Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.03 kDa 
• Atom Count: 3249 
• Modelled Residue Count: 357 
• Deposited Residue Count: 360 
• Unique protein chains: 1

3SA0

Complex of ERK2 with norathyriol

• PDB DOI: 10.2210/pdb3SA0/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-02 Released: 2011-12-14 
• Deposition Author(s): Kurinov, I., Malakhova, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.200 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Norathyriol Suppresses Skin Cancers Induced by Solar Ultraviolet Radiation by Targeting ERK Kinases.

Li, J., Malakhova, M., Mottamal, M., Reddy, K., Kurinov, I., Carper, A., Langfald, A., Oi, N., Kim, M.O., Zhu, F., Sosa, C.P., Zhou, K., Bode, A.M., Dong, Z.

(2012) Cancer Res 72: 260-270

• PubMed: 22084399 
• DOI: 10.1158/0008-5472.CAN-11-2596
• Primary Citation of Related Structures:  
  3SA0


• PubMed Abstract: 
  

Ultraviolet (UV) irradiation is the leading factor in the development of skin cancer, prompting great interest in chemopreventive agents for this disease. In this study, we report the discovery of norathyriol, a plant-derived chemopreventive compound identified through an in silico virtual screening of the Chinese Medicine Library. Norathyriol is a metabolite of mangiferin found in mango, Hypericum elegans, and Tripterospermum lanceolatum and is known to have anticancer activity. Mechanistic investigations determined that norathyriol acted as an inhibitor of extracellular signal-regulated kinase (ERK)1/2 activity to attenuate UVB-induced phosphorylation in mitogen-activated protein kinases signaling cascades. We confirmed the direct and specific binding of norathyriol with ERK2 through a cocrystal structural analysis. The xanthone moiety in norathyriol acted as an adenine mimetic to anchor the compound by hydrogen bonds to the hinge region of the protein ATP-binding site on ERK2. Norathyriol inhibited in vitro cell growth in mouse skin epidermal JB6 P+ cells at the level of G(2)-M phase arrest. In mouse skin tumorigenesis assays, norathyriol significantly suppressed solar UV-induced skin carcinogenesis. Further analysis indicated that norathyriol mediates its chemopreventive activity by inhibiting the ERK-dependent activity of transcriptional factors AP-1 and NF-κB during UV-induced skin carcinogenesis. Taken together, our results identify norathyriol as a safe new chemopreventive agent that is highly effective against development of UV-induced skin cancer.

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Organizational Affiliation: 

The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	360	Homo sapiens	Mutation(s): 0  Gene Names: ERK2, MAPK1, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NRA	B [auth A]	norathyriol C13 H8 O6 ZHTQCPCDXKMMLU-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.200 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.687	α = 90
b = 69.411	β = 108.99
c = 59.721	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-02 
• Released Date: 2011-12-14 
Deposition Author(s): Kurinov, I., Malakhova, M.

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2012-01-18
  Changes: Database references