Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 35.05 kDa 
• Atom Count: 2500 
• Residue Count: 287 
• Unique protein chains: 2

4NRG

Crystal Structure of a human Mms2/Ubc13 D118G mutant

• DOI: 10.2210/pdb4NRG/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-11-26 Released: 2014-12-10 
• Deposition Author(s): Hodge, C.D., Edwards, R.A., Glover, J.N.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Stochastic gate dynamics regulate the catalytic activity of ubiquitination enzymes.

Rout, M.K., Hodge, C.D., Markin, C.J., Xu, X., Glover, J.N., Xiao, W., Spyracopoulos, L.

(2014) J Am Chem Soc 136: 17446-17458

• PubMed: 25423605 
• DOI: 10.1021/ja505440b
• Primary Citation of Related Structures:  
  4NR3, 4NRI, 4NRG


• PubMed Abstract: 
  

Initiation of the DNA damage and innate immune responses is dependent upon the flow of chemical information through coupled protein-protein interaction networks and driven by the synthesis and recognition of Lys 63 linked polyubiquitin (polyUb) chains on adaptor proteins. The central chemical step in Lys 63-linked protein ubiquitination involves the reaction of a specific lysine on a target protein with Ub that is covalently attached as a thioester conjugate to the Ub conjugating enzyme (E2) Ubc13. The active site cysteine of Ubc13, and E2 enzymes in general, is buttressed by a flexible loop. The role of loop dynamics in catalysis was investigated by mutating the central and hinge residues to glycine. The loop dynamics were experimentally characterized through measurement of enzyme kinetics, main chain NMR relaxation, X-ray crystallographic studies, and in vivo studies in yeast. The experimental data were complemented by analysis of MD simulations of the dynamics and kinetics for the loop motion. The results show that fast pico- to nanosecond time scale active site loop fluctuations play a crucial role in regulating the catalytic activity of Ubc13 by functioning as a stochastic active site gate, which is characterized by precisely balanced rates of opening and closing. In vivo functional complementation assays in yeast demonstrate that defects within this regulatory mechanism can have profound biological consequences, given that Ubc13 is the only E2 dedicated to synthesizing Lys 63-linked polyUb chains.

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Organizational Affiliation: 

Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G 2H7, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 variant 2	A	153	Homo sapiens	Mutation(s): 0  Gene Names: MMS2, UBE2V2, UEV2
Find proteins for Q15819 (Homo sapiens) Explore Q15819  Go to UniProtKB:  Q15819
NIH Common Fund Data Resources
PHAROS:  Q15819 GTEx:  ENSG00000169139

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	B	160	Homo sapiens	Mutation(s): 1  Gene Names: BLU, UBE2N EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens) Explore P61088  Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS:  P61088 GTEx:  ENSG00000177889

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.272	α = 90
b = 73.616	β = 90
c = 92.093	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-11-26 
• Released Date: 2014-12-10 
Deposition Author(s): Hodge, C.D., Edwards, R.A., Glover, J.N.M.

Revision History 

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references