1YOV

Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8

Walden, H.Podgorski, M.S.Schulman, B.A.

(2003) Nature 422: 330-334

  • DOI: 10.1038/nature01456
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Post-translational modification by ubiquitin-like proteins (Ublps) is an essential cellular regulatory mechanism. The Ublp NEDD8 regulates cell division, signalling and embryogenesis. Ublps are conjugated to their targets by the sequential action of ...

    Post-translational modification by ubiquitin-like proteins (Ublps) is an essential cellular regulatory mechanism. The Ublp NEDD8 regulates cell division, signalling and embryogenesis. Ublps are conjugated to their targets by the sequential action of E1, E2 and often E3 enzymes. Each Ublp has a dedicated E1, or activating enzyme, that initiates its conjugation cascade. First, E1 associates with the Ublp and catalyses adenylation of the carboxy terminus of the Ublp. Second, E1 forms a thioester between its catalytic cysteine and the Ublp. Next, E1 is loaded with a second Ublp molecule, adenylating the C terminus of this second Ublp while still carrying the first thioester-bound Ublp. Last, E1 binds E2 and promotes Ublp transfer to the catalytic cysteine of E2. We report here the structure and mutational analysis of human APPBP1-UBA3, the heterodimeric E1 enzyme for NEDD8 (ref. 11). Each E1 activity is specified by a domain: an adenylation domain resembling bacterial adenylating enzymes, an E1-specific domain organized around the catalytic cysteine, and a domain involved in E2 recognition resembling ubiquitin. The domains are arranged around two clefts that coordinate protein and nucleotide binding so that each of E1's reactions drives the next, in an assembly-line fashion.


    Organizational Affiliation

    Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amyloid protein-binding protein 1
A, C
537Homo sapiensMutation(s): 0 
Gene Names: NAE1 (APPBP1)
Find proteins for Q13564 (Homo sapiens)
Go to Gene View: NAE1
Go to UniProtKB:  Q13564
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1C
B, D
444Homo sapiensMutation(s): 0 
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
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.400α = 90.00
b = 123.600β = 90.00
c = 198.200γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance