5KNL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    5KNL

  • 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 structure of S ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-activating enzyme E1 1A, D1001Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ptr3SPBC1604.21cSPBC211.09
EC: 6.2.1.45
UniProt
Find proteins for O94609 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O94609 
Go to UniProtKB:  O94609
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB, E96Moesziomyces antarcticusMutation(s): 8 
Gene Names: PAN0_008c3613PAN0_007c3281PSANT_03630
UniProt
Find proteins for A0A081CEG8 (Pseudozyma antarctica)
Explore A0A081CEG8 
Go to UniProtKB:  A0A081CEG8
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 15C, F175Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ubc15SPBC1105.09
EC: 2.3.2.23
UniProt
Find proteins for Q9Y818 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9Y818 
Go to UniProtKB:  Q9Y818
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth B] , L [auth D] , M [auth D] , N [auth D] , 
G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth B],  L [auth D],  M [auth D],  N [auth D],  O [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.111α = 102.1
b = 82.238β = 95.78
c = 135.376γ = 90.86
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115568

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence