PDBsum entry 4yfc

Immune system/hydrolase

PDB id: 4yfc

Contents

Protein chains

322 a.a.

209 a.a.

Ligands

NAG-NAG-FUL

NAG-NAG

NAG-NAG-BMA-FUL

NAG ×2

Waters ×77

Obsolete entry

PDB id:

4yfc

Name:

Immune system/hydrolase

Title:

Crystal structure of ptp delta ig1-ig2 in complex with il1rapl1

Structure:

Interleukin-1 receptor accessory protein-like 1. Chain: b. Fragment: unp residues 19-352. Synonym: il1rapl-1,x-linked interleukin-1 receptor accessory protein- like 1. Engineered: yes. Receptor-type tyrosine-protein phosphatase delta. Chain: a. Fragment: unp residues 21-318.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: il1rapl1. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: freestyle 293-f. Gene: ptprd. Expression_system_cell_line: freestyle 293-f

Resolution:

2.70Å R-factor: 0.228 R-free: 0.263

Authors:

A.Yamagata,S.Fukai

Key ref:

A.Yamagata et al. (2015). Mechanisms of splicing-dependent trans-synaptic adhesion by PTPδ-IL1RAPL1/IL-1RAcP for synaptic differentiation. Nat Commun, 6, 6926. PubMed id: 25908590 DOI: 10.1038/ncomms7926

Date:

25-Feb-15 Release date: 06-May-15

Protein chain

P59823  (IRPL1_MOUSE) -  Interleukin-1 receptor accessory protein-like 1 from Mus musculus

Seq: 695 a.a.

Struc: 322 a.a.

Protein chain

Q64487  (PTPRD_MOUSE) -  Receptor-type tyrosine-protein phosphatase delta from Mus musculus

Seq: 1912 a.a.

Struc: 209 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.3.1.3.48 - protein-tyrosine-phosphatase.
• Reaction: O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate

O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] (Bound ligand (Het Group name = NAG) matches with 47.62% similarity) + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1038/ncomms7926

Nat Commun 6:6926 (2015)

PubMed id: 25908590

Mechanisms of splicing-dependent trans-synaptic adhesion by PTPδ-IL1RAPL1/IL-1RAcP for synaptic differentiation.

A.Yamagata, T.Yoshida, Y.Sato, S.Goto-Ito, T.Uemura, A.Maeda, T.Shiroshima, S.Iwasawa-Okamoto, H.Mori, M.Mishina, S.Fukai.

ABSTRACT

Synapse formation is triggered through trans-synaptic interaction between pairs of pre- and postsynaptic adhesion molecules, the specificity of which depends on splice inserts known as 'splice-insert signaling codes'. Receptor protein tyrosine phosphatase δ (PTPδ) can bidirectionally induce pre- and postsynaptic differentiation of neurons by trans-synaptically binding to interleukin-1 receptor accessory protein (IL-1RAcP) and IL-1RAcP-like-1 (IL1RAPL1) in a splicing-dependent manner. Here, we report crystal structures of PTPδ in complex with IL1RAPL1 and IL-1RAcP. The first immunoglobulin-like (Ig) domain of IL1RAPL1 directly recognizes the first splice insert, which is critical for binding to IL1RAPL1. The second splice insert functions as an adjustable linker that positions the Ig2 and Ig3 domains of PTPδ for simultaneously interacting with the Ig1 domain of IL1RAPL1 or IL-1RAcP. We further identified the IL1RAPL1-specific interaction, which appears coupled to the first-splice-insert-mediated interaction. Our results thus reveal the decoding mechanism of splice-insert signaling codes for synaptic differentiation induced by trans-synaptic adhesion between PTPδ and IL1RAPL1/IL-1RAcP.