Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>.
The block schematics were created with DSSR and
rendered using PyMOL.
- PDB-id
- 5VMW
- Class
- transcription-DNA
- Method
- X-ray (2.4 Å)
- Summary
- Kaiso (zbtb33) zinc finger DNA binding domain in complex with a double cpg-methylated DNA resembling the specific kaiso binding sequence (kbs)
List of 4 5mC-amino acid contacts:
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D.5CM8: stacking-with-A.ARG511 is-WC-paired is-in-duplex [+]:CcG/cGG
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D.5CM10: other-contacts is-WC-paired is-in-duplex [+]:GcG/cGc
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E.5CM26: stacking-with-A.ARG511 is-WC-paired is-in-duplex [-]:cGA/TcG
-
E.5CM28: other-contacts is-WC-paired is-in-duplex [-]:cGc/GcG
direct SNAP output · DNAproDB 2.0
- Reference
- Nikolova, E.N., Stanfield, R.L., Dyson, H.J., Wright, P.E.: (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120.
- Abstract
- Many eukaryotic transcription factors recognize the epigenetic marker 5-methylcytosine (mC) at CpG sites in DNA. Despite their structural diversity, methyl-CpG-binding proteins (MBPs) share a common mode of recognition of mC methyl groups that involves hydrophobic pockets and weak hydrogen bonds of the CH···O type. The zinc finger protein Kaiso possesses a remarkably high specificity for methylated over unmethylated CpG sites. A key contribution to this specificity is provided by glutamate 535 (E535), which is optimally positioned to form multiple interactions with mCpG, including direct CH···O hydrogen bonds. To examine the role of E535 and CH···O hydrogen bonding in the preferential recognition of mCpG sites, we determined the structures of wild type Kaiso (WT) and E535 mutants and characterized their interactions with methylated DNA by nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography, and in vitro protein-DNA binding assays. Our data show that Kaiso favors an mCpG over a CpG site by 2 orders of magnitude in affinity and that an important component of this effect is the presence of hydrophobic and CH···O contacts involving E535. Moreover, we present the first direct evidence for formation of a CH···O hydrogen bond between an MBP and 5-methylcytosine by using experimental (NMR) and quantum mechanical chemical shift analysis of the mC methyl protons. Together, our findings uncover a critical function of methyl-specific interactions, including CH···O hydrogen bonds, that optimize the specificity and affinity of MBPs for methylated DNA and contribute to the precise control of gene expression.
- The 5-methylcytosine group (PDB ligand '5CM') is shown in space-filling model,
with the methyl-carbon atom in black.
- Watson-Crick base pairs are represented as long rectangular blocks with the
minor-groove edge in black. Color code: A-T red, C-G yellow, G-C green, T-A blue.
- Protein is shown as cartoon in purple. DNA backbones are shown ribbon, colored code
by chain identifier.
- The block schematics were created with 3DNA-DSSR,
and images were rendered using PyMOL.
- Download the PyMOL session file corresponding to the top-left
image in the following panel.
- The contacts include paired nucleotides (mostly a G in G-C pairing), and
amino-acids within a 4.5-A distance cutoff to the base atoms of 5mC.
- The structure is oriented in the 'standard' base reference frame of 5mC, allowing for easy comparison
and direct superimposition between entries.
- The black sphere (•) denotes the 5-methyl carbon atom in 5mC.
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No. 1 D.5CM8: download PDB file
for the 5mC entry
stacking-with-A.ARG511 is-WC-paired is-in-duplex [+]:CcG/cGG
|
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No. 2 D.5CM10: download PDB file
for the 5mC entry
other-contacts is-WC-paired is-in-duplex [+]:GcG/cGc
|
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No. 3 E.5CM26: download PDB file
for the 5mC entry
stacking-with-A.ARG511 is-WC-paired is-in-duplex [-]:cGA/TcG
|
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No. 4 E.5CM28: download PDB file
for the 5mC entry
other-contacts is-WC-paired is-in-duplex [-]:cGc/GcG
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