Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.75 kDa 
• Atom Count: 3713 
• Residue Count: 461 
• Unique protein chains: 2

5VA6

CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METHYLATED ON R26

• DOI: 10.2210/pdb5VA6/pdb

• Classification: TRANSFERASE/DNA BINDING PROTEIN
• Organism(s): Ricinus communis, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-24 Released: 2017-04-19 
• Deposition Author(s): Bergamin, E., Sarvan, S., Malette, J., Eram, M., Yeung, S., Mongeon, V., Joshi, M., Brunzelle, J.S., Michaels, S.D., Blais, A., Vedadi, M., Couture, J.-F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.297 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 

Literature

Molecular basis for the methylation specificity of ATXR5 for histone H3.

Bergamin, E., Sarvan, S., Malette, J., Eram, M.S., Yeung, S., Mongeon, V., Joshi, M., Brunzelle, J.S., Michaels, S.D., Blais, A., Vedadi, M., Couture, J.F.

(2017) Nucleic Acids Res 45: 6375-6387

• PubMed: 28383693 
• DOI: 10.1093/nar/gkx224
• Primary Citation of Related Structures:  
  5VA6, 5VAH, 5VAC, 5VAB, 5VBC


• PubMed Abstract: 
  

In plants, the histone H3.1 lysine 27 (H3K27) mono-methyltransferases ARABIDOPSIS TRITHORAX RELATED PROTEIN 5 and 6 (ATXR5/6) regulate heterochromatic DNA replication and genome stability. Our initial studies showed that ATXR5/6 discriminate between histone H3 variants and preferentially methylate K27 on H3.1. In this study, we report three regulatory mechanisms contributing to the specificity of ATXR5/6. First, we show that ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Second, we demonstrate that post-transcriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. Third, we show that ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Finally, we demonstrate that deletion or mutation of the PHD domain reduces the catalytic efficiency (kcat/Km of AdoMet) of ATXR5 up to 58-fold, highlighting the multifunctional nature of ATXR5 PHD domain. Overall, our results suggest that several molecular determinants regulate ATXR5/6 methyltransferase activity and epigenetic inheritance of H3.1 K27me1 mark in plants.

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Organizational Affiliation: 

Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable Histone-lysine N-methyltransferase ATXR5	A, B	229	Ricinus communis	Mutation(s): 0  Gene Names: ATXR5, RCOM_1460410 EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
Find proteins for B9RU15 (Ricinus communis) Explore B9RU15  Go to UniProtKB:  B9RU15

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C, D	18	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
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS:  P68431 GTEx:  ENSG00000197409ENSG00000197153ENSG00000278828ENSG00000275714ENSG00000273983ENSG00000274750ENSG00000275379ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	A, B	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NMM	C,D	L-PEPTIDE LINKING	C7 H16 N4 O2		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.297 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.31	α = 90
b = 86.81	β = 127.83
c = 74.04	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-24 
• Released Date: 2017-04-19 
Deposition Author(s): Bergamin, E., Sarvan, S., Malette, J., Eram, M., Yeung, S., Mongeon, V., Joshi, M., Brunzelle, J.S., Michaels, S.D., Blais, A., Vedadi, M., Couture, J.-F.

Revision History 

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Database references