The expression of Pin1 is regulated by both transcriptional regulation and post-translational modification. In transcriptional regulation, Pin1 is regulated by transcription factor E2F, which activates PIN1 promoter specifically through the E2F binding sites. Moreover, different SNPs can activate or suppress Pin1 protein expression. The transcriptional repressor AP4 binds to a repressor SNP (rSNP) and thus suppresses Pin1 promoter activity. However, Pin1 could also regulate through activator SNPs (aSNPs). Through the post-translational modification, DAPK1 phosphorylates Pin1 at Ser71 residue in the PPIase catalytic site and inactivates the Pin1 catalytic activity presumably because the phosphate might form a hydrogen bond with the critical residue Arg69, and thus inhibits Pin1 nuclear localization and cellular function. Similarly, Pin1 is phosphorylated at Ser16 in the WW domain possibly by PKA and this phosphorylation inhibits the Pin1 WW domain to bind substrates presumably because the phosphate might form a hydrogen bond with the critical residue Arg17.

Pin1 regulates phosphorylated proteins through several mechanisms. (a) Recycle phosphoproteins; by controlling the conformation of specific phosphorylated Ser/Thr-Pro motifs, Pin1 regulates the function of its phospho-substrates by modulating their phosphorylation/dephosphorylation state. (b) Enhance degradation; Pin1 would boost cis/trans isomerization rate to grant the right conformation for subsequent ubiquitylation of phospho-proteins by E3 ligase and activate proteasome mediated protein degradation. (c) Prevent degradation; Pin1 could render the protein unfavorable for ubiquitin ligase binding or inhibit ubiquitin ligase access to the phosphorylated sites to increase the half-life of the substrate protein. (d) Regulate other post-translational modifications (PTMs); Pin1 regulates the cross-talk between several post-translational modification mechanisms such as phosphorylation and ubiquitylation (Ub); phosphorylation and sumoylation (sumo) and others such as acetylation (Ac).

Pin1 plays a critical role in regulating phosphorylation-dependent ubiquitylation pathway by catalyzing the intrinsically slow prolyl cis/trans isomerization. The catalytic processes of phosphorylation and ubiquitylation occur very rapidly under normal condition. However, the cis/trans conformation conversion of phosphorylated protein which is crucial for SCF complex or E3 ligase recognition occurs slowly. In the absence of Pin1, the trans to cis conformation conversion occurs very rarely due to difficulty in overcoming a high predicted energy barrier (ΔG_tc=30 kcal/mol) of this conformational change. In addition, using NMR, the rate of the cis to trans conversion is shown to be slow on the order of <0.002/sec at 25 °C [3]. However, in the presence of Pin1, Pin1 enhances the cis/trans conformational changes by reducing the free energy barrier, resulting in a markedly increased conversion rate up to 100- to 1000-fold. Therefore, the prolyl cis/trans isomerization mediated by Pin1 could be a critical step in controlling the phosphorylation-dependent ubiquitylation pathway.