PDBsum entry 1p13

Transferase

PDB id

1p13

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Contents

			Protein chains

					102 a.a. *

			Ligands

					CYS-ASP


					PTR-ALA-ASN-PHE- LYS


					CYS-ASP-PTR


					ALA-ASN-PHE-LYS


					CAC ×4

			Waters ×273

* Residue conservation analysis

PDB id:

1p13

Links

Name:

Transferase

Title:

Crystal structure of the src sh2 domain complexed with peptide (sdpyanfk)

Structure:

Proto-oncogene tyrosine-protein kinase src. Chain: a, b. Fragment: sh2 domain. Synonym: p60-src, c-src. Engineered: yes. Peptide. Chain: c, d. Engineered: yes

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Gene: src. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was chemically synthesized.

Biol. unit:

Dimer (from PQS)

Resolution:

1.63Å

R-factor:

0.207

R-free:

0.252

Authors:

E.D.Sonnenburg,A.Bilwes,T.Hunter,J.P.Noel

Key ref:

E.D.Sonnenburg et al. (2003). The structure of the membrane distal phosphatase domain of RPTPalpha reveals interdomain flexibility and an SH2 domain interaction region. Biochemistry, 42, 7904-7914. PubMed id: 12834342 DOI: 10.1021/bi0340503

Date:

11-Apr-03

Release date:

19-Aug-03

PROCHECK

	Headers

	References

Protein chains

P00523 (SRC_CHICK) - Proto-oncogene tyrosine-protein kinase Src from Gallus gallus

Seq: Struc:

Seq: Struc:					533 a.a. 102 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.2.7.1.112 - Transferred entry: 2.7.10.1 and 2.7.10.2.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + a protein tyrosine = ADP + protein tyrosine phosphate

Bound ligand (Het Group name = PTR)
matches with 76.19% similarity

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

reference

DOI no: 10.1021/bi0340503	Biochemistry 42:7904-7914 (2003)
PubMed id: 12834342

The structure of the membrane distal phosphatase domain of RPTPalpha reveals interdomain flexibility and an SH2 domain interaction region.
E.D.Sonnenburg, A.Bilwes, T.Hunter, J.P.Noel.

ABSTRACT

The receptor protein tyrosine phosphatase alpha (RPTPalpha) is a transmembrane receptor with two intracellular protein tyrosine phosphatase domains, a catalytically active membrane proximal domain (D1) and a membrane distal phosphatase domain with minimal catalytic activity (D2). Here we elucidate the crystal structure of RPTPalpha's D2 domain. Unlike D1, D2 exists as a monomer and lacks the N-terminal inhibitory wedge motif. The N-terminal portion of D2 is disordered, and this region linking D1 to D2 is proteolytically labile in solution whether part of D2 alone or tethered to D1, indicating that the polypeptide backbone of this part of D2 is highly flexible, and therefore accessible to proteases under native conditions. Furthermore, we have crystallized the SH2 domain of the protein tyrosine kinase c-Src, a RPTPalpha substrate, with a phosphopeptide encompassing the C-terminal phosphorylation site of D2 (pTyr789). The SH2 domain of Src binds RPTPalpha in an extended conformation. The structural and functional data support a D1-D2 arrangement with significant flexibility between phosphatase domains of RPTPalpha that is likely to be important for dynamic alterations in intra- and/or intermolecular interactions that are critical for RPTPalpha function.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20385765

A.M.Vacaru, and J.den Hertog (2010).
Serine dephosphorylation of receptor protein tyrosine phosphatase alpha in mitosis induces Src binding and activation.

Mol Cell Biol, 30, 2850-2861.

19167335

A.J.Barr, E.Ugochukwu, W.H.Lee, O.N.King, P.Filippakopoulos, I.Alfano, P.Savitsky, N.A.Burgess-Brown, S.Müller, and S.Knapp (2009).
Large-scale structural analysis of the classical human protein tyrosine phosphatome.

Cell, 136, 352-363.

PDB codes:

2ahs 2b49 2cfv 2cjz 2gjt 2h4v 2i75 2jjd 2nlk 2nz6 2oc3 2ooq 2p6x 2pa5 2qep 3b7o

18422654

A.Groen, J.Overvoorde, T.van der Wijk, and J.den Hertog (2008).
Redox regulation of dimerization of the receptor protein-tyrosine phosphatases RPTPalpha, LAR, RPTPmu and CD45.

FEBS J, 275, 2597-2604.

16423050

N.Holmes (2006).
CD45: all is not yet crystal clear.

Immunology, 117, 145-155.

16914752

N.J.Hassan, S.J.Simmonds, N.G.Clarkson, S.Hanrahan, M.J.Puklavec, M.Bomb, A.N.Barclay, and M.H.Brown (2006).
CD6 regulates T-cell responses through activation-dependent recruitment of the positive regulator SLP-76.

Mol Cell Biol, 26, 6727-6738.

15623519

A.Groen, S.Lemeer, T.van der Wijk, J.Overvoorde, A.J.Heck, A.Ostman, D.Barford, M.Slijper, and J.den Hertog (2005).
Differential oxidation of protein-tyrosine phosphatases.

J Biol Chem, 280, 10298-10304.

14734566

D.F.McCain, L.Wu, P.Nickel, M.U.Kassack, A.Kreimeyer, A.Gagliardi, D.C.Collins, and Z.Y.Zhang (2004).
Suramin derivatives as inhibitors and activators of protein-tyrosine phosphatases.

J Biol Chem, 279, 14713-14725.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.