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

  • Thomas W. Traut
Part of the EJB Reviews 1994 book series (EJB REVIEWS, volume 1994)

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-1 and NMP-2 bind to the pentose and phosphate of the bound ligand. NMP-1 is found in almost all the kinases that phosphorylate AMP, CMP, GMP, dTMP, or UMP. NMP-3 a 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 γ-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.

Keywords

Regulatory Site Adenylate Kinase Consensus Motif Phosphoglycerate Kinase tRNA Synthetase 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

Ap5A

adenosine(5′)pentaphospho(5′)adenosine

Ef

elongation factor

PFru

phosphofructo

PGri

phosphoglycerate

RS

tRNA synthetase.

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Copyright information

© FEBS 1994

Authors and Affiliations

  • Thomas W. Traut
    • 1
  1. 1.Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillUSA

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