PDBsum entry 1ywo

Hydrolase, signaling protein

PDB id: 1ywo

Contents

Protein chain

55 a.a. *

Ligands

GLN-PRO-PRO-VAL-PRO-PRO-GLN-ARG-PRO-MET

Waters ×67

* Residue conservation analysis

PDB id:

1ywo

Name:

Hydrolase, signaling protein

Title:

Phospholipase cgamma1 sh3 in complex with a slp-76 motif

Structure:

1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1. Chain: a. Synonym: phosphoinositide phospholipasE C, plc-gamma-1, phospholipasE C-gamma-1, plc-ii, plc-148. Engineered: yes. Mutation: yes. Lymphocyte cytosolic protein 2. Chain: p.

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: plcg1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Homo sapiens. Human. Organism_taxid: 9606

Biol. unit:

Dimer (from PQS)

Resolution:

1.81Å R-factor: 0.173 R-free: 0.221

Authors:

L.Deng,C.A.Velikovsky,C.P.Swaminathan,S.Cho,R.A.Mariuzza

Key ref:

L.Deng et al. (2005). Structural basis for recognition of the T cell adaptor protein SLP-76 by the SH3 domain of phospholipase Cgamma1. J Mol Biol, 352, 1. PubMed id: 16061254 DOI: 10.1016/j.jmb.2005.06.072

Date:

18-Feb-05 Release date: 16-Aug-05

Protein chain

P10686  (PLCG1_RAT) -  1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 from Rattus norvegicus

Seq: 1290 a.a.

Struc: 55 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.4.11 - phosphoinositide phospholipase C.
• Pathway: myo-Inositol Phosphate Metabolism
• Reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) + H2O = 1D-myo-inositol 1,4,5-trisphosphate + a 1,2-diacyl-sn-glycerol + H⁺

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

Added reference

DOI no: 10.1016/j.jmb.2005.06.072

J Mol Biol 352:1 (2005)

PubMed id: 16061254

Structural basis for recognition of the T cell adaptor protein SLP-76 by the SH3 domain of phospholipase Cgamma1.

L.Deng, C.A.Velikovsky, C.P.Swaminathan, S.Cho, R.A.Mariuzza.

ABSTRACT

The enzyme phospholipase Cgamma1 (PLCgamma1) is essential for T cell signaling and activation. Following T cell receptor ligation, PLCgamma1 interacts through its SH2 and SH3 domains with the adaptors LAT and SLP-76, respectively, to form a multiprotein signaling complex that leads to activation of PLCgamma1 by Syk tyrosine kinases. To identify the binding site for PLCgamma1 in SLP-76, we used isothermal titration calorimetry to measure affinities for the interaction of PLCgamma1-SH3 with a set of overlapping peptides spanning the central proline-rich region of SLP-76. PLCgamma1-SH3 bound with high specificity to the SLP-76 motif 186PPVPPQRP193, which represents the minimal binding site. To understand the basis for selective recognition, we determined the crystal structures of PLCgamma1-SH3 in free form, and bound to a 10-mer peptide containing this site, to resolutions of 1.60 A and 1.81 A, respectively. The structures reveal that several key contacting residues of the SH3 shift toward the SLP-76 peptide upon complex formation, optimizing the fit and strengthening hydrophobic interactions. Selectivity results mainly from strict shape complementarity between protein and peptide, rather than sequence-specific hydrogen bonding. In addition, Pro193 of SLP-76 assists in positioning Arg192 into the compass pocket of PLCgamma1-SH3, which coordinates the compass residue through an unusual aspartate. The PLCgamma1-SH3/SLP-76 structure provides insights into ligand binding by SH3 domains related to PLCgamma1-SH3, as well as into recognition by PLCgamma1 of signaling partners other than SLP-76.

Selected figure(s)

Figure 3.
Figure 3. Comparison of PLCg1-SH3 in free and SLP-76-bound forms. (a) Superposition of the polypeptide chain of unbound PLCg1-SH3 (gold) onto that of PLCg1-SH3 in the PLCg1-SH3/SLP-76 complex (cyan). The SLP-76 peptide is drawn in ball-and-stick representation. The arrow points to the region where the two structures deviate most. (b) Close-up view of the rearrangement of the n-Src loop of PLCg1-SH3 following peptide binding. Glycine residues are represented by their carbonyl oxygen atoms. (c) Adjustments in the PLCg1-SH3 binding site upon ligation of SLP-76 peptide. Free PLCg1-SH3 was superposed on SLP-76-bound PLCg1-SH3. The view is looking down on the binding groove. The SLP-76 peptide and the rest of the SH3 structure are omitted for clarity. Only residues contacting the ligand are shown. Glycine residues are represented by their carbonyl oxygen atoms. Dual conformations were observed for the side-chains Gln805 and Arg806 in the PLCg1-SH3/SLP-76 complex.

Figure 4.
Figure 4. (a) Structure-based sequence alignment of the SH3 domains of PLCg1, PLCg2 and Lck. Secondary structure elements are denoted by violet arrows (b-strands) and a pink cylinder (3[10] helix). These, and the loop regions (brown lines), are labeled according to the nomenclature for Src-SH3.22 Residues of PLCg1-SH3 making van der Waals contacts with SLP-76 are shaded yellow; residues interacting with SLP-76 through hydrogen bonds are shaded cyan. Asp808, which forms a salt-bridge with the bound peptide, is shaded red. (b) Superposition of PLCg1-SH3 in bound form (cyan) onto free Lck-SH3 (green; PDB accession code 1LCK).28 The view is the same as that in Figure 3(c). Residues of Lck-SH3 that potentially contact bound peptide, based on sequence alignment with PLCg1-SH3 (a), are shown. (c) Interactions at the SH3 compass pocket. The PLCg1/SLP-76 complex (cyan) was superposed onto the Src-SH3/App12 complex (PDB accession code 1QWE)30 and free Lck-SH3. Only interactions with the compass residue of the bound peptide (Arg192 of SLP-76 and Arg9 of App12) are shown. Salt-bridges are drawn as broken lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 1-0) copyright 2005.

Figures were selected by an automated process.