PDBsum entry 1j6y

Isomerase

PDB id: 1j6y

Contents

Protein chain

120 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Solution structure of the single-Domain prolyl cis/trans isomerase pin1at from arabidopsis thaliana.

Authors

I.Landrieu, J.M.Wieruszeski, R.Wintjens, D.Inzé, G.Lippens.

Ref.

J Mol Biol, 2002, 320, 321-332. [DOI no: 10.1016/S0022-2836(02)00429-1]

PubMed id

12079389

Abstract

The 119-amino acid residue prolyl cis/trans isomerase from Arabidopsis thaliana (PIN1At) is similar to the catalytic domain of the human hPIN1. However, PIN1At lacks the N-terminal WW domain that appears to be essential for the hPIN1 function. Here, the solution structure of PIN1At was determined by three-dimensional nuclear magnetic resonance spectroscopy. The PIN1At fold could be superimposed on that of the catalytic domain of hPIN1 and had a 19 residue flexible loop located between strand beta1 and helix alpha1. The dynamical features of this beta1/alpha1-loop, which are characteristic for a region involved in protein-protein interactions, led to exchange broadening in the NMR spectra. When sodium sulfate salt was added to the protein sample, the beta1/alpha1 loop was stabilized and, hence, a complete backbone resonance assignment was obtained. Previously, with a phospho-Cdc25 peptide as substrate, PIN1At had been shown to catalyze the phosphoserine/phosphothreonine prolyl cis/trans isomerization specifically. To map the catalytic site of PIN1At, the phospho-Cdc25 peptide or sodium sulfate salt was added in excess to the protein and chemical shift changes in the backbone amide protons were monitored in the (1)H(N)-(15)N heteronuclear single quantum coherence spectrum. The peptide caused perturbations in the loops between helix alpha4 and strand beta3, between strands beta3 and beta4, in the alpha3 helix, and in the beta1/alpha1 loop. The amide groups of the residues Arg21 and Arg22 showed large chemical shift perturbations upon phospho-Cdc25 peptide or sulfate addition. We conclude that this basic cluster formed by Arg21 and Arg22, both located in the beta1/alpha1 loop, is homologous to that found in the hPIN1 crystal structure (Arg68 and Arg69), which also is involved in sulfate ion binding. We showed that the sulfate group competed for the interaction between PIN1At and the phospho-Cdc25 peptide. In the absence of the WW domain, three hydrophobic residues (Ile33, Ile34, and Leu35) located in the long flexible loop and specific for the plant PIN-type peptidyl prolyl cis/trans isomerases (PPIases) could be an additional interaction site in PIN1At. However, phospho-peptide addition did not affect the resonances of these residues significantly. Electrostatic potential calculations revealed a negatively charged area not found in hPIN1 on the PIN1At molecular surface, which corresponds to the surface shielded by the WW domain in hPIN1. Based on our experimental results and the molecular specificities of the PIN1At enzyme, functional implications of the lack of WW domains in this plant PIN-type PPIase will be discussed.

Figure 3.
Figure 3. Ribbon representations of (a) hPIN1 (residues 9-37 and 50-163) and (b) representative NMR PIN1At conformer (residues 6-120). The coordinates of hPIN1 are from PDB:1PIN.5 Secondary structure elements are colored and labeled. The sulfate molecule and the Ala-Pro dipeptide are represented by the space-filling model and are colored blue and green, respectively. The picture in (a) was obtained using a combination of MOLSCRIPT and Raster3D programs.

Figure 6.
Figure 6. Accessible molecular surface representation of (a) hPIN1 and (b) PIN1At in similar orientation, colored according to the electrostatic potential and displayed with GRASP program. Color codes for the electric potential are -5kT/e (red, acidic residues), 0kT/e (white), +5kT/e (blue, basic residues). The WW domain of hPIN1 (a) is drawn as a yellow line. The view is along the surface shielded in hPIN1 by the WW domain and corresponds to a 20° rotation to the left around the ordinate when compared with Figure 3.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 321-332) copyright 2002.

Secondary reference #1

Title

Letter to the editor: sequence-Specific 1h, 13c and 15n chemical shift backbone nmr assignment and secondary structure of the arabidopsis thaliana pin1at protein.

Authors

I.Landrieu, J.M.Wieruszeski, B.Odaert, D.Inzé, S.Grzesiek, G.Lippen.

Ref.

J Biomol Nmr, 2000, 17, 271-272.

PubMed id

10959635

Secondary reference #2

Title

The arabidopsis thaliana pin1at gene encodes a single-Domain phosphorylation-Dependent peptidyl prolyl cis/trans isomerase.

Authors

I.Landrieu, L.De veylder, J.S.Fruchart, B.Odaert, P.Casteels, D.Portetelle, M.Van montagu, D.Inzé, G.Lippens.

Ref.

J Biol Chem, 2000, 275, 10577-10581. [DOI no: 10.1074/jbc.275.14.10577]

PubMed id

10744752

Figure 1.
Fig. 1. Amino acid sequence alignment of the PIN-type PPIases of the parvulin family using the CLUSTALW program. Residues identical to the column consensus are white on a black background; similar residues to the column consensus are shaded in gray. PIN1At (this work) is from A. thaliana (accession number AAD20122), PIN1 is from human (AAC50492), DODO is from D. melanogaster (AAC28408), PINA is from A. nidulans (AAC49984), SSP1 is from N. crassa (CAA06818), SPCC16C4.03 is from Schizosaccharomyces pombe (CAA20742), ESS1/PTF1 is from S. cerevisiae (S52764/CAA59961), and Par10 is from E. coli (S48658). Asterisks indicate the potential anion-binding sites, and secondary structure elements of the human PIN1 are indicated above the alignment (6).

Figure 2.
Fig. 2. Expression analysis of PIN1At. Reverse transcription PCRs were performed using total RNA harvested from seedlings, rosette leaves, stems, flowers, roots, and dividing cell suspensions. Primers specific to PIN1At and ACT2 (control) were used.

The above figures are reproduced from the cited reference with permission from the ASBMB