5N1U

Structure of xEco2 acetyltransferase domain

• PDB DOI: https://doi.org/10.2210/pdb5N1U/pdb

• Classification: CELL CYCLE
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-06 Released: 2017-03-15 
• Deposition Author(s): Chao, W.C.H., Wade, B.O., Singleton, M.R.
• Funding Organization(s): Cancer Research UK, Wellcome Trust, Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.268 
• R-Value Work: 0.223 
• R-Value Observed: 0.228 

Literature

Structural Basis of Eco1-Mediated Cohesin Acetylation.

Chao, W.C., Wade, B.O., Bouchoux, C., Jones, A.W., Purkiss, A.G., Federico, S., O'Reilly, N., Snijders, A.P., Uhlmann, F., Singleton, M.R.

(2017) Sci Rep 7: 44313-44313

• PubMed: 28290497 
• DOI: https://doi.org/10.1038/srep44313
• Primary Citation of Related Structures:  
  5N1U, 5N1W, 5N22


• PubMed Abstract: 
  

  Sister-chromatid cohesion is established by Eco1-mediated acetylation on two conserved tandem lysines in the cohesin Smc3 subunit. However, the molecular basis of Eco1 substrate recognition and acetylation in cohesion is not fully understood. Here, we discover and rationalize the substrate specificity of Eco1 using mass spectrometry coupled with in-vitro acetylation assays and crystallography. Our structures of the X. laevis Eco2 (xEco2) bound to its primary and secondary Smc3 substrates demonstrate the plasticity of the substrate-binding site, which confers substrate specificity by concerted conformational changes of the central β hairpin and the C-terminal extension.

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Organizational Affiliation: 

Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.25 kDa 
• Atom Count: 2,725 
• Modelled Residue Count: 340 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XEco2	A, B	183	Xenopus laevis	Mutation(s): 0  Gene Names: xeco2
UniProt
Find proteins for A8QZK6 (Xenopus laevis) Explore A8QZK6  Go to UniProtKB:  A8QZK6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	C [auth A], D [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.268 
• R-Value Work: 0.223 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.475	α = 90
b = 66.287	β = 90
c = 109.763	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Chao, W.C.H., Wade, B.O., Singleton, M.R.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	FC001155
Wellcome Trust	United Kingdom	FC001155
Medical Research Council (United Kingdom)	United Kingdom	FC001155

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-03-29
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description