ISDA

Deposition Date 2021-03-20

Release Date 2021-06-30

Last Version Date 2023-11-29

Entry Detail

PDB ID:

7EF2

Keywords:

GENE REGULATION

Title:

Crystal structure of maize SHH2 SAWADEE domain in complex with an H3K9me3 peptide

Biological Source:

Source Organism:

Zea mays (Taxon ID: 4577)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.24

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

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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:158
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
M3L	C	LYS	modified residue

Ligand Molecules

Primary Citation

Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2.

Wang, Y, Zhou, X, Luo, J, Lv, S, Liu, R, Du, X, Jia, B, Yuan, F, Zhang, H, Du, J.Show

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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Disease

Primary Citation of related structures