5KNL

Crystal structure of S. pombe ubiquitin E1 (Uba1) in complex with Ubc15 and ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

S. pombe Uba1-Ubc15 Structure Reveals a Novel Regulatory Mechanism of Ubiquitin E2 Activity.

Lv, Z.Rickman, K.A.Yuan, L.Williams, K.Selvam, S.P.Woosley, A.N.Howe, P.H.Ogretmen, B.Smogorzewska, A.Olsen, S.K.

(2017) Mol. Cell 65: 699-714.e6

  • DOI: 10.1016/j.molcel.2017.01.008

  • PubMed Abstract: 
  • Ubiquitin (Ub) E1 initiates the Ub conjugation cascade by activating and transferring Ub to tens of different E2s. How Ub E1 cooperates with E2s that differ substantially in their predicted E1-interacting residues is unknown. Here, we report the stru ...

    Ubiquitin (Ub) E1 initiates the Ub conjugation cascade by activating and transferring Ub to tens of different E2s. How Ub E1 cooperates with E2s that differ substantially in their predicted E1-interacting residues is unknown. Here, we report the structure of S. pombe Uba1 in complex with Ubc15, a Ub E2 with intrinsically low E1-E2 Ub thioester transfer activity. The structure reveals a distinct Ubc15 binding mode that substantially alters the network of interactions at the E1-E2 interface compared to the only other available Ub E1-E2 structure. Structure-function analysis reveals that the intrinsically low activity of Ubc15 largely results from the presence of an acidic residue at its N-terminal region. Notably, Ub E2 N termini are serine/threonine rich in many other Ub E2s, leading us to hypothesize that phosphorylation of these sites may serve as a novel negative regulatory mechanism of Ub E2 activity, which we demonstrate biochemically and in cell-based assays.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA. Electronic address: olsensk@musc.edu.,Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA.,Laboratory of Genome Maintenance, Rockefeller University, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1 1
A, D
1001Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
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
B, E
96Pseudozyma antarcticaMutation(s): 8 
Find proteins for A0A081CEG8 (Pseudozyma antarctica)
Go to UniProtKB:  A0A081CEG8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 15
C, F
175Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: ubc15
EC: 2.3.2.23
Find proteins for Q9Y818 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9Y818
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 77.111α = 102.10
b = 82.238β = 95.78
c = 135.376γ = 90.86
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM115568

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence