7EF1 image
Deposition Date 2021-03-20
Release Date 2021-06-30
Last Version Date 2023-11-29
Entry Detail
PDB ID:
7EF1
Keywords:
GENE REGULATION
Title:
crystal structure of maize SHH2 SAWADEE domain in complex with and H3K9me1 peptide
Biological Source:
Source Organism:
Zea mays (Taxon ID: 4577)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.90 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
7EF1 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:HB transcription factor
Gene (Uniprot):100279552
Mutagens:R235G
Chain IDs:A, B
Chain Length:157
Number of Molecules:2
Biological Source:Zea mays
UniProt ID:B7ZYP9 Pfam ID:PF16719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Gene (Uniprot):H3C2, H3C3, H3C4
Chain IDs:C (auth: P), D (auth: Q)
Chain Length:10
Number of Molecules:2
Biological Source:Zea mays
UniProt ID:P69246
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MLZ C LYS modified residue
Ligand Molecules
ZN
Primary Citation
Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2.
J Integr Plant Biol 63 1091 1096 (2021)
PMID: 33913587 DOI: 10.1111/jipb.13103

Abstact

RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation pathway, which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2 (SHH2) is an H3K9me1 reader. Our structural studies reveal that H3K9me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di- and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a mono-methyllysine recognition mechanism which potentially links RdDM to H3K9me1 in maize.

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Primary Citation of related structures
7EF1