1JAT

Mms2/Ubc13 Ubiquitin Conjugating Enzyme Complex

• PDB DOI:  https://doi.org/10.2210/pdb1JAT/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-05-31 Released: 2001-06-20 
• Deposition Author(s): VanDemark, A.P., Hofmann, R.M., Tsui, C., Pickart, C.M., Wolberger, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.239 
• R-Value Work: 0.203 

Literature

Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer.

VanDemark, A.P., Hofmann, R.M., Tsui, C., Pickart, C.M., Wolberger, C.

(2001) Cell 105: 711-720

• PubMed: 11440714 
• DOI: https://doi.org/10.1016/s0092-8674(01)00387-7
• Primary Citation of Related Structures:  
  1JAT, 1JBB


• PubMed Abstract: 
  

While the signaling properties of ubiquitin depend on the topology of polyubiquitin chains, little is known concerning the molecular basis of specificity in chain assembly and recognition. UEV/Ubc complexes have been implicated in the assembly of Lys63-linked polyubiquitin chains that act as a novel signal in postreplicative DNA repair and I kappa B alpha kinase activation. The crystal structure of the Mms2/Ubc13 heterodimer shows the active site of Ubc13 at the intersection of two channels that are potential binding sites for the two substrate ubiquitins. Mutations that destabilize the heterodimer interface confer a marked UV sensitivity, providing direct evidence that the intact heterodimer is necessary for DNA repair. Selective mutations in the channels suggest a molecular model for specificity in the assembly of Lys63-linked polyubiquitin signals.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.28 kDa 
• Atom Count: 2,576 
• Modelled Residue Count: 284 
• Deposited Residue Count: 293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-Conjugating Enzyme E2-17.5 KDA	A	155	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: UBC13 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for P52490 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P52490  Go to UniProtKB:  P52490

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-Conjugating Enzyme Variant Mms2	B	138	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: MMS2
UniProt
Find proteins for P53152 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53152  Go to UniProtKB:  P53152

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.239 
• R-Value Work: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.158	α = 90
b = 63.797	β = 105.83
c = 53.152	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-06-20 
Deposition Author(s): VanDemark, A.P., Hofmann, R.M., Tsui, C., Pickart, C.M., Wolberger, C.

Revision History  

• Version 1.0: 2001-06-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance