Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.93 kDa 
• Atom Count: 979 
• Modelled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 2

2MC1

Solution structure of the Vav1 SH2 domain complexed with a Syk-derived singly phosphorylated peptide

• PDB DOI: 10.2210/pdb2MC1/pdb
• BMRB: 19423

• Classification: SIGNALING PROTEIN/PROTEIN BINDING
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-13 Released: 2013-08-28 
• Deposition Author(s): Chen, C., Piraner, D., Gorenstein, N.M., Geahlen, R.L., Post, C.B.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Differential recognition of syk-binding sites by each of the two phosphotyrosine-binding pockets of the Vav SH2 domain.

Chen, C.H., Piraner, D., Gorenstein, N.M., Geahlen, R.L., Beth Post, C.

(2013) Biopolymers 99: 897-907

• PubMed: 23955592 
• DOI: 10.1002/bip.22371
• Primary Citation of Related Structures:  
  2MC1


• PubMed Abstract: 
  

The association of spleen tyrosine kinase (Syk), a central tyrosine kinase in B cell signaling, with Vav SH2 domain is controlled by phosphorylation of two closely spaced tyrosines in Syk linker B: Y342 and Y346. Previous studies established both singly phosphorylated and doubly phosphorylated forms play a role in signaling. The structure of the doubly phosphorylated form identified a new recognition of phosphotyrosine whereby two phosphotyrosines bind simultaneously to the Vav SH2 domain, one in the canonical pTyr pocket and one in the specificity pocket on the opposite side of the central β-sheet. It is unknown if the specificity pocket can bind phosphotyrosine independent of phosphotyrosine binding the pTyr pocket. To address this gap in knowledge, we determined the structure of the complex between Vav1 SH2 and a peptide (SykLB-YpY) modeling the singly phosphorylated-Y346 form of Syk with unphosphorylated Y342. The nuclear magnetic resonance (NMR) data conclusively establish that recognition of phosphotyrosine is swapped between the two pockets; phosphorylated pY346 binds the specificity pocket of Vav1 SH2, and unphosphorylated Y342 occupies what is normally the pTyr binding pocket. Nearly identical changes in chemical shifts occurred upon binding all three forms of singly and doubly phosphorylated peptides; however, somewhat smaller shift perturbations for SykLB-YpY from residues in regions of high internal mobility suggest that internal motions are coupled to binding affinity. The differential recognition that includes this swapped binding of phosphotyrosine to the specificity pocket of Vav SH2 increases the repertoire of possible phosphotyrosine binding by SH2 domains in regulating protein-protein interactions in cellular signaling.

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Organizational Affiliation: 

Department of Medicinal Chemistry and Molecular Pharmacology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47907.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene vav	A	107	Homo sapiens	Mutation(s): 0  Gene Names: VAV1, VAV
UniProt & NIH Common Fund Data Resources
Find proteins for P15498 (Homo sapiens) Explore P15498  Go to UniProtKB:  P15498
PHAROS:  P15498

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	B	13	Mus musculus	Mutation(s): 0  Gene Names: Syk, ptk72, Sykb EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P48025 (Mus musculus) Explore P48025  Go to UniProtKB:  P48025
IMPC:  MGI:99515

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2MC1 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-13 
• Released Date: 2013-08-28 
Deposition Author(s): Chen, C., Piraner, D., Gorenstein, N.M., Geahlen, R.L., Post, C.B.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2013-10-02
  Changes: Database references