5L6H

Uba1 in complex with Ub-ABPA3 covalent adduct

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


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:  
    5L6H, 5L6I, 5L6J

  • 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 crystal structures of the yeast ubiquitin E1 (Uba1) with three adenosyl sulfamate inhibitors exhibiting different E1 specificities, which are all covalently linked to ubiquitin ...

    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. Electronic address: hermann.schindelin@virchow.uni-wuerzburg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-activating enzyme E1 1A, C1024Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UBA1, YKL210W
EC: 6.2.1.45
UniProt
Find proteins for P22515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22515 
Go to UniProtKB:  P22515
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22515
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31B, D, E76Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS31, RPS37, UBI3, YLR167W, L9470.14
UniProt
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05759 
Go to UniProtKB:  P05759
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05759
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6O2
Query on 6O2
Download Ideal Coordinates CCD File 
DA [auth D],
R [auth B]		[(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
C18 H18 N6 O6 S
LZNFQRSVDZCPTR-SCFUHWHPSA-N		 Ligand Interaction
SO4
Query on SO4
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F [auth A],
S [auth C]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
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AA [auth C],
BA [auth C],
K [auth A],
L [auth A],
M [auth A],
AA [auth C],
BA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
CA [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CL
Query on CL
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G [auth A],
H [auth A],
I [auth A],
J [auth A],
T [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
T [auth C],
U [auth C],
V [auth C],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
X [auth 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: 2.30 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.048α = 90
b = 194.098β = 90
c = 230.172γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyFZ82; HS

Revision History  (Full details and data files)

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