Receptor tyrosine kinases undergo ligand-induced dimerization that promotes kinase domain trans-autophosphorylation. However, the kinase domains of the insulin receptor are effectively dimerized because of the covalent alpha2beta2 holomeric structure. This fact has made it difficult to determine the molecular mechanism of intraholomeric autophosphorylation, but there is evidence for both cis- and trans-autophosphorylation in the absence and presence of insulin. Here, using the cytoplasmic kinase domain (CKD) of the human insulin receptor, we demonstrate that autophosphorylation in the juxtamembrane (JM) subdomain follows a cis-reaction pathway. JM autophosphorylation was independent of CKD concentration over the range 6 nM-3 microM and was characterized kinetically: Half-saturation (K(ATP)) was observed at 75 microM ATP [5 mM Mn(CH3CO2)2] with a maximal rate of 0.24 mol of PO4 (mol of CKD)(-1) min(-1). Pairwise substitutions of Phe for Tyr in the other two autophosphorylation subdomains, generated by site-directed mutagenesis, altered the kinetics of JM autophosphorylation but did not change the pathway from a cis-reaction. Tyr(1328,1334) to Phe (in the carboxy-terminal subdomain) yielded <2-fold increase in the efficiency of JM autophosphorylation, whereas Tyr(1162,1163) to Phe (in the activation loop subdomain) yielded approximately 38-fold increased efficiency of JM autophosphorylation, due predominantly to a 23-fold decreased K(ATP). These findings demonstrate basal state binding of ATP to the CKD leading to cis-autophosphorylation and novel basal state regulatory interactions among the subdomains of the insulin receptor kinase. On the basis of these results and the crystal structure of the conserved catalytic core of this kinase [Hubbard, S. R., et al. (1994) Nature 372, 746], a model is proposed which reconciles the JM cis-reaction and the activation loop cis-inhibition/trans-reaction with the complex kinetics of insulin receptor autophosphorylation [Kohanski, R. A. (1993) Biochemistry 32, 5766].