PDBsum entry 1nmv

Isomerase

PDB id: 1nmv

Contents

Protein chain

163 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural analysis of the mitotic regulator hpin1 in solution: insights into domain architecture and substrate binding.

Authors

E.Bayer, S.Goettsch, J.W.Mueller, B.Griewel, E.Guiberman, L.M.Mayr, P.Bayer.

Ref.

J Biol Chem, 2003, 278, 26183-26193. [DOI no: 10.1074/jbc.M300721200]

PubMed id

12721297

Abstract

The peptidyl-prolyl cis/trans isomerase hPin1 is a phosphorylation-dependent regulatory enzyme whose substrates are proteins involved in regulation of cell cycle, transcription, Alzheimer's disease, and cancer pathogenesis. We have determined the solution structure of the two domain protein hPin1-(1-163) and its separately expressed PPIase domain (50-163) (hPin1PPIase) with an root mean square deviation of <0.5 A over backbone atoms using NMR. Domain organization of hPin1 differs from that observed in structures solved by x-ray crystallography. Whereas PPIase and WW domain are tightly packed onto each other and share a common binding interface in crystals, our NMR-based data revealed only weak interaction of both domains at their interface in solution. Interaction between the two domains of full-length hPin1 is absent when the protein is dissected into the catalytic and the WW domain. It indicates that the flexible linker, connecting both domains, promotes binding. By evaluation of NOESY spectra we can show that the alpha1/beta1 loop, which was proposed to undergo a large conformational rearrangement in the absence of sulfate and an Ala-Pro peptide, remained in the closed conformation under these conditions. Dissociation constants of 0.4 and 2.0 mm for sulfate and phosphate ions were measured at 12 degrees C by fluorescence spectroscopy. Binding of sulfate prevents hPin1 aggregation and changes surface charges across the active center and around the reactive and catalytically essential Cys113. In the absence of sulfate and/or reducing agent this residue seems to promote aggregation, as observed in hPin1 solutions in vitro.

Figure 4.
FIG. 4. Structural comparison of solution and crystal structures of the PPIase domain of hPin1. Top, the C[ ]trace of the PPIase domain of the solution structure (red) is superimposed with the crystal structure solved by Verdecia et al. (13) (blue) (A) and Ranganathan et al. (14) (cyan) (B). Bottom, differences in angles between the solution structure and crystal structures from A and B are plotted.

Figure 9.
FIG. 9. GRASP surface representation of hPin1[PPIase]. Molecular surfaces are colored according to electric potential. Blue colors represent positive charges, red colors are negative charges, and neutral areas are gray. Calculation of electric potential was done, including the potential of the complexed sulfate ion (A) or excluding it (B). Indicated are charged residues and amino acids of the active center.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 26183-26193) copyright 2003.

Secondary reference #1

Title

A human peptidyl-Prolyl isomerase essential for regulation of mitosis.

Authors

K.P.Lu, S.D.Hanes, T.Hunter.

Ref.

Nature, 1996, 380, 544-547.

PubMed id

8606777

Secondary reference #2

Title

Structural and functional analysis of the mitotic rotamase pin1 suggests substrate recognition is phosphorylation dependent.

Authors

R.Ranganathan, K.P.Lu, T.Hunter, J.P.Noel.

Ref.

Cell, 1997, 89, 875-886. [DOI no: 10.1016/S0092-8674(00)80273-1]

PubMed id

9200606

Figure 1.
Figure 1. Overall Fold of Human Pin1(A) Ribbon representation of Pin1. Residues 1–6 and 40–44 are not visible in electron density maps and are disordered. Apostrophes distinguish the WW domain secondary structural elements from the PPIase domain's secondary structural features. Atoms are color coded for clarity (oxygen is red, nitrogen is blue, carbon is black, and sulfur is yellow). The HPO[4]^2− label reflects the possible substitution of sulfate by phosphate in phosphate-soaked crystals. Produced with MOLSCRIPT ([25]) and Raster3D ( [2]).(B) Ribbon and molecular surface representation of the Pin1 interdomain cavity. View is the same as in (A). The WW domain is orange and the PPIase domain is light blue. The dotted surface depicts the solvent-accessible surface for residues lining the interdomain cavity. The cavity presents a largely hydrophobic composite surface as indicated by the predominance of carbon atoms lining the cavity. Produced with RIBBONS ([5]).

Figure 3.
Figure 3. Structural Comparison of Representative PPIases(A) Cα stereo pair of FKBP (PDB code 1FKF), Pin1, and cyclophilin (PDB code 1CYH) aligned and offset. The backbone atoms of Pin1 and FKBP were aligned in O ([22]). Pin1 and cyclophilin (CyPA) were aligned by superimposing the backbone atoms of the cis AlaPro dipeptides. Active site residues are shown and color coded for clarity. The white line serves as a visual clue for the aligned active sites.(B) Active site views. A portion of FK506 bound to FKBP, and the AlaPro dipeptides bound to Pin1 and CyPA are shown. The psi (ψ) rotation for the alanine in the dipeptide bound to Pin1 relative to the same alanine in the dipeptide bound to CyPA likely occurs to avoid a steric clash between the β-methyl group of alanine and the bound sulfate anion. In Pin1, dashed gray lines emphasize the relationship of Cys-113 and His-59 to the peptide bond of the AlaPro peptide. Both panels were produced with the conic option ([20]) of MIDAS ( [11]).

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #3

Title

Structural basis for phosphoserine-Proline recognition by group IV ww domains.

Authors

M.A.Verdecia, M.E.Bowman, K.P.Lu, T.Hunter, J.P.Noel.

Ref.

Nat Struct Biol, 2000, 7, 639-643. [DOI no: 10.1038/77929]

PubMed id

10932246

Figure 1.
Figure 1. Overall architecture of human Pin1. a, Ribbon representation of the Pin1 -CTD peptide complex. Residues 1 -5 of Pin1 are visible in the electron density maps but not shown here for clarity; residues 39 -50 are disordered. Apostrophes distinguish the WW domain colored purple from the PPIase domain colored blue. The CTD peptide backbone is yellow. Residues of the CTD peptide are labeled with primes. Atoms are colored according to type: carbon, light gray; nitrogen, blue; phosphorus, black; oxygen, red; sulfur, yellow. Dotted green lines depict hydrogen bonds. b, Ribbon representation of the Pin1 -PEG complex19. c, Stereo view of the SIGMAA weighted |2F[o] - F[c]| electron density map contoured at 1.0 around the Tyr 23-Trp 34 clamp.

Figure 2.
Figure 2. The Pin1 -CTD peptide binding interface. a, Ribbon diagram of the Pin1 WW domain bound to Tyr-P.Ser-Pro-Thr-P.Ser-Pro-Ser depicted after a 90° rotation around a vertical axis from the view shown in Fig. 1a. This view is looking onto the concave WW domain peptide binding surface opposite the PPIase domain. The carbon atoms of the CTD peptide are colored gold to distinguish them from the WW domain side chain atoms. The water molecule mediating Tyr 23 -phosphate contacts is shown as a cyan sphere. Hydrogen bonds are shown as green dotted spheres. b, Molecular surface representation of the WW domain -peptide interface rendered after a slight rotation around the vertical axis from the view depicted in (a). The solvent accessible surface for the Pin1 WW domain residues was calculated in GRASP33, and the acidic and basic residues colored red and blue, respectively. c, Schematic and energetic view of the Pin1 -phosphopeptide complex. Pin1 residues are purple and CTD residues black. Residues participating in van der Waals contacts are highlighted with gold and the extended van der Waals surfaces appear as dotted gold curves. Hydrogen bonds are shown as dashed green lines. In the case of the S16H and W34H mutants, some of the apparent binding is likely being contributed by the PPIase domain. Residues are given in the single letter code. Values in parentheses represent deviations from theoretical binding isotherms.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd