Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 10.07 kDa 
• Atom Count: 698 
• Modelled Residue Count: 88 
• Deposited Residue Count: 88 
• Unique protein chains: 2

6QXZ

Solution structure of the ASHH2 CW domain with the N-terminal histone H3 tail mimicking peptide monomethylated on lysine 4

• PDB DOI: 10.2210/pdb6QXZ/pdb
• Entry: 6QXZ supersedes: 6HBO
• BMRB: 27251

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-08 Released: 2019-12-04 
• Deposition Author(s): Dobrovolska, O., Madeleine, N., Teigen, K., Halskau, O., Bril'kov, M.
• Funding Organization(s): Research Council of Norway

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection.

Dobrovolska, O., Brilkov, M., Madeleine, N., Odegard-Fougner, O., Stromland, O., Martin, S.R., De Marco, V., Christodoulou, E., Teigen, K., Isaksson, J., Underhaug, J., Reuter, N., Aalen, R.B., Aasland, R., Halskau, O.

(2020) FEBS J 287: 4458-4480

• PubMed: 32083791 
• DOI: 10.1111/febs.15256
• Primary Citation of Related Structures:  
  6QXZ


• PubMed Abstract: 
  

Chromatin post-translational modifications are thought to be important for epigenetic effects on gene expression. Methylation of histone N-terminal tail lysine residues constitutes one of many such modifications, executed by families of histone lysine methyltransferase (HKMTase). One such protein is ASHH2 from the flowering plant Arabidopsis thaliana, equipped with the interaction domain, CW, and the HKMTase domain, SET. The CW domain of ASHH2 is a selective binder of monomethylation at lysine 4 on histone H3 (H3K4me1) and likely helps the enzyme dock correctly onto chromatin sites. The study of CW and related interaction domains has so far been emphasizing lock-key models, missing important aspects of histone-tail CW interactions. We here present an analysis of the ASHH2 CW-H3K4me1 complex using NMR and molecular dynamics, as well as mutation and affinity studies of flexible coils. β-augmentation and rearrangement of coils coincide with changes in the flexibility of the complex, in particular the η1, η3 and C-terminal coils, but also in the β1 and β2 strands and the C-terminal part of the ligand. Furthermore, we show that mutating residues with outlier dynamic behaviour affect the complex binding affinity despite these not being in direct contact with the ligand. Overall, the binding process is consistent with conformational selection. We propose that this binding mechanism presents an advantage when searching for the correct post-translational modification state among the highly modified and flexible histone tails, and also that the binding shifts the catalytic SET domain towards the nucleosome. DATABASES: Structural data are available in the PDB database under the accession code 6QXZ. Resonance assignments for CW42 in its apo- and holo-forms are available in the BMRB database under the accession code 27251.

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Related Citations: 

• 1H, 13C, and 15N resonance assignments of CW domain of the N-methyltransferase ASHH2 free and bound to the mono-, di- and tri-methylated histone H3 tail peptides.
  Dobrovolska, O., Bril'kov, M., Odegard-Fougner, O., Aasland, R., Halskau, O.
  (2018) Biomol NMR Assign 12: 215

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Organizational Affiliation: 

Department of Biological Sciences, University of Bergen, Norway, Bergen.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase ASHH2	A	79	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ASHH2, EFS, LAZ2, SDG8, SET8, At1g77300, T14N5.15 EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
UniProt
Find proteins for Q2LAE1 (Arabidopsis thaliana) Explore Q2LAE1  Go to UniProtKB:  Q2LAE1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ARG-THR-MLZ-GLN-THR-ALA-ARG-TYR	B	9	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	B	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 6QXZ Olderado

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-08 
• Released Date: 2019-12-04 
Deposition Author(s): Dobrovolska, O., Madeleine, N., Teigen, K., Halskau, O., Bril'kov, M.
• This entry supersedes: 6HBO

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Funding Organization	Location	Grant Number
Research Council of Norway	Norway	226244/F50

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2020-12-16
  Changes: Database references, Derived calculations
• Version 1.2: 2020-12-23
  Changes: Database references