spacer
spacer

PDBsum entry 2jt4

Go to PDB code: 
protein Protein-protein interface(s) links
Signaling protein PDB id
2jt4
Jmol
Contents
Protein chains
71 a.a. *
76 a.a. *
* Residue conservation analysis
PDB id:
2jt4
Name: Signaling protein
Title: Solution structure of the sla1 sh3-3-ubiquitin complex
Structure: Cytoskeleton assembly control protein sla1. Chain: a. Engineered: yes. Ubiquitin. Chain: b. Fragment: sh3 domain sequence database residues 350-420. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: sla1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ubi1, rpl40a.
NMR struc: 20 models
Authors: Y.He,I.Radhakrishnan
Key ref:
Y.He et al. (2007). Structural Basis for Ubiquitin Recognition by SH3 Domains. J Mol Biol, 373, 190-196. PubMed id: 17765920 DOI: 10.1016/j.jmb.2007.07.074
Date:
18-Jul-07     Release date:   25-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P32790  (SLA1_YEAST) -  Actin cytoskeleton-regulatory complex protein SLA1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1244 a.a.
71 a.a.
Protein chain
Pfam   ArchSchema ?
P0CG63  (UBI4P_YEAST) -  Polyubiquitin
Seq:
Struc:
381 a.a.
76 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/j.jmb.2007.07.074 J Mol Biol 373:190-196 (2007)
PubMed id: 17765920  
 
 
Structural Basis for Ubiquitin Recognition by SH3 Domains.
Y.He, L.Hicke, I.Radhakrishnan.
 
  ABSTRACT  
 
The SH3 domain is a protein-protein interaction module commonly found in intracellular signaling and adaptor proteins. The SH3 domains of multiple endocytic proteins have been recently implicated in binding ubiquitin, which serves as a signal for diverse cellular processes including gene regulation, endosomal sorting, and protein destruction. Here we describe the solution NMR structure of ubiquitin in complex with an SH3 domain belonging to the yeast endocytic protein Sla1. The ubiquitin binding surface of the Sla1 SH3 domain overlaps substantially with the canonical binding surface for proline-rich ligands. Like many other ubiquitin-binding motifs, the SH3 domain engages the Ile44 hydrophobic patch of ubiquitin. A phenylalanine residue located at the heart of the ubiquitin-binding surface of the SH3 domain serves as a key specificity determinant. The structure of the SH3-ubiquitin complex explains how a subset of SH3 domains has acquired this non-traditional function.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Economy in conformational rearrangements upon complex formation between Sla1 SH3-3 and ubiquitin and basis for specificity of SH3–ubiquitin interactions. (a) Stereo views of the C^α traces of Sla1 SH3-3 and ubiquitin following a best-fit superposition of backbone atoms corresponding to residues 357–415 of Sla1 and 1–73 of ubiquitin in the NMR structure of the complex with the corresponding segments in the crystal structures of the apo forms. The Sla1 SH3-3 domain is colored blue (complex) and orange (apo; PDB code, 1Z9Z) whereas ubiquitin is shown in yellow (complex) and green (apo; PDB code, 1UBQ^9). (b) Stereo views of the ubiquitin-binding residues of Sla1 SH3-3 in the apo (orange) and ubiquitin-bound (blue) states and comparison with the equivalent residues in the Grb2 SH3 domain (light pink).^10 The side-chains are shown in stick representation whereas the backbones are shown as worms. Residues and important structural landmarks are annotated. Notice also the relatively modest changes in side-chain conformation for Sla1 SH3-3 upon complex formation with ubiquitin.
Figure 3.
Figure 3. Sequence conservation and non-covalent interactions mediated by residues of SH3 domains with ubiquitin-binding activity. (a) CLUSTAL W-guided multiple sequence alignment of a selection of SH3 domains. The proteins were grouped into three functional classes including Sla1 orthologs (top), proteins with demonstrable ubiquitin-binding activity (middle) and those lacking this activity (bottom).^3 Conserved and invariant residues in each group are shaded green and yellow, respectively. The continuous pink circles and red inverted triangles denote Sla1 SH3-3 residues deemed to contact ubiquitin in the NMR structure and those residues that when mutated to alanine diminish monoubiquitin binding,^3 respectively. A cartoon depicting the location of secondary structural elements in Sla1 SH3-3 is shown on top. (b) A catalog of non-covalent intermolecular interactions in the Sla1 SH3-3–ubiquitin complex detected in ≥60% of conformers in the NMR ensemble.^27 Sla1 SH3-3 and ubiquitin residues are colored in blue and yellow, respectively. The lines connect interacting residues. Line colors indicate the type of interaction (green, electrostatic; red, hydrogen bonding; purple, salt bridge; gray, hydrophobic).
 
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 373, 190-196) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20541996 J.M.Winget, and T.Mayor (2010).
The diversity of ubiquitin recognition: hot spots and varied specificity.
  Mol Cell, 38, 627-635.  
19361414 A.Severin, R.E.Joseph, S.Boyken, D.B.Fulton, and A.H.Andreotti (2009).
Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain.
  J Mol Biol, 387, 726-743.  
20064468 J.F.Trempe, C.X.Chen, K.Grenier, E.M.Camacho, G.Kozlov, P.S.McPherson, K.Gehring, and E.A.Fon (2009).
SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination.
  Mol Cell, 36, 1034-1047.
PDB code: 3iql
19359362 J.L.Ortega-Roldan, M.R.Jensen, B.Brutscher, A.I.Azuaga, M.Blackledge, and N.A.van Nuland (2009).
Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.
  Nucleic Acids Res, 37, e70.  
19627600 W.Dampier, P.Evans, L.Ungar, and A.Tozeren (2009).
Host sequence motifs shared by HIV predict response to antiretroviral therapy.
  BMC Med Genomics, 2, 47.  
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 code is shown on the right.