4NNJ

Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the ubiquitin-activating enzyme loaded with two ubiquitin molecules.

Schafer, A.Kuhn, M.Schindelin, H.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1311-1320

  • DOI: 10.1107/S1399004714002910
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The activation of ubiquitin by the ubiquitin-activating enzyme Uba1 (E1) constitutes the first step in the covalent modification of target proteins with ubiquitin. This activation is a three-step process in which ubiquitin is adenylated at its C-term ...

    The activation of ubiquitin by the ubiquitin-activating enzyme Uba1 (E1) constitutes the first step in the covalent modification of target proteins with ubiquitin. This activation is a three-step process in which ubiquitin is adenylated at its C-terminal glycine, followed by the covalent attachment of ubiquitin to a catalytic cysteine residue of Uba1 and the subsequent adenylation of a second ubiquitin. Here, a ubiquitin E1 structure loaded with two ubiquitin molecules is presented for the first time. While one ubiquitin is bound in its adenylated form to the active adenylation domain of E1, the second ubiquitin represents the status after transfer and is covalently linked to the active-site cysteine. The covalently linked ubiquitin enables binding of the E2 enzyme without further modification of the ternary Uba1-ubiquitin2 arrangement. This doubly loaded E1 structure constitutes a missing link in the structural analysis of the ubiquitin-transfer cascade.


    Organizational Affiliation

    Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1 1A, C1040Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UBA1YKL210W
EC: 6.2.1.45
Find proteins for P22515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22515 
Go to UniProtKB:  P22515
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Uba1B, D, E79Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCD2UBI4YLL039C
Find proteins for P0CG63 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CG63 
Go to UniProtKB:  P0CG63
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download CCD File 
B, D
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

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A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.04α = 90
b = 195.651β = 90
c = 230.629γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
EDNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references