the SAPs and in dlg-Ap (Fig.…”

Functional Inactivation of the Human Guanylyl Cyclase C Receptor: Modeling and Mutation of the Protein Kinase-like Domain

“…ATP binding sites in proteins may be classified into two broad types based on function (22). These are catalytic sites, which include protein kinases, ATP synthases, and adenyltransferases, and regulatory sites, such as those found in aspartate carbamoyl-transferase and phosphofructokinase.…”