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Official Full Name
l(3)mbt-like 3 (Drosophila)
L3MBTL3; l(3)mbt-like 3 (Drosophila); lethal(3)malignant brain tumor-like protein 3; KIAA1798; Hl(3)mbt like protein; l(3)mbt like 3 (Drosophila); l(3)mbt like 3; L(3)mbt like 3 protein; Lethal(3)malignant brain tumor like 3 protein; MBT1; l(3)mbt-like protein 3; H-l(3)mbt-like protein 3; MBT-1; RP11-73O6.1; MBT1, MBT-1, RP11-73O6.1; si:ch211-45m15.2; CH211-45M15.3

Recent Progress

To understand L3MBTL3, it is important to understand "readers" of the histone code, which are proteins binding methylated lysines. These proteins are important components in the epigenetic regulation of gene expression. They also play a role in modulating other proteins with methyl-lysine such as p53 and Rb. Compaction of chromatin and a repressed transcriptional state have been identified with recognition of methyl-lysine marks by MBT domains.

UNC1215 was discovered by the researchers as a potential chemical probe for the methyl-lysine (Kme) reading function of L3MBTL3. Specifically speaking, UNC1215 binds L3MBTL3 with a K(d) of 120 nM and is greater than 50-fold more potent toward L3MBTL3 compared with other members of the MBT family. Its selectivity against more than 200 other reader domains examined was not compromised. The 2:2 polyvalent mode of interaction between UNC1215 and L3MBTL3 was revealed by X-ray crystallography. It is discovered that the cellular mobility of GFP-L3MBTL3 fusion proteins could be increased through UNC1215. Moreover, a new Kme-dependent interaction between L3MBTL3 and BCLAF1(a protein associated with DNA damage repair and apoptosis) was revealed through usage of UNC1215(Fig. 1).

Fig. 1. X-ray crystal structure of the UNC1215-3MBT complex. (LI James et al, 2013)

Antagonists of MBT domains could serve as probes to interrogate the functional role of "readers" of the histone code. first using a chemi-luminescent assay and ITC to determine the structure of histone peptide-MBT complexes and their interaction with MBT domains, investigators then designed small-molecule MBT antagonists based on findings. They discovered ligands that antagonize native histone peptide binding, what is more, they displayed 5-fold stronger binding affinity to L3MBTL1 than its preferred histone peptide. They also defined the first cocrystal structure of a small molecule bound to L3MBTL1.

After the discovery of UNC1215 as a potent and selective chemical probe for the L3MBTL3 methyllysine reader domain, researchers further described the development of structure activity relationships (SAR) of a second series of potent L3MBTL3 antagonists. These proteins developed from the structure of the chemical probe UNC1215. As mentioned before, these compounds are selective for L3MBTL3 against a panel of methyl-lysine reader proteins, in particular the related MBT family proteins, L3MBTL1 and MBTD1. Through studying the co-crystal structure of L3MBTL3 along with one of the most potent compounds, it is revealed by the investigator that the L3MBTL3 dimer rotates about the dimer interface to accommodate ligand binding.

Based on the above mentioned findings, researchers took the study further to describe in vitro analysis of L3MBTL3 dimerization through its MBT domains. Results indicated that this dimerization occurs within a cellular context, in particular when the small molecule ligands are absent. More intriguingly, both in vitro and in cells, mutations occurred at the first and second MBT domains abrogated L3MBTL3 dimerization. These findings taken together provide a more solid foundation for the hypothesis, that L3MBTL3 interacts with methylated histone tails as a dimer. These results also offer an explanation for the presence of repeated MBT domains within L3MBTL3.

DNMT1 is considered as a major DNA methyl-transferase that preserves epigenetic inheritance of DNA methylation patterns during DNA replication. Researchers have reported that the methylated lysine 142 of DNMT1 is de-methylated by LSD1. It has been revealed that L3MBTL3 binds the K142-methylated DNMT1 and recruits a novel CRL4DCAF5 ubiquitin ligase to degrade DNMT1. LSD1 and PHF20L1 both act primarily during S phase. This is thought to prevent DNMT1 degradation by L3MBTL3-CRL4DCAF5. Deletion of L3MBTL3/MBT-1 in mouse can cause accumulation of DNMT1 protein, increase in genomic DNA methylation, along with late embryonic lethality. Results indicated that L3MBTL3-CRL4DCAF5 can modulate the methylation-dependent E2F1 degradation.


  1. James, L. I., et al. "Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. " Nature Chemical Biology 9.3(2013):184-191.
  2. James, Lindsey I., et al. "Small-Molecule Ligands of Methyl-Lysine Binding Proteins: Optimization of Selectivity for L3MBTL3." Journal of Medicinal Chemistry 56.18(2013):2504-2511.
  3. Zhong, N, et al. "Crystal structure of the complex of the 3-MBT repeat domain of L3MBTL3 and UNC1215." Nature Chemical Biology 9.3(2013):184-191.
  4. Camerino, M. A., et al. "The structure-activity relationships of L3MBTL3 inhibitors: flexibility of the dimer interface. " Medchemcomm 4.11(2013):1501-1507.
  5. Baughman, B. M., et al. "Retraction of "The L3MBTL3 Methyl-Lysine Reader Domain Functions As a Dimer". " Acs Chemical Biology 11.3(2015):722.
  6. Leng, F., et al. "Methylated DNMT1 and E2F1 are targeted for proteolysis by L3MBTL3 and CRL4DCAF5 ubiquitin ligase. " Nature Communications 9.1(2018).