PDBsum entry 1d4w

Signaling protein

PDB id: 1d4w

Contents

Protein chain

104 a.a. *

Ligands

SER-LEU-THR-ILE-PTR-ALA-GLN-VAL-GLN-LYS ×2

Waters ×413

* Residue conservation analysis

PDB id:

1d4w

Name:

Signaling protein

Title:

Crystal structure of the xlp protein sap in complex with slam phosphopeptide

Structure:

T cell signal transduction molecule sap. Chain: a, b. Fragment: sh2 domain. Synonym: sap. Engineered: yes. Mutation: yes. Signaling lymphocytic activation molecule. Chain: c, d. Fragment: cytoplasmic tail synthetic phospopeptide.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Cell: t cell. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this peptide was chemically synthesized.

Biol. unit:

Octamer (from PQS)

Resolution:

1.80Å R-factor: 0.172 R-free: 0.240

Authors:

F.Poy,M.B.Yaffe,J.Sayos,K.Saxena,M.J.Eck

Key ref:

F.Poy et al. (1999). Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition. Mol Cell, 4, 555-561. PubMed id: 10549287 DOI: 10.1016/S1097-2765(00)80206-3

Date:

06-Oct-99 Release date: 14-Oct-99

Protein chains

O60880  (SH21A_HUMAN) -  SH2 domain-containing protein 1A from Homo sapiens

Seq: 128 a.a.

Struc: 104 a.a.

DOI no: 10.1016/S1097-2765(00)80206-3

Mol Cell 4:555-561 (1999)

PubMed id: 10549287

Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition.

F.Poy, M.B.Yaffe, J.Sayos, K.Saxena, M.Morra, J.Sumegi, L.C.Cantley, C.Terhorst, M.J.Eck.

ABSTRACT

SAP, the product of the gene mutated in X-linked lymphoproliferative syndrome (XLP), consists of a single SH2 domain that has been shown to bind the cytoplasmic tail of the lymphocyte coreceptor SLAM. Here we describe structures that show that SAP binds phosphorylated and nonphosphorylated SLAM peptides in a similar mode, with the tyrosine or phosphotyrosine residue inserted into the phosphotyrosine-binding pocket. We find that specific interactions with residues N-terminal to the tyrosine, in addition to more characteristic C-terminal interactions, stabilize the complexes. A phosphopeptide library screen and analysis of mutations identified in XLP patients confirm that these extended interactions are required for SAP function. Further, we show that SAP and the similar protein EAT-2 recognize the sequence motif TIpYXX(V/I).

Selected figure(s)

Figure 1.
Figure 1. Structure of SAP and the Location of Missense Mutations Identified in XLP Patients(A) Ribbon diagram showing the SAP/SLAM pY281 complex. The bound phosphopeptide is shown in a stick representation (yellow). Selected SAP residues that form the binding site are shown in blue. Elements of secondary structure are labeled using the standard SH2 domain nomenclature ([8]). Note that the pY −3 to pY −1 residues of the peptide make a parallel β sheet interaction with strand βD; the side chains of these peptide residues make hydrophobic contacts with Tyr-50, Ile-51, and Tyr-52 in strand βD, and with Leu-21. Thr (pY −2) in the peptide hydrogen bonds with Glu-17 and with a buried water molecule. The phosphotyrosine is coordinated in a manner similar to that observed in the N-terminal domain of SHP-2, and as in SHP-2, the phosphate group is rotated “above” the plane of the phosphotyrosine ring. Interestingly, arginine 13 (at position αA2), which is conserved in almost all SH2 domains and usually contributes to phosphotyrosine coordination, does not participate in phosphate binding in the SAP complex. Instead, arginine 55 (βD6) hydrogen bonds with the phosphate group. C-terminal to phosphotyrosine, Val(pY +3) binds in a mostly hydrophobic cleft.(B) Point mutations identified in XLP patients cluster along the peptide-binding site and at the back of the domain. Mutations that would be expected to directly disrupt the phosphotyrosine-binding pocket are shown in green, and those that would disrupt C-terminal interactions in magenta. The remaining mutations (gold) are remote from the peptide-binding surface and may destabilize the folded protein (see text).(C) Structure-based sequence comparisons of human SAP, murine EAT-2, and other SH2 domains. Elements of secondary structure are indicated above the alignment. Numbering corresponds to human SAP. The black diamonds indicate the mutations illustrated in (B).

Figure 2.
Figure 2. Structure and Comparisons of the SAP/SLAM Y281 Complex(A) Surface representation of the SAP domain with the bound nonphosphorylated peptide shown in green. Hydrophobic residues at the −1 and −3 positions of the peptide intercalate with hydrophobic and aromatic residues on the surface of the domain (see also [D] and Figure 1A). C-terminal to phosphotyrosine, Val+3 is buried in a mostly hydrophobic groove.(B) Superposition of the phosphorylated and nonphosphorylated peptides shows that they adopt an essentially identical conformation. An alpha-carbon trace of the domain is shown in gray.(C) Superposition of the unliganded domain (blue) and the phosphopeptide (yellow) and nonphosphorylated peptide complexes (green). In the absence of bound peptide, the EF and BG loops fold inward to close the hydrophobic +3 binding groove. The conformation of the phosphotyrosine-binding pocket is essentially the same in all structures. In the unliganded structure, a sulfate ion occupies the position of the phosphate group in the phosphopeptide complex.(D) Detail of the phosphotyrosine-binding pocket in the SLAM/pY281 complex. Red spheres represent ordered water molecules. The pY281 peptide is shown in yellow. Thin cyan lines indicate potential hydrogen bonds. Note that Arg-13 is poorly ordered and does not participate in phosphotyrosine coordination.(E) Detail of the phosphotyrosine-binding pocket in the nonphosphorylated SLAM/Y281 complex. Red spheres represent ordered water molecules. The Y281 peptide is shown in green. Thin cyan lines indicate potential hydrogen bonds. Note that Arg-32 organizes an extensive network of hydrogen bonds in spite of the lack of phosphorylation of Tyr-281.

The above figures are reprinted by permission from Cell Press: Mol Cell (1999, 4, 555-561) copyright 1999.

Figures were selected by the author.