1Y8X

Structural basis for recruitment of Ubc12 by an E2-binding domain in NEDD8's E1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1.

Huang, D.T.Paydar, A.Zhuang, M.Waddell, M.B.Holton, J.M.Schulman, B.A.

(2005) Mol.Cell 17: 341-350

  • DOI: 10.1016/j.molcel.2004.12.020

  • PubMed Abstract: 
  • E2 conjugating enzymes play a central role in ubiquitin and ubiquitin-like protein (ublp) transfer cascades: the E2 accepts the ublp from the E1 enzyme and then the E2 often interacts with an E3 enzyme to promote ublp transfer to the target. We repor ...

    E2 conjugating enzymes play a central role in ubiquitin and ubiquitin-like protein (ublp) transfer cascades: the E2 accepts the ublp from the E1 enzyme and then the E2 often interacts with an E3 enzyme to promote ublp transfer to the target. We report here the crystal structure of a complex between the C-terminal domain from NEDD8's heterodimeric E1 (APPBP1-UBA3) and the catalytic core domain of NEDD8's E2 (Ubc12). The structure and associated mutational analyses reveal molecular details of Ubc12 recruitment by NEDD8's E1. Interestingly, the E1's Ubc12 binding domain resembles ubiquitin and recruits Ubc12 in a manner mimicking ubiquitin's interactions with ubiquitin binding domains. Structural comparison with E2-E3 complexes indicates that the E1 and E3 binding sites on Ubc12 may overlap and raises the possibility that crosstalk between E1 and E3 interacting with an E2 could influence the specificity and processivity of ublp transfer.


    Organizational Affiliation

    Department of Structural Biology, Department of Genetics/Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 M
A
160Homo sapiensMutation(s): 0 
Gene Names: UBE2M (UBC12)
EC: 2.3.2.-
Find proteins for P61081 (Homo sapiens)
Go to Gene View: UBE2M
Go to UniProtKB:  P61081
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1C
B
98Homo sapiensMutation(s): 1 
Gene Names: UBA3 (UBE1C)
EC: 6.2.1.-
Find proteins for Q8TBC4 (Homo sapiens)
Go to Gene View: UBA3
Go to UniProtKB:  Q8TBC4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.606α = 90.00
b = 61.518β = 90.00
c = 125.938γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance