5L6H

Uba1 in complex with Ub-ABPA3 covalent adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dissecting the Specificity of Adenosyl Sulfamate Inhibitors Targeting the Ubiquitin-Activating Enzyme.

Misra, M.Kuhn, M.Lobel, M.An, H.Statsyuk, A.V.Sotriffer, C.Schindelin, H.

(2017) Structure 25: 1120-1129.e3

  • DOI: 10.1016/j.str.2017.05.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeting the activating enzymes (E1) of ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) has emerged as a promising anti-cancer strategy, possibly overcoming the ineffectiveness of proteasome inhibitors against solid tumors. Here, we report crysta ...

    Targeting the activating enzymes (E1) of ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) has emerged as a promising anti-cancer strategy, possibly overcoming the ineffectiveness of proteasome inhibitors against solid tumors. Here, we report crystal structures of the yeast ubiquitin E1 (Uba1) with three adenosyl sulfamate inhibitors exhibiting different E1 specificities, which are all covalently linked to ubiquitin. The structures illustrate how the chemically diverse inhibitors are accommodated within the adenylation active site. When compared with the previously reported structures of various E1 enzymes, our structures provide the basis of the preferences of these inhibitors for different Ub/Ubl-activating enzymes. In vitro inhibition assays and molecular dynamics simulations validated the specificities of the inhibitors as deduced from the structures. Taken together, the structures establish a framework for the development of additional compounds targeting E1 enzymes, which will display higher potency and selectivity.


    Organizational Affiliation

    Institute of Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany; Institute of Pharmacy and Food Chemistry, Department of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-activating enzyme E1 1
A, C
1024Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UBA1
EC: 6.2.1.45
Find proteins for P22515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: UBA1
Go to UniProtKB:  P22515
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
B, D, E
76Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS31 (RPS37, UBI3)
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05759
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6O2
Query on 6O2

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B, D
[(2~{R},3~{S},4~{R},5~{R})-5-[6-[(3-ethynylphenyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate
ABPA3
C18 H18 N6 O6 S
LZNFQRSVDZCPTR-SCFUHWHPSA-N
 Ligand Interaction
SO4
Query on SO4

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

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C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, C
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.048α = 90.00
b = 194.098β = 90.00
c = 230.172γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFZ82; HS

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence