4NRG

Crystal Structure of a human Mms2/Ubc13 D118G mutant

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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

  • DOI: 10.1021/ja505440b
  • Primary Citation of Related Structures:  

  • 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) chain ...

    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.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 variant 2
A
153Homo sapiensMutation(s): 0 
Gene Names: UBE2V2 (MMS2, UEV2)
Find proteins for Q15819 (Homo sapiens)
Go to Gene View: UBE2V2
Go to UniProtKB:  Q15819
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
B
160Homo sapiensMutation(s): 1 
Gene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.272α = 90.00
b = 73.616β = 90.00
c = 92.093γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
CrystalCleardata collection
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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