4II2

Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer.

Olsen, S.K.Lima, C.D.

(2013) Mol.Cell 49: 884-896

  • DOI: 10.1016/j.molcel.2013.01.013
  • Primary Citation of Related Structures:  4II3

  • PubMed Abstract: 
  • Ubiquitin (Ub) conjugation is initiated by an E1 enzyme that catalyzes carboxy-terminal Ub adenylation, thioester bond formation to a catalytic cysteine in the E1 Cys domain, and thioester transfer to a catalytic cysteine in E2 conjugating enzymes. H ...

    Ubiquitin (Ub) conjugation is initiated by an E1 enzyme that catalyzes carboxy-terminal Ub adenylation, thioester bond formation to a catalytic cysteine in the E1 Cys domain, and thioester transfer to a catalytic cysteine in E2 conjugating enzymes. How the E1 and E2 active sites come together during thioester transfer and how Ub E1 interacts with diverse Ub E2s remains unclear. Here we present a crystal structure of a Ub E1-E2(Ubc4)/Ub/ATP·Mg complex that was stabilized by induction of a disulfide bond between the E1 and E2 active sites. The structure reveals combinatorial recognition of the E2 by the E1 ubiquitin-fold domain (UFD) and Cys domain and mutational analysis, coupled with thioester transfer assays with E1, Ubc4, and other Ub E2s, show that both interfaces are important for thioester transfer. Comparison to a Ub E1/Ub/ATP·Mg structure reveals conformational changes in the E1 that bring the E1 and E2 active sites together.


    Organizational Affiliation

    Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1 1
A
1001Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: ptr3
EC: 6.2.1.45
Find proteins for O94609 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94609
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
B
83Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: uep1 (ubi2)
Find proteins for P0CH07 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P0CH07
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 4
C
163Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: ubc4
EC: 2.3.2.23
Find proteins for P46595 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P46595
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PG0
Query on PG0

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Download CCD File 
A
2-(2-METHOXYETHOXY)ETHANOL
PEG 6000
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.600α = 90.00
b = 111.200β = 90.00
c = 181.300γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
DENZOdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description