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P II  protein is one of the largest families of signal transduction proteins in archaea, bacteria, and plants, controlling key processes of nitrogen assimilation. An intriguing characteristic for many P II  proteins is that the three ligand binding sites exhibit anticooperative allosteric regulation. In this work, P II  protein from  Synechococcus elongatus , a model for cyanobacteria and plant P II  proteins, is utilized to reveal the anticooperative mechanism upon binding of 2‐oxoglutarate (2‐OG). To this end, a method is proposed to define the binding pocket size by identifying residues that contribute greatly to the binding of 2‐OG. It is found that the anticooperativity is realized through population shift of the binding pocket size in an asymmetric manner. Furthermore, a new algorithm based on the dynamic correlation analysis is developed and utilized to discover residues that mediate the anticooperative process with high probability. It is surprising to find that the T‐loop, which is believed to be responsible for mediating the binding of P II  with its target proteins, also takes part in the intersubunit signal transduction process. Experimental results of P II  variants further confirmed the influence of T‐loop on the anticooperative regulation, especially on binding of the third 2‐OG. These discoveries extend our understanding of the P II  T‐loop from being essential in versatile binding of target protein to signal‐mediating in the anticooperative allosteric regulation. Proteins 2014; 82:1048–1059. © 2013 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Population shift of binding pocket size and dynamic correlation analysis shed new light on the anticooperative mechanism of P II protein