PDBsum entry 2fpd

Signaling protein

PDB id: 2fpd

Contents

Protein chains

62 a.a. *

Ligands

GLC-GLC

SO4 ×2

Waters ×249

* Residue conservation analysis

PDB id:

2fpd

Name:

Signaling protein

Title:

Sad structure determination: crystal structure of the intrinsic dimerization sh3 domain of the ib1 scaffold protein

Structure:

C-jun-amino-terminal kinase interacting protein 1. Chain: a, b, c, d. Fragment: sh3 domain, residues 1-60. Synonym: jnk-interacting protein 1, jip-1, jnk map kinase scaffold protein 1, islet-brain-1, ib-1, mitogen-activated protein kinase 8- interacting protein 1, jip-1-related protein, jrp. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: mapk8ip1, ib1, jip1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.05Å R-factor: 0.184 R-free: 0.228

Authors:

O.Kristensen,I.Dar,M.Gajhede

Key ref:

O.Kristensen et al. (2006). A unique set of SH3-SH3 interactions controls IB1 homodimerization. EMBO J, 25, 785-797. PubMed id: 16456539 DOI: 10.1038/sj.emboj.7600982

Date:

16-Jan-06 Release date: 28-Feb-06

Protein chains

Q9R237  (JIP1_RAT) -  C-Jun-amino-terminal kinase-interacting protein 1 from Rattus norvegicus

Seq: 708 a.a.

Struc: 62 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1038/sj.emboj.7600982

EMBO J 25:785-797 (2006)

PubMed id: 16456539

A unique set of SH3-SH3 interactions controls IB1 homodimerization.

O.Kristensen, S.Guenat, I.Dar, N.Allaman-Pillet, A.Abderrahmani, M.Ferdaoussi, R.Roduit, F.Maurer, J.S.Beckmann, J.S.Kastrup, M.Gajhede, C.Bonny.

ABSTRACT

Islet-brain 1 (IB1 or JIP-1) is a scaffold protein that interacts with components of the c-Jun N-terminal kinase (JNK) signal-transduction pathway. IB1 is expressed at high levels in neurons and in pancreatic beta-cells, where it controls expression of several insulin-secretory components and secretion. IB1 has been shown to homodimerize, but neither the molecular mechanisms nor the function of dimerization have yet been characterized. Here, we show that IB1 homodimerizes through a novel and unique set of Src homology 3 (SH3)-SH3 interactions. X-ray crystallography studies show that the dimer interface covers a region usually engaged in PxxP-mediated ligand recognition, even though the IB1 SH3 domain lacks this motif. The highly stable IB1 homodimer can be significantly destabilized in vitro by three individual point mutations directed against key residues involved in dimerization. Each mutation reduces IB1-dependent basal JNK activity in 293T cells. Impaired dimerization also results in a reduction in glucose transporter type 2 expression and in glucose-dependent insulin secretion in pancreatic beta-cells. Taken together, these results indicate that IB1 homodimerization through its SH3 domain has pleiotropic effects including regulation of the insulin secretion process.

Selected figure(s)

Figure 1.
Figure 1 Protein interaction domains of IB1. (A) IB1 is characterized by a JBD (gray box, residues 154–182), SH3 (yellow box, residues 494–553) and a PID (orange box, residues 570–704). Residues are numbered according to the full-length rat IB1 sequence (GenBank, AF108959). The seven PxxP motifs are shown in black and red. Motifs marked in red are conserved in rat, human and mouse IB1 and IB2. MKK7 and MLK3, two of the known partners of IB1, bind to regions 287–472 and 473–709 of IB1, respectively. (B) Schematic representations of full-length and C-terminal deletion mutants of IB1. Numbering corresponds to the last amino-acid expressed in the various constructs. Binding results described in Figure 2 are summarized for all constructs. ND: not determined. (C) Sequence alignment of rat, mouse and human IB1/JIP1 and IB2/JIP2 SH3 domains. The sequence of rat IB1 (GenBank, AF108959), human JIP1 (Ensembl, ENSP00000241014), mouse JIP1 (Ensembl, ENSMUSP00000050773), rat IB2 (Ensembl, ENSRNOP00000050155), human IB2 (GenBank, AF218778) and mouse JIP2 (Ensembl, ENSMUSP00000023291) are included. The IB1 SH3 region is identical in all three species. Residues that participate to IB1 dimerization as well as those expected to do so in IB2 are shown in bold blue. Residues at the dimer interface involved in inter-protomer salt bridges or hydrogen bonds are shaded in green. Nonconserved amino acids between IB1 and IB2 are indicated with a star in the consensus sequence. The positions of the strands 1–5 and the 3[10]-helix are indicated in yellow.

Figure 4.
Figure 4 Stereographic representation of the IB1 SH3 domain. (A) The solvent-accessible surface of the IB1 SH3 domain. Contact residues from the other molecule of the homodimer colored after atom type are shown as sticks. Carbon atoms from residues 500 to 510 are colored in gray, those from residues 525 to 529 are in yellow and the 542 to 547 region is shown in magenta. Residues 506 and 507 from both monomers are colored in cyan. (B) The solvent-accessible surfaces of the IB1 and SEM-5 SH3 domains. The surface of the IB1 SH3 domain is colored after atom type. The superimposed solvent-accessible surface of SEM-5 (Lim et al, 1994) is shown as a yellow mesh, along with the bound mSos-derived peptide PPPVPPR in sticks representation. The canonical PPII binding sites are labeled (Yu et al, 1994).

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 785-797) copyright 2006.

Figures were selected by an automated process.