4N0S | pdb_00004n0s

Complex of ERK2 with caffeic acid

• PDB DOI: https://doi.org/10.2210/pdb4N0S/pdb

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


• Deposited: 2013-10-02 Released: 2014-08-27 
• Deposition Author(s): Kurinov, I., Malakhova, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.189 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Caffeic Acid Directly Targets ERK1/2 to Attenuate Solar UV-Induced Skin Carcinogenesis.

Yang, G., Fu, Y., Malakhova, M., Kurinov, I., Zhu, F., Yao, K., Li, H., Chen, H., Li, W., Lim, D.Y., Sheng, Y., Bode, A.M., Dong, Z., Dong, Z.

(2014) Cancer Prev Res (phila) 7: 1056-1066

• PubMed: 25104643 
• DOI: https://doi.org/10.1158/1940-6207.CAPR-14-0141
• Primary Citation Related Structures: 
  4N0S


• PubMed Abstract: 
  

  Caffeic acid (3,4-dihydroxycinnamic acid) is a well-known phenolic phytochemical present in coffee and reportedly has anticancer activities. However, the underlying molecular mechanisms and targeted proteins involved in the suppression of carcinogenesis by caffeic acid are not fully understood. In this study, we report that caffeic acid significantly inhibits colony formation of human skin cancer cells and EGF-induced neoplastic transformation of HaCaT cells dose-dependently. Caffeic acid topically applied to dorsal mouse skin significantly suppressed tumor incidence and volume in a solar UV (SUV)-induced skin carcinogenesis mouse model. A substantial reduction of phosphorylation in mitogen-activated protein kinase signaling was observed in mice treated with caffeic acid either before or after SUV exposure. Caffeic acid directly interacted with ERK1/2 and inhibited ERK1/2 activities in vitro. Importantly, we resolved the cocrystal structure of ERK2 complexed with caffeic acid. Caffeic acid interacted directly with ERK2 at amino acid residues Q105, D106, and M108. Moreover, A431 cells expressing knockdown of ERK2 lost sensitivity to caffeic acid in a skin cancer xenograft mouse model. Taken together, our results suggest that caffeic acid exerts chemopreventive activity against SUV-induced skin carcinogenesis by targeting ERK1 and 2.

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Organizational Affiliation: 
• The Hormel Institute, University of Minnesota, Austin, Minnesota. Physiology and Pathophysiology, Basic Medical College, Zhengzhou University, ZhengZhou, China. The First Affiliated Hospital of Zhengzhou University, ZhengZhou, China.
The Hormel Institute, University of Minnesota, Austin, Minnesota. The First Affiliated Hospital of Zhengzhou University, ZhengZhou, China.
The Hormel Institute, University of Minnesota, Austin, Minnesota.
Cornell University, NE-CAT, APS, Argonne, Illinois.
Physiology and Pathophysiology, Basic Medical College, Zhengzhou University, ZhengZhou, China. [e-mail] [e-mail].
The Hormel Institute, University of Minnesota, Austin, Minnesota. [e-mail] [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 42.48 kDa 
• Atom Count: 3,347 
• Modeled Residue Count: 352 
• Deposited Residue Count: 360 
• Unique protein chains: 1

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: MAPK1, ERK2, 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 GTEx:  ENSG00000100030

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHC	B [auth A]	CAFFEIC ACID C9 H8 O4 QAIPRVGONGVQAS-DUXPYHPUSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	G [auth A], H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

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: 1.80 Å
• R-Value Free:  0.189 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.748	α = 90
b = 69.932	β = 109.16
c = 59.989	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

• Released Date: 2014-08-27 
Deposition Author(s): Kurinov, I., Malakhova, M.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary