7UBU | pdb_00007ubu

Crystal structure of ZMET2 in complex with hemimethylated CAG DNA and a histone H3Kc9me2 peptide

• PDB DOI: https://doi.org/10.2210/pdb7UBU/pdb
• NAKB: 7UBU

• Classification: TRANSFERASE/DNA
• Organism(s): Zea mays
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-15 Released: 2022-06-08 
• Deposition Author(s): Fang, J., Song, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Mechanistic basis for maintenance of CHG DNA methylation in plants.

Fang, J., Jiang, J., Leichter, S.M., Liu, J., Biswal, M., Khudaverdyan, N., Zhong, X., Song, J.

(2022) Nat Commun 13: 3877-3877

• PubMed: 35790763 
• DOI: https://doi.org/10.1038/s41467-022-31627-3
• Primary Citation Related Structures: 
  7UBU


• PubMed Abstract: 
  

  DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, DNA methylation widely occurs in the CG, CHG, and CHH (H = A, C, or T) contexts, with the maintenance of CHG methylation mediated by CMT3 chromomethylase. However, how CMT3 interacts with the chromatin environment for faithful maintenance of CHG methylation is unclear. Here we report structure-function characterization of the H3K9me2-directed maintenance of CHG methylation by CMT3 and its Zea mays ortholog ZMET2. Base-specific interactions and DNA deformation coordinately underpin the substrate specificity of CMT3 and ZMET2, while a bivalent readout of H3K9me2 and H3K18 allosterically stimulates substrate binding. Disruption of the interaction with DNA or H3K9me2/H3K18 led to loss of CMT3/ZMET2 activity in vitro and impairment of genome-wide CHG methylation in vivo. Together, our study uncovers how the intricate interplay of CMT3, repressive histone marks, and DNA sequence mediates heterochromatic CHG methylation.

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Organizational Affiliation: 
• Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.
Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA. [e-mail].
Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA. [e-mail].
Department of Biochemistry, University of California, Riverside, CA, 92521, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 105.97 kDa 
• Atom Count: 6,690 
• Modeled Residue Count: 776 
• Deposited Residue Count: 885 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 1	A	783	Zea mays	Mutation(s): 0  Gene Names: MET2A EC: 2.1.1.37
UniProt
Find proteins for Q9AXT8 (Zea mays) Explore Q9AXT8  Go to UniProtKB:  Q9AXT8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	B [auth P], E [auth Q]	33	Zea mays	Mutation(s): 0  Gene Names: H3C2, H3C3, H3C4
UniProt
Find proteins for P69246 (Zea mays) Explore P69246  Go to UniProtKB:  P69246

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5MC SSDNA	C [auth B]	18	Zea mays

Entity ID: 4
Molecule	Chains	Length	Organism	Image
C49 SSDNA	D [auth C]	18	Zea mays

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M2L	B [auth P], E [auth Q]	L-PEPTIDE LINKING	C7 H16 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.574	α = 90
b = 121.392	β = 90
c = 160.446	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
PHASER	phasing
HKL-3000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Fang, J., Song, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM119721

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2022-07-20
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-23
  Changes: Data collection, Structure summary