PDBsum entry 1f8h

Endocytosis/exocytosis

PDB id: 1f8h

Contents

Protein chain

95 a.a. *

Ligands

SER-THR-ASN-PRO-PHE-ARG

Metals

_CA

* Residue conservation analysis

PDB id:

1f8h

Name:

Endocytosis/exocytosis

Title:

Structure of the second eps15 homology domain of human eps15 in complex with ptgssstnpfr

Structure:

Epidermal growth factor receptor substrate 15. Chain: a. Fragment: residues 121-218 of human eps15. Engineered: yes. Ptgssstnpfr. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: homo, sapiens. Synthetic: yes. Other_details: chemically synthesized peptide

NMR struc:

20 models

Authors:

T.De Beer,A.N.Hoofnagle,J.L.Enmon,R.C.Bowers,M.Yamabhai,B.K.Kay, M.Overduin

Key ref:

T.de Beer et al. (2000). Molecular mechanism of NPF recognition by EH domains. Nat Struct Biol, 7, 1018-1022. PubMed id: 11062555 DOI: 10.1038/80924

Date:

30-Jun-00 Release date: 01-Nov-00

Protein chain

P42566  (EPS15_HUMAN) -  Epidermal growth factor receptor substrate 15 from Homo sapiens

Seq: 896 a.a.

Struc: 95 a.a.

DOI no: 10.1038/80924

Nat Struct Biol 7:1018-1022 (2000)

PubMed id: 11062555

Molecular mechanism of NPF recognition by EH domains.

T.de Beer, A.N.Hoofnagle, J.L.Enmon, R.C.Bowers, M.Yamabhai, B.K.Kay, M.Overduin.

ABSTRACT

Eps15 homology (EH) domains are protein interaction modules that recognize Asn-Pro-Phe (NPF) motifs in their biological ligands to mediate critical events during endocytosis and signal transduction. To elucidate the structural basis of the EH-NPF interaction, the solution structures of two EH-NPF complexes were solved using NMR spectroscopy. The first complex contains a peptide representing the Hrb C-terminal NPFL motif; the second contains a peptide in which an Arg residue substitutes the C-terminal Leu. The NPF residues are almost completely embedded in a hydrophobic pocket on the EH domain surface and the backbone of NPFX adopts a conformation reminiscent of the Asx-Pro type I beta-turn motif. The residue directly following NPF is crucial for recognition and is required to complete the beta-turn. Five amino acids on the EH surface mediate specific recognition of this residue through hydrophobic and electrostatic contacts. The complexes explain the selectivity of the second EH domain of Eps15 for NPF over DPF motifs and reveal a critical aromatic interaction that provides a conserved anchor for the recognition of FW, WW, SWG and HTF ligands by other EH domains.

Selected figure(s)

Figure 1.
Figure 1. Structures of EH[2] in complex with NPF[Hrb] and with NPF[Hrb(L arrow R)]. a, Stereo view showing C traces of 20 superimposed NMR structures of the EH[2] -NPF[Hrb(L arrow R)] complex. The backbone C', N, and C atoms of residues 145 -175 of EH[2], which include helices B and C, were used for superposition. The TNPFR sequence of NPF[Hrb(L arrow R)] is indicated in black. The backbone of EH[2] is color coded as follows: helix A consists of residues 126 -136 and is depicted in dark blue; B, 148 -156, in orange; C, 162 -172, in red; and D, 182 -197, in light blue. Loops connecting the helices are indicated in different shades of green. The calcium ion in the second EF-hand is represented as an orange sphere. N and C indicate the N- and C-termini of EH[2], respectively. b, Stereo view showing C traces of 20 superimposed NMR structures of the EH[2] -NPF[Hrb] complex using the same color scheme as in (a). The slightly different orientation of the Phe side chain in the structures can be attributed to a few NOEs that could not be assigned in spectra of EH[2] -NPF[Hrb] due to spectral overlap. c, Ribbon and surface representation of EH[2] -NPF[ Hrb(L arrow R)]. The TNPFR part of the peptide is shown with C, N and O atoms colored yellow, blue and red, respectively. The Phe and +3 residue HN protons that interact with the Asn side chain oxygen atoms are shown in white. Val 151, Leu 155, Leu 165 and Trp 169 at the base of the NPF binding site of EH[2] are displayed as stick models in green. The helices are color coded as in (a). d, Ribbon and surface diagram of EH[2] -NPF[Hrb] using the same color scheme as in ( c).

Figure 3.
Figure 3. Residues of the EH domain interacting with NPF[Hrb(L arrow R)]. a, Binding site interactions. EH[2] is represented as a partially transparent surface with the protein backbone from residue 145 -175 displayed as a blue ribbon. Black arrows at the top of the figure indicate the direction of the backbone. Residues of EH[2] are depicted in ball-and-stick representation with C, N, O, and calcium atoms in blue, dark blue, red, and green, respectively. The peptide residues NPFR are displayed as stick models with C, N, and O atoms colored orange, blue and red, respectively. Phe, Arg and Asn side chain protons are shown in white. Potential hydrogen bonds involving NPF[Hrb(L arrow R)] are indicated by green lines. The carbonyl atoms of Leu 165 and Gly 166 are part of helix C, and putative hydrogen bonds with the HN protons (in white) of Trp 169 and Glu 170 are indicated by yellow lines. b, View of the binding site rotated 180° about a vertical axis to highlight the interactions with the Pro and Phe residues of NPF, using the same color scheme as in (a). c, Degree of amino acid conservation of EH residues that contact the TNPFR sequence. EH[ 2] is shown as a color coded surface with different shades of blue representing the degree of conservation as defined in the insert. The labeling stands for a single, pair or triplet of amino acids that are conserved at that position. The first letter and the number indicate the residue and sequence number of EH[2], respectively. NPF residues are shown in orange, T and R are displayed in yellow. Figs 1, 3a, b were generated using InsightII (Biosym Inc.), and Fig. 3c using VMD^30.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 1018-1022) copyright 2000.

Figures were selected by an automated process.