3CMM

Crystal Structure of the Uba1-Ubiquitin Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into E1-catalyzed ubiquitin activation and transfer to conjugating enzymes.

Lee, I.Schindelin, H.

(2008) Cell 134: 268-278

  • DOI: 10.1016/j.cell.2008.05.046

  • PubMed Abstract: 
  • Ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are conjugated to their targets by specific cascades involving three classes of enzymes, E1, E2, and E3. Each E1 adenylates the C terminus of its cognate Ubl, forms a E1 approximately Ubl thioester in ...

    Ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are conjugated to their targets by specific cascades involving three classes of enzymes, E1, E2, and E3. Each E1 adenylates the C terminus of its cognate Ubl, forms a E1 approximately Ubl thioester intermediate, and ultimately generates a thioester-linked E2 approximately Ubl product. We have determined the crystal structure of yeast Uba1, revealing a modular architecture with individual domains primarily mediating these specific activities. The negatively charged C-terminal ubiquitin-fold domain (UFD) is primed for binding of E2s and recognizes their positively charged first alpha helix via electrostatic interactions. In addition, a mobile loop from the domain harboring the E1 catalytic cysteine contributes to E2 binding. Significant, experimentally observed motions in the UFD around a hinge in the linker connecting this domain to the rest of the enzyme suggest a conformation-dependent mechanism for the transthioesterification function of Uba1; however, this mechanism clearly differs from that of other E1 enzymes.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1 1
A, C
1015Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: UBA1
EC: 6.2.1.45
Find proteins for P22515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: UBA1
Go to UniProtKB:  P22515
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, D
76Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: UBI4 (SCD2)
Find proteins for P0CG63 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CG63
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRO
Query on PRO

Download SDF File 
Download CCD File 
A, C
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 115.363α = 90.00
b = 118.564β = 90.00
c = 207.567γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CBASSdata collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description