Structure and Activity of the Peptidyl-Prolyl Isomerase Domain from the Histone Chaperone Fpr4 toward Histone H3 Proline Isomerization

Yoan R Monneau,Heddy Soufari,Christopher J Nelson,Cameron D Mackereth

doi:10.1074/jbc.m113.479964

Abstract

The FK506-binding protein (FKBP) family of peptidyl-prolyl isomerases (PPIases) is characterized by a common catalytic domain that binds to the inhibitors FK506 and rapamycin. As one of four FKBPs within the yeast Saccharomyces cerevisiae, Fpr4 has been described as a histone chaperone, and is in addition implicated in epigenetic function in part due to its mediation of cis-trans conversion of proline residues within histone tails. To better understand the molecular details of this activity, we have determined the solution structure of the Fpr4 C-terminal PPIase domain by using NMR spectroscopy. This canonical FKBP domain actively increases the rate of isomerization of three decapeptides derived from the N terminus of yeast histone H3, whereas maintaining intrinsic cis and trans populations. Observation of the uncatalyzed and Fpr4-catalyzed isomerization rates at equilibrium demonstrate Pro(16) and Pro(30) of histone H3 as the major proline targets of Fpr4, with little activity shown against Pro(38). This alternate ranking of the three target prolines, as compared with affinity determination or the classical chymotrypsin-based fluorescent assay, reveals the mechanistic importance of substrate residues C-terminal to the peptidyl-prolyl bond.

Highlights

The yeast histone chaperone Fpr4 harbors a peptidyl-prolyl isomerase domain of the FK506-binding protein (FKBP) family
The FK506-binding protein (FKBP) family of peptidyl-prolyl isomerases (PPIases) is characterized by a common catalytic domain that binds to the inhibitors FK506 and rapamycin
The FKBP family of PPIases share a canonical domain fold consisting of a ␤-sheet composed of four large and two small ␤-strands, opposed by a single main ␣-helix [27, 28]

Summary

Background

The yeast histone chaperone Fpr harbors a peptidyl-prolyl isomerase domain of the FK506-binding protein (FKBP) family. To better understand the molecular details of this activity, we have determined the solution structure of the Fpr C-terminal PPIase domain by using NMR spectroscopy This canonical FKBP domain actively increases the rate of isomerization of three decapeptides derived from the N terminus of yeast histone H3, whereas maintaining intrinsic cis and trans populations. Observation of the uncatalyzed and Fpr4-catalyzed isomerization rates at equilibrium demonstrate Pro and Pro of histone H3 as the major proline targets of Fpr, with little activity shown against Pro38 This alternate ranking of the three target prolines, as compared with affinity determination or the classical chymotrypsin-based fluorescent assay, reveals the mechanistic importance of substrate residues C-terminal to the peptidylprolyl bond. The remaining two FKBPs, Fpr and Fpr, share significant similarity to one another (58% identity), and are located in the nucleus and nucleolus Both proteins include an extended and highly charged region N-terminal to the FKBP catalytic domain. Specific inclusion of residues downstream from the target proline reveals a substrate preference that differs from previous characterization of Fpr activity, and highlights a possible mechanistic importance for this often absent substrate element

EXPERIMENTAL PROCEDURES

RESULTS

DISCUSSION