PDBsum entry 1jpp

Cell adhesion

PDB id: 1jpp

Contents

Protein chains

499 a.a. *

11 a.a. *

14 a.a. *

Ligands

GOL

Waters ×72

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Molecular mechanisms of beta-Catenin recognition by adenomatous polyposis coli revealed by the structure of an apc-Beta-Catenin complex.

Authors

K.Eklof spink, S.G.Fridman, W.I.Weis.

Ref.

EMBO J, 2001, 20, 6203-6212. [DOI no: 10.1093/emboj/20.22.6203]

PubMed id

11707392

Abstract

The adenomatous polyposis coli (APC) tumor suppressor protein plays a critical role in regulating cellular levels of the oncogene product beta-catenin. APC binds to beta-catenin through a series of homologous 15 and 20 amino acid repeats. We have determined the crystal structure of a 15 amino acid beta-catenin binding repeat from APC bound to the armadillo repeat region of beta-catenin. Although it lacks significant sequence homology, the N-terminal half of the repeat binds in a manner similar to portions of E-cadherin and XTcf3, but the remaining interactions are unique to APC. We discuss the implications of this new structure for the design of therapeutics, and present evidence from structural, biochemical and sequence data, which suggest that the 20 amino acid repeats can adopt two modes of binding to beta-catenin.

Figure 1.
Figure 1 The -catenin-binding sites of APC. (A) Schematic of the APC primary structure. The conserved axin binding (SAMP1-3), oligomerization (olig.), armadillo repeat (arm.), basic and discs large interaction (dlg) regions are indicated. The 15 amino acid -catenin-binding repeats are labeled A, B and C (white boxes). The 20 amino acid -catenin-binding repeats are labeled 1 -7 (black boxes). Truncations in the midpoint cluster region (MCR), which eliminate all of the axin-binding and most of the -catenin-binding repeats, account for >60% of oncogenic mutations in APC (Miyoshi et al., 1992). The APC constructs used in binding experiments and crystallization are shown, with the beginning and end residue numbers in human APC indicated. (B) Alignment of the APC 15 and 20 amino acid repeats with E-cadherin and XTcf3. The alignment of the 15mers with E-cadherin and XTcf3 was performed based on the homologous regions of the E-cadherin - -catenin, XTcf3 - -catenin and APC-rA - -catenin structures (boxed). The 20mers were aligned with the 15mers based on alignment of the core homology regions. For an alternative alignment using the SLSSL sequences of E-cadherin and the 20mers, see Figure 4A, bottom panel. The residues that constitute the 15 and 20 amino acid repeat sequences are in bold. The homologous residues of the 15 and 20mer 'core homology region' are shaded gray; those conserved only in the 15mers are blue. The phosphorylation-specific binding motif of E-cadherin and the homologous APC 20mer sequences are highlighted in yellow. Beginning residue numbers based on the full-length proteins are indicated before the alignment. Residues from APC-rA that form contacts with -catenin are indicated by asterisks (contacts by side chain only or main chain and side chain atoms) or plus signs (contacts by mainchain atoms only) above the alignment. hAPC-A, hAPC-B, hAPC-C: human APC 15mer repeats A, B and C. hAPC-D: hypothesized fourth human 15mer. dAPC-A, dAPC-B: Drosophila APC 15mers. eAPC-A, eAPC-B: Drosophila APC2 15mers. hAPC-1, hAPC-2, etc.: human APC 20mers. (C) Competition experiments to test the relative affinities of several -catenin-binding peptides. GST-pulldown assays were performed using GST - -catenin (full length) in the presence of a 5-fold excess of APC-fA. Increasing quantities of the APC-rA, APC-rAL, Tcf-ext or Cad-ext peptides were tested for their ability to compete with APC-fA for binding to limiting -catenin. Fold molar excess of peptide (as compared with APC-fA) is plotted on the x-axis, as a pseudo log base-4 plot. APC-fA band intensities were quantified using the NIH Image program and are shown on the y-axis as percent of binding relative to that with no peptide competitor. Each point is plotted as mean SD of three experiments, except for the 256-fold excess of APC-rA, for which only two data points were obtained. APC-fA did not bind to GST alone (data not shown). See Materials and methods for details.

Figure 3.
Figure 3 Interactions in the -catenin -APC-rA complex. (A) Comparison of -catenin-bound APC-rA, XTcf3 and E-cadherin in the core homology region of APC-rA. -catenin residues are labeled in gray boxes. Other colors are as in Figure 2B. Contacts between APC-rA and -catenin are drawn as solid lines (non-polar interactions), dotted lines (hydrogen bonds) or dashed lines (salt bridges). APC-rA residue numbers are indicated in green. (B) Comparison of -catenin bound APC-rA, XTcf3 and E-cadherin in the region of the APC-rA bulge. Coloring and labeling is as in (A). Contacts of -catenin with APC-rA are drawn in gray, and those with XTcf3 and E-cadherin in red. (C) Stabilizing forces in the APC-rA C-terminal bulge. -catenin is drawn in a surface representation, colored blue for positive and red for negative electrostatic potential at the 10 kT/e level. The APC-rA peptide is colored by atom type with carbon white, oxygen red and nitrogen blue. Although no density is seen for the APC-rA Lys1030 or Asp1033 side chains in the structure, they are modeled (gray side chains) to demonstrate their likely interactions with regions of electrostatic potential on the surface of -catenin. Hydrogen bonds between backbone and side chain atoms within the peptide are drawn as dotted lines. The Leu 1029 side chain is not shown for clarity. (A) and (B) were generated using Molscript and Raster3D (Kraulis, 1991; Merrit and Murphy, 1994).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 6203-6212) copyright 2001.

Secondary reference #1

Title

The structure of the beta-Catenin/e-Cadherin complex and the molecular basis of diverse ligand recognition by beta-Catenin.

Authors

A.H.Huber, W.I.Weis.

Ref.

Cell, 2001, 105, 391-402. [DOI no: 10.1016/S0092-8674(01)00330-0]

PubMed id

11348595

Figure 2.
Figure 2. Interaction Regions I and IIβ-catenin is represented as in Figure 1, and the arm repeats are marked “R.” Residues of β-catenin are labeled in bold italics, and residues of E-cadherin in plain text. Oxygen, nitrogen, and sulfur are shown as red, blue, and green spheres, respectively. Individual side chains of β-catenin are shown in purple (H3) or gray (others). In this and Figures 3, 5, and 6, only those β-catenin residues that form direct contacts with E-cadherin are shown. E-cadherin is shown with yellow bonds. Hydrogen bonds and salt bridges are shown as thin pink lines. (A) Region I. Nearby region III residues are shown in light yellow. (B) Region II

Figure 6.
Figure 6. Comparison of E[cyto] and XTcf-3 Binding to β-CateninE-cadherin is shown in yellow and XTcf-3 in green. (A) Overall comparison of E-cadherin and XTcf-3 bound to β-catenin. (B) Overlay of the extended region III of E-cadherin with the corresponding portion of XTcf-3. (C) Comparison of the phosphorylated region IV interaction. Figure colored as in Figure 2 and Figure 4

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

Secondary reference #2

Title

Crystal structure of a beta-Catenin/tcf complex.

Authors

T.A.Graham, C.Weaver, F.Mao, D.Kimelman, W.Xu.

Ref.

Cell, 2000, 103, 885-896. [DOI no: 10.1016/S0092-8674(00)00192-6]

PubMed id

11136974

Figure 3.
Figure 3. The Interactions between β-Catenin and the β Strand in the Extended Region of XTcf3-CBD(A) Stereo 2F[o]−F[c] simulated annealed omit map of XTcf3-CBD. XTcf3 residues are denoted in yellow and β-catenin residues are denoted in red. Solvent molecules are shown in turquoise. The map is shown at a level of 1σ.(B) Structure of the XTcf3 extended region on the top of the β-catenin molecular surface. Two semi-buried charged buttons, Lys-435 and Lys-312, are critical for the β-catenin/Tcf interactions. The β-catenin surface was cut off in the upper part of the figure to be able to view the extended region of XTcf3-CBD. XTcf3 residues are shown in white and exposed β-catenin residues due to the cut surface are shown in green. XTcf3 residues are labeled in yellow and β-catenin residues are labeled in white. The equipotential contours at the relative levels of 10, 20, 30, 40, and 50 were calculated with GRASP and are shown in white.(C) XTcf3 extended region bonding diagram. The same conventions are used as in Figure 2B.

Figure 4.
Figure 4. The Interactions between β-Catenin and the XTcf3-CBD Helix(A) Molecular model of the XTcf3 helical region. XTcf3 residues are labeled in yellow and β-catenin residues are labeled in white.(B) XTcf3 helix module bonding diagram. The same conventions are used as in Figure 2B.

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

Secondary reference #3

Title

Three-Dimensional structure of the armadillo repeat region of beta-Catenin.

Authors

A.H.Huber, W.J.Nelson, W.I.Weis.

Ref.

Cell, 1997, 90, 871-882. [DOI no: 10.1016/S0092-8674(00)80352-9]

PubMed id

9298899

Figure 2.
Figure 2. Stereo Views of Electron Density MapsThe region near Trp-338, which interacts with Arg residues in the groove of β59, is shown. The upper panel shows a portion of the refined Form A model in the experimental 2.4 Å MAD-phased map. The lower panel shows the same region of the Form B model in the final 2.9 Å Form B 2F[o] − F[c] map. Both maps are contoured at 1.0 σ.

Figure 5.
Figure 5. Stereo View Showing Relative Motion of the Two Halves of β59The Cαs from residues 193–390 from Form A (gray) and Form B (black) have been superimposed. The COOH-terminal portions of the two structures are related by an 11.5° rotation about the axis shown as a straight vertical line. The asterisk marks the middle of the loop that replaces H1 in repeat 7. This figure was made with MOLSCRIPT ([21]).

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