PDBsum entry 3sem

Signaling protein/inhibitor

PDB id: 3sem

Contents

Protein chains

58 a.a. *

Ligands

PRO-PRO-PRO-VAL-NMC-PRO-ARG

PRO-PRO-PRO-VAL-NMC-PRO

Waters ×28

* Residue conservation analysis

PDB id:

3sem

Name:

Signaling protein/inhibitor

Title:

Sem5 sh3 domain complexed with peptoid inhibitor

Structure:

Sex muscle abnormal protein 5. Chain: a, b. Fragment: c-terminal sh3. Engineered: yes. Sh3 peptoid inhibitor. Chain: c, d. Engineered: yes

Source:

Caenorhabditis elegans. Organism_taxid: 6239. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.248 R-free: 0.310

Authors:

J.T.Nguyen,C.W.Turck,F.E.Cohen,R.N.Zuckermann,W.A.Lim

Key ref:

J.T.Nguyen et al. (1998). Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science, 282, 2088-2092. PubMed id: 9851931 DOI: 10.1126/science.282.5396.2088

Date:

02-Nov-98 Release date: 06-Jan-99

Protein chains

P29355  (SEM5_CAEEL) -  Sex muscle abnormal protein 5 from Caenorhabditis elegans

Seq: 228 a.a.

Struc: 58 a.a.

DOI no: 10.1126/science.282.5396.2088

Science 282:2088-2092 (1998)

PubMed id: 9851931

Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors.

J.T.Nguyen, C.W.Turck, F.E.Cohen, R.N.Zuckermann, W.A.Lim.

ABSTRACT

Src homology 3 (SH3) and WW protein interaction domains bind specific proline-rich sequences. However, instead of recognizing critical prolines on the basis of side chain shape or rigidity, these domains broadly accepted amide N-substituted residues. Proline is apparently specifically selected in vivo, despite low complementarity, because it is the only endogenous N-substituted amino acid. This discriminatory mechanism explains how these domains achieve specific but low-affinity recognition, a property that is necessary for transient signaling interactions. The mechanism can be exploited: screening a series of ligands in which key prolines were replaced by nonnatural N-substituted residues yielded a ligand that selectively bound the Grb2 SH3 domain with 100 times greater affinity.

Selected figure(s)

Figure 1.
Fig. 1. Backbone substitution requirements for SH3 and WW domain recognition. (A) Structural mapping of alanine and sarcosine scanning results (Table 1). Peptide/domain complex interfaces (8, 9) shown schematically. Ligands adopt a PPII conformation, depicted schematically as a triangular prism. Residue positions (spheres) are color-coded by class: white--does not require either C^ - or N-substitution (alanine and sarcosine tolerant); green--requires C^ -substitution (alanine tolerant, sarcosine intolerant); orange--requires N-substitution (sarcosine tolerant, alanine intolerant). (B) Minimally sufficient recognition unit for SH3 and WW domain binding grooves. Schematic view of a single binding groove cross-section, looking down the PPII helical axis (viewed from left side of Fig. 1A). Minimally required atoms defined in this study, a sequential pair of C^ - and N-substituted residues, are solid black. The van der Waals binding surface that these atoms present is shaded. (C) Distinct mechanisms of proline recognition. Proline can be recognized by a lock and key mechanism, utilizing the full chemical potential of the side chain. In contrast, SH3 and WW domains recognized key prolines based on N-substitution. This mechanism utilizes relatively little of the binding potential of ligand or protein (hatched surface) but is still highly discriminatory for proline among natural amino acids.

Figure 3.
Fig. 3. Structural basis of peptoid recognition. (A) Structure of wild-type Sos peptide (PPPVPPRRR) bound to Crk SH3 domain (20). Proline-rich core binding grooves are indicated by dashed boxes. Highly conserved surface residues among the four SH3 domains studied here (one or two conservative amino acid types) are green. Variable surface residues (3+ amino acid types) are brown. The ligand PXXP core binds at the most conserved surface on the protein. (B) Structure of peptide 34 bound to Crk SH3 domain. N-(S)-1-Phenylethyl peptoid side chain (orange) bound at site P[2]. Close-up view from the same perspective as above. (C) Structure of peptide 39 bound to the Sem5 SH3 domain. N-Cyclopropylmethyl peptoid side chain (orange) bound at site P[ 1]. Close-up view from the same perspective as above.

The above figures are reprinted by permission from the AAAs: Science (1998, 282, 2088-2092) copyright 1998.

Figures were selected by an automated process.