1Z7L

Crystal structure of fragment of mouse ubiquitin-activating enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.277 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a fragment of mouse ubiquitin-activating enzyme.

Szczepanowski, R.H.Filipek, R.Bochtler, M.

(2005) J.Biol.Chem. 280: 22006-22011

  • DOI: 10.1074/jbc.M502583200

  • PubMed Abstract: 
  • Protein ubiquitination requires the sequential activity of three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin-ligase (E3). The ubiquitin-transfer machinery is hierarchically organized; for every ub ...

    Protein ubiquitination requires the sequential activity of three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin-ligase (E3). The ubiquitin-transfer machinery is hierarchically organized; for every ubiquitin-activating enzyme, there are several ubiquitin-conjugating enzymes, and most ubiquitin-conjugating enzymes can in turn interact with multiple ubiquitin ligases. Despite the central role of ubiquitin-activating enzyme in this cascade, a crystal structure of a ubiquitin-activating enzyme is not available. The enzyme is thought to consist of an adenylation domain, a catalytic cysteine domain, a four-helix bundle, and possibly, a ubiquitin-like domain. Its adenylation domain can be modeled because it is clearly homologous to the structurally known adenylation domains of the activating enzymes for the small ubiquitin-like modifier (SUMO) and for the protein encoded by the neuronal precursor cell-expressed, developmentally down-regulated gene 8 (NEDD8). Low sequence similarity and vastly different domain lengths make modeling difficult for the catalytic cysteine domain that results from the juxtaposition of two catalytic cysteine half-domains. Here, we present a biochemical and crystallographic characterization of the two half-domains and the crystal structure of the larger, second catalytic cysteine half-domain of mouse ubiquitin-activating enzyme. We show that the domain is organized around a conserved folding motif that is also present in the NEDD8- and SUMO-activating enzymes, and we propose a tentative model for full-length ubiquitin-activating enzyme.


    Organizational Affiliation

    International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1 1
A, B, C
276Mus musculusMutation(s): 0 
Gene Names: Uba1 (Sbx, Ube1, Ube1ax, Ube1x)
EC: 6.2.1.45
Find proteins for Q02053 (Mus musculus)
Go to UniProtKB:  Q02053
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TBR
Query on TBR

Download SDF File 
Download CCD File 
A, B, C
HEXATANTALUM DODECABROMIDE
DODECABROMOHEXATANTALUM
Br12 Ta6
YWYIQTPPCOBSGN-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.277 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 216.123α = 90.00
b = 216.123β = 90.00
c = 196.092γ = 120.00
Software Package:
Software NamePurpose
MLPHAREphasing
DMphasing
SHELXEmodel building
SIGMAAphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance