4FH1

S. cerevisiae Ubc13-N79A

• PDB DOI: https://doi.org/10.2210/pdb4FH1/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-06-05 Released: 2013-01-09 
• Deposition Author(s): Berndsen, C.E., Wolberger, C., Wiener, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.246 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

A conserved asparagine has a structural role in ubiquitin-conjugating enzymes.

Berndsen, C.E., Wiener, R., Yu, I.W., Ringel, A.E., Wolberger, C.

(2013) Nat Chem Biol 9: 154-156

• PubMed: 23292652 
• DOI: https://doi.org/10.1038/nchembio.1159
• Primary Citation of Related Structures:  
  4FH1


• PubMed Abstract: 
  

  It is widely accepted that ubiquitin-conjugating enzymes contain an active site asparagine that serves as an oxyanion hole, thereby stabilizing a negatively charged transition state intermediate and promoting ubiquitin transfer. Using structural and biochemical approaches to study the role of the conserved asparagine to ubiquitin conjugation by Ubc13-Mms2, we conclude that the importance of this residue stems primarily from its structural role in stabilizing an active site loop.

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Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 17.64 kDa 
• Atom Count: 1,130 
• Modelled Residue Count: 145 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 13	A	153	Saccharomyces cerevisiae S288C	Mutation(s): 2  Gene Names: UBC13, YDR092W, YD6652.04 EC: 6.3.2.19
UniProt
Find proteins for P52490 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52490  Go to UniProtKB:  P52490

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	B [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.246 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.026	α = 90
b = 77.026	β = 90
c = 68.35	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Berndsen, C.E., Wolberger, C., Wiener, R.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description