Abstract
Parvulins are a group of peptidyl-prolyl isomerases (PPIases) responsible for important biological processes in all kingdoms of life. The PinA protein from the psychrophilic archaeon Cenarchaeum symbiosum is a parvulin-like PPIase. Due to its striking similarity to the human parvulins Pin1 and Par14, PinA constitutes an interesting subject for structural and functional studies. Here, we present the first high resolution NMR structure of an archaeal parvulin, PinA, based on 1798 conformational restraints. Structure calculation yields an ensemble of 20 convergent low energy structures with a backbone r.m.s.d. value of 0.6 Å within the secondary structure elements. The overall fold of PinA comprises the β-α3-β-α-β2 fold typical for all parvulin structures known so far, but with helix III being a short 310-helix. A detailed comparison of this high resolution structure of the first archaeal PinA protein with bacterial and eukaryotic parvulin PPIase structures reveals an atypically large catalytic binding site. This feature provides an explanation for cold-adapted protein function. Moreover, the residues in and around 310-helix III exhibit strong intramolecular dynamics on a microsecond to millisecond timescale and display structural heterogeneity within the NMR ensemble. A putative peptide ligand was found for PinA by phage display and was used for 1H-15N-HSQC titrations. Again, the flexible region around 310-helix III as well as residues of the peptide binding pocket showed the strongest chemical shift perturbations upon peptide binding. The local flexibility of this region also was modulated by ligand binding. A glycine and two positively charged residues are conserved in most parvulin proteins in this flexible loop region, which may be of general functional importance for parvulin-type PPIases.
Highlights
Positively charged residues are conserved in most parvulin proteins in this flexible loop region, which may be of general functional importance for parvulin-type Peptidyl-prolyl isomerases (PPIases)
Sequence-specific Resonance Assignment—Sequence-specific assignment of backbone 1H, 13C, and 15N resonances of protein isomerase (PinA) from C. symbiosum was obtained from analyzing tripleresonance HNCACB, CBCA(CO)NH, HNCO, HNCA, and HN(CO)CA spectra
The overall three-dimensional structure of the PinA protein from C. symbiosum is characterized by the typical parvulin-like -␣3--␣-2 fold, classifying CsPinA as a member of the FK506-binding protein (FKBP)-superfold family
Summary
Positively charged residues are conserved in most parvulin proteins in this flexible loop region, which may be of general functional importance for parvulin-type PPIases. Pin proteins are small parvulin-type PPIases found in bacteria and all eukaryotes [1] and are involved in key steps of cell cycle regulation and protein quality control This latter function relates parvulin proteins to folding disorders in human brain tissues such as Alzheimer and Parkinson diseases [2, 3]. The symbiotic archaeon C. symbiosum belongs to a large group of marine Archaea that eluded cultivation [7] It was initially classified as a member of the phylum of Crenarchaeota, but its optimal growth temperature at 10 °C differed strongly from the ones of any other cultivated member of that phylum [5]. There is nothing yet known about cold-optimized parvulins or about archaeal Pin proteins in general but only the PinA protein sequence from C. symbiosum This protein comprises 92 amino acids without N- or C-terminal extensions to its PPIase domain similar to Escherichia coli Par. Though the function of this conserved protein within the psychrophilic endosymbiont is not known, it is tempting to
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