PDBsum entry: 1bw8

Peptide binding protein

PDB id: 1bw8

Contents

Protein chain

256 a.a. *

Ligands

PHE-TYR-ARG-ALA-LEU-MET

Waters ×51

* Residue conservation analysis

PDB id:

1bw8

Name:

Peptide binding protein

Title:

Mu2 adaptin subunit (ap50) of ap2 adaptor (second domain), complexed with egfr internalization peptide fyralm

Structure:

Protein (mu2 adaptin subunit). Chain: a. Fragment: internalization signal binding domain. Synonym: ap50. Engineered: yes. Protein (internalization signal from egfr). Chain: p. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: the protein was chemically synthesized

Biol. unit:

Tetramer (from PQS)

Resolution:

2.65Å R-factor: 0.272 R-free: 0.296

Authors:

D.J.Owen,P.R.Evans

Key ref:

D.J.Owen and P.R.Evans (1998). A structural explanation for the recognition of tyrosine-based endocytotic signals. Science, 282, 1327-1332. PubMed id: 9812899 DOI: 10.1126/science.282.5392.1327

Date:

30-Sep-98 Release date: 25-Nov-98

Protein chain

P84092  (AP2M1_RAT) -  AP-2 complex subunit mu

Seq: 435 a.a.

Struc: 256 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: clathrin coat of coated pit (2 terms)
• Biological process: vesicle-mediated transport (2 terms)
• Biochemical function: protein binding (1 term)

DOI no: 10.1126/science.282.5392.1327

Science 282:1327-1332 (1998)

PubMed id: 9812899

A structural explanation for the recognition of tyrosine-based endocytotic signals.

D.J.Owen, P.R.Evans.

ABSTRACT

Many cell surface proteins are marked for endocytosis by a cytoplasmic sequence motif, tyrosine-X-X-(hydrophobic residue), that is recognized by the mu2 subunit of AP2 adaptors. Crystal structures of the internalization signal binding domain of mu2 complexed with the internalization signal peptides of epidermal growth factor receptor and the trans-Golgi network protein TGN38 have been determined at 2.7 angstrom resolution. The signal peptides adopted an extended conformation rather than the expected tight turn. Specificity was conferred by hydrophobic pockets that bind the tyrosine and leucine in the peptide. In the crystal, the protein forms dimers that could increase the strength and specificity of binding to dimeric receptors.

Selected figure(s)

Figure 3.
Fig. 3. The peptide binding site. (A) The binding of the tyrosine residue of the internalization signal peptide is in a hydrophobic pocket created by Phe^174, Trp421, and Arg423, with a hydrogen-bonding network between the tyrosine OH and Asp176, Lys203, and Arg423. The structure shown is that of the DYQRLN TGN38 peptide. (B) The binding pocket for the bulky hydrophobic residue at Y+3 (Leu in both peptides) is lined with aliphatic side chains of Leu173, Leu175, Val401, Leu404, Val422, and the aliphatic portion of Lys420. ArgY+2 of the TGN38 peptide is packed against Trp421. (C) Schematic representation of the interactions between the internalization signal of TGN38 and µ2, showing both side chain contacts and the short stretch of sheet formed between the peptide and strand 16. The peptide is shown with bold lines.

Figure 4.
Fig. 4. The crystallographic dimer. (A and B) Orthogonal views of the dimer formed in the crystal, along and perpendicular to the crystallographic twofold axis. The A subdomains are colored gold and green; the B subdomains are blue and purple. (C and D) The surface of the µ2 dimer colored according to electrostatic surface potential (blue positive, red negative; scale from -30 to +30 kT e^-1) in the same view as (A) and (B). The planar face at the top of (D) may interact with the membrane.

The above figures are reprinted by permission from the AAAs: Science (1998, 282, 1327-1332) copyright 1998.

Figures were selected by the author.