PDBsum entry 2jm9

Structural protein

PDB id: 2jm9

Contents

Protein chain

62 a.a. *

* Residue conservation analysis

PDB id:

2jm9

Name:

Structural protein

Title:

R21a spc-sh3 bound

Structure:

Spectrin alpha chain, brain. Chain: a. Fragment: sh3 domain, residues 965-1025. Synonym: spectrin, non-erythroid alpha chain, fodrin alpha chain, alpha spectrin. Engineered: yes. Mutation: yes

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Gene: sptan1, spta2. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

N.A.J.Van Nuland,S.Casares,E.Ab,H.Eshuis,O.Lopez-Mayorga,F.Conejero- Lara

Key ref:

S.Casares et al. (2007). The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3. Bmc Struct Biol, 7, 22. PubMed id: 17407569

Date:

25-Oct-06 Release date: 24-Apr-07

Protein chain

P07751  (SPTN1_CHICK) -  Spectrin alpha chain, non-erythrocytic 1 from Gallus gallus

Seq: 2477 a.a.

Struc: 62 a.a.*

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

Bmc Struct Biol 7:22 (2007)

PubMed id: 17407569

The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3.

S.Casares, E.Ab, H.Eshuis, O.Lopez-Mayorga, N.A.van Nuland, F.Conejero-Lara.

ABSTRACT

BACKGROUND: SH3 domains are small protein modules of 60-85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation of many cellular processes (some are related to cancer and AIDS) and have thus been interesting targets in drug design. The decapeptide APSYSPPPPP (p41) binds with relatively high affinity to the SH3 domain of the Abl tyrosine kinase (Abl-SH3), while it has a 100 times lower affinity for the alpha-spectrin SH3 domain (Spc-SH3). RESULTS: Here we present the high-resolution structure of the complex between the R21A mutant of Spc-SH3 and p41 derived from NMR data. Thermodynamic parameters of binding of p41 to both WT and R21A Spc-SH3 were measured by a combination of isothermal titration and differential scanning calorimetry. Mutation of arginine 21 to alanine in Spc-SH3 increases 3- to 4-fold the binding affinity for p41 due to elimination at the binding-site interface of the steric clash produced by the longer arginine side chain. Amide hydrogen-deuterium experiments on the free and p41-bound R21A Spc-SH3 domain indicate that binding elicits a strong reduction in the conformational flexibility of the domain. Despite the great differences in the thermodynamic magnitudes of binding, the structure of the R21A Spc-SH3:P41 complex is remarkably similar to that of the Abl-SH3:P41 complex, with only few differences in protein-ligand contacts at the specificity pocket. Using empirical methods for the prediction of binding energetics based on solvent-accessible surface area calculations, the differences in experimental energetics of binding between the two complexes could not be properly explained only on the basis of the structural differences observed between the complexes. We suggest that the experimental differences in binding energetics can be at least partially ascribed to the absence in the R21A Spc-SH3:P41 complex of several buried water molecules, which have been proposed previously to contribute largely to the highly negative enthalpy and entropy of binding in the Abl-SH3:P41 complex. CONCLUSION: Based on a deep structural and thermodynamic analysis of a low and high affinity complex of two different SH3 domains with the same ligand p41, we underline the importance of taking into account in any effective strategy of rational design of ligands, factors different from the direct protein-ligand interactions, such as the mediation of interactions by water molecules or the existence of cooperative conformational effects induced by binding.