Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger.

Human L3MBTL1, which contains three malignant brain tumor (MBT) repeats, binds monomethylated and dimethylated lysines, but not trimethylated lysines, in several histone sequence contexts. In crystal structures of L3MBTL1 complexes, the monomethyl- and dimethyllysines insert into a narrow and deep cavity of aromatic residue-lined pocket 2, while a proline ring inserts into shallower pocket 1. We have also engineered a single Y to E substitution within the aromatic cage of the BPTF PHD finger, resulting in a reversal of binding preference from trimethyl- to dimethyllysine in an H3K4 sequence context. In both the "cavity insertion" (L3MBTL1) and "surface groove" (PHD finger) modes of methyllysine recognition, a carboxylate group both hydrogen bonds and ion pairs to the methylammonium proton. Our structural and binding studies of these two modules provide insights into the molecular principles governing the decoding of lysine methylation states, thereby highlighting a methylation state-specific layer of histone mark readout impacting on epigenetic regulation.

[1]  Scott A. Busby,et al.  Modifications of human histone H3 variants during mitosis. , 2005, Biochemistry.

[2]  J. Rice,et al.  Human SFMBT is a transcriptional repressor protein that selectively binds the N‐terminal tail of histone H3 , 2007, FEBS letters.

[3]  V. Verkhusha,et al.  Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2 , 2006, Nature.

[4]  John D Aitchison,et al.  Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. , 2006, Molecular cell.

[5]  P. Boccuni,et al.  The Human L(3)MBT Polycomb Group Protein Is a Transcriptional Repressor and Interacts Physically and Functionally with TEL (ETV6)* , 2003, The Journal of Biological Chemistry.

[6]  Alexey G. Murzin,et al.  Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9 , 2002, Nature.

[7]  D. A. Dougherty,et al.  The Cationminus signpi Interaction. , 1997, Chemical reviews.

[8]  Geoff Kelly,et al.  Structure and catalytic mechanism of the human histone methyltransferase SET7/9 , 2003, Nature.

[9]  Ian M. Fingerman,et al.  Proteome-wide Analysis in Saccharomyces cerevisiae Identifies Several PHD Fingers as Novel Direct and Selective Binding Modules of Histone H3 Methylated at Either Lysine 4 or Lysine 36* , 2007, Journal of Biological Chemistry.

[10]  Youngchang Kim,et al.  Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. , 2003, Genes & development.

[11]  Sebastian Maurer-Stroh,et al.  The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. , 2003, Trends in biochemical sciences.

[12]  Cyrus Martin,et al.  The diverse functions of histone lysine methylation , 2005, Nature Reviews Molecular Cell Biology.

[13]  Yi Zhang,et al.  Regulation of histone methylation by demethylimination and demethylation , 2007, Nature Reviews Molecular Cell Biology.

[14]  Yi Zhang,et al.  Tudor, MBT and chromo domains gauge the degree of lysine methylation , 2006, EMBO reports.

[15]  D. Reinberg,et al.  L3MBTL1, a Histone-Methylation-Dependent Chromatin Lock , 2007, Cell.

[16]  J. Min,et al.  Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. , 2003, Genes & development.

[17]  Malgorzata Schelder,et al.  DNA-binding and selective methyl-lysine-binding activities A Polycomb group protein complex with sequence-specific Material Supplemental , 2006 .

[18]  S. Khorasanizadeh,et al.  Double chromodomains cooperate to recognize the methylated histone H3 tail , 2005, Nature.

[19]  Georges Mer,et al.  Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair , 2006, Cell.

[20]  Thomas A. Milne,et al.  A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling , 2006, Nature.

[21]  J. Simon,et al.  Expression and properties of wild-type and mutant forms of the Drosophila sex comb on midleg (SCM) repressor protein. , 1998, Genetics.

[22]  Yi Zhang,et al.  Recognition of Histone H3 Lysine-4 Methylation by the Double Tudor Domain of JMJD2A , 2006, Science.

[23]  A. Murzin,et al.  Crystal Structure of the Malignant Brain Tumor (MBT) Repeats in Sex Comb on Midleg-like 2 (SCML2)* , 2003, Journal of Biological Chemistry.

[24]  Thomas A. Milne,et al.  Physical Association and Coordinate Function of the H3 K4 Methyltransferase MLL1 and the H4 K16 Acetyltransferase MOF , 2005, Cell.

[25]  D. Patel,et al.  Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets. , 2003, Structure.

[26]  S. Jacobs,et al.  Structure of HP1 Chromodomain Bound to a Lysine 9-Methylated Histone H3 Tail , 2002, Science.

[27]  Yang Shi,et al.  Dynamic regulation of histone lysine methylation by demethylases. , 2007, Molecular cell.

[28]  C. Allis,et al.  Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. , 2007, Molecular cell.

[29]  D. Patel,et al.  Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF , 2006, Nature.

[30]  H. Saya,et al.  A human homolog of Drosophila lethal(3)malignant brain tumor (l(3)mbt) protein associates with condensed mitotic chromosomes , 1999, Oncogene.