Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A5B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A4B3 Local Symmetry: Helical - H  (3D View)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Helical - H  (3D View)
Local Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 111.06 kDa 
• Atom Count: 5,732 
• Modelled Residue Count: 732 
• Deposited Residue Count: 959 
• Unique protein chains: 1

 4ZWS

Crystal Structure of the Bacteriophage T4 recombination mediator protein UvsY, Lattice Type III

• PDB DOI: 10.2210/pdb4ZWS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia virus T4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-19 Released: 2016-03-02 
• Deposition Author(s): Gajewski, S., White, S.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), American Lebanese-Syrian Associated Charities (ALSAC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.236 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structure and mechanism of the phage T4 recombination mediator protein UvsY.

Gajewski, S., Waddell, M.B., Vaithiyalingam, S., Nourse, A., Li, Z., Woetzel, N., Alexander, N., Meiler, J., White, S.W.

(2016) Proc Natl Acad Sci U S A 113: 3275-3280

• PubMed: 26951671 
• DOI: 10.1073/pnas.1519154113
• Primary Citation of Related Structures:  
  4ZWQ, 4ZWR, 4ZWS, 4ZWT


• PubMed Abstract: 
  

The UvsY recombination mediator protein is critical for efficient homologous recombination in bacteriophage T4 and is the functional analog of the eukaryotic Rad52 protein. During T4 homologous recombination, the UvsX recombinase has to compete with the prebound gp32 single-stranded binding protein for DNA-binding sites and UvsY stimulates this filament nucleation event. We report here the crystal structure of UvsY in four similar open-barrel heptameric assemblies and provide structural and biophysical insights into its function. The UvsY heptamer was confirmed in solution by centrifugation and light scattering, and thermodynamic analyses revealed that the UvsY-ssDNA interaction occurs within the assembly via two distinct binding modes. Using surface plasmon resonance, we also examined the binding of UvsY to both ssDNA and the ssDNA-gp32 complex. These analyses confirmed that ssDNA can bind UvsY and gp32 independently and also as a ternary complex. They also showed that residues located on the rim of the heptamer are required for optimal binding to ssDNA, thus identifying the putative ssDNA-binding surface. We propose a model in which UvsY promotes a helical ssDNA conformation that disfavors the binding of gp32 and initiates the assembly of the ssDNA-UvsX filament.

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Organizational Affiliation: 

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombination protein uvsY	A, B, C, D, E, F, G	137	Escherichia virus T4	Mutation(s): 0  Gene Names: uvsY
UniProt
Find proteins for P04537 (Enterobacteria phage T4) Explore P04537  Go to UniProtKB:  P04537

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.236 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.571	α = 90
b = 123.571	β = 90
c = 332.465	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Gajewski, S., White, S.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM066934
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA21765
American Lebanese-Syrian Associated Charities (ALSAC)	United States	--

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Database references
• Version 1.2: 2016-04-20
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence