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Structural studies of a four-MBT repeat protein MBTD1.

Eryilmaz J, Pan P, Amaya MF, Allali-Hassani A, Dong A, Adams-Cioaba MA, Mackenzie F, Vedadi M, Min J - PLoS ONE (2009)

Bottom Line: All known MBT-peptide complex structures characterized to date do not exhibit strong histone peptide sequence selectivity, and use a "cavity insertion recognition mode" to recognize the methylated lysine with the deeply buried methyl-lysine forming extensive interactions with the protein while the peptide residues flanking methyl-lysine forming very few contacts [1].Please note that a web plugin is required to access this enhanced functionality.Instructions for the installation and use of the web plugin are available in Text S1.

View Article: PubMed Central - PubMed

Affiliation: Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

ABSTRACT

Background: The Polycomb group (PcG) of proteins is a family of important developmental regulators. The respective members function as large protein complexes involved in establishment and maintenance of transcriptional repression of developmental control genes. MBTD1, Malignant Brain Tumor domain-containing protein 1, is one such PcG protein. MBTD1 contains four MBT repeats.

Methodology/principal findings: We have determined the crystal structure of MBTD1 (residues 130-566aa covering the 4 MBT repeats) at 2.5 A resolution by X-ray crystallography. The crystal structure of MBTD1 reveals its similarity to another four-MBT-repeat protein L3MBTL2, which binds lower methylated lysine histones. Fluorescence polarization experiments confirmed that MBTD1 preferentially binds mono- and di-methyllysine histone peptides, like L3MBTL1 and L3MBTL2. All known MBT-peptide complex structures characterized to date do not exhibit strong histone peptide sequence selectivity, and use a "cavity insertion recognition mode" to recognize the methylated lysine with the deeply buried methyl-lysine forming extensive interactions with the protein while the peptide residues flanking methyl-lysine forming very few contacts [1]. Nevertheless, our mutagenesis data based on L3MBTL1 suggested that the histone peptides could not bind to MBT repeats in any orientation.

Conclusions: The four MBT repeats in MBTD1 exhibits an asymmetric rhomboid architecture. Like other MBT repeat proteins characterized so far, MBTD1 binds mono- or dimethylated lysine histones through one of its four MBT repeats utilizing a semi-aromatic cage.

Enhanced version: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

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MBTD1 lysine-binding pocket.The MBTD1 binding pocket is formed by aromatic residues Phe526, Trp529, Tyr533, negatively charged Asp502 and Leu508. The binding pocket is occupied by Arg325 from a symmetry related molecule.
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pone-0007274-g004: MBTD1 lysine-binding pocket.The MBTD1 binding pocket is formed by aromatic residues Phe526, Trp529, Tyr533, negatively charged Asp502 and Leu508. The binding pocket is occupied by Arg325 from a symmetry related molecule.

Mentions: Although the four MBT repeats of MBTD1 have similar three-dimensional structures and high sequence identity, only the fourth MBT repeat (MBT4) contains the semi-aromatic cage, which is formed by the loops between the first and second strands and the third and fourth strands of the β- barrel core domain and constitutes the binding site for methyllysine residue, analogous to L3MBTL2. The binding pocket of the MBTD1-MBT4 is shown in Figure 4, where an open cage in MBTD1 is formed by aromatic residues Phe526, Trp529, Tyr533, negatively charged Asp502, and Leu508. Three highly conserved aromatic residues Phe526, Trp529 and Tyr533 form the base and the walls of the hydrophobic pocket. Interestingly, Arg325 from a symmetry related molecule is inserted into the binding pocket, mimicking the methyl-lysine binding in L3MBTL2 [1]. The arginine residue 325 is stabilized by a salt bridge with the pocket residue Asp502, and cation-π and van der Waals and interactions with the aromatic cage residues.


Structural studies of a four-MBT repeat protein MBTD1.

Eryilmaz J, Pan P, Amaya MF, Allali-Hassani A, Dong A, Adams-Cioaba MA, Mackenzie F, Vedadi M, Min J - PLoS ONE (2009)

MBTD1 lysine-binding pocket.The MBTD1 binding pocket is formed by aromatic residues Phe526, Trp529, Tyr533, negatively charged Asp502 and Leu508. The binding pocket is occupied by Arg325 from a symmetry related molecule.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2747274&req=5

pone-0007274-g004: MBTD1 lysine-binding pocket.The MBTD1 binding pocket is formed by aromatic residues Phe526, Trp529, Tyr533, negatively charged Asp502 and Leu508. The binding pocket is occupied by Arg325 from a symmetry related molecule.
Mentions: Although the four MBT repeats of MBTD1 have similar three-dimensional structures and high sequence identity, only the fourth MBT repeat (MBT4) contains the semi-aromatic cage, which is formed by the loops between the first and second strands and the third and fourth strands of the β- barrel core domain and constitutes the binding site for methyllysine residue, analogous to L3MBTL2. The binding pocket of the MBTD1-MBT4 is shown in Figure 4, where an open cage in MBTD1 is formed by aromatic residues Phe526, Trp529, Tyr533, negatively charged Asp502, and Leu508. Three highly conserved aromatic residues Phe526, Trp529 and Tyr533 form the base and the walls of the hydrophobic pocket. Interestingly, Arg325 from a symmetry related molecule is inserted into the binding pocket, mimicking the methyl-lysine binding in L3MBTL2 [1]. The arginine residue 325 is stabilized by a salt bridge with the pocket residue Asp502, and cation-π and van der Waals and interactions with the aromatic cage residues.

Bottom Line: All known MBT-peptide complex structures characterized to date do not exhibit strong histone peptide sequence selectivity, and use a "cavity insertion recognition mode" to recognize the methylated lysine with the deeply buried methyl-lysine forming extensive interactions with the protein while the peptide residues flanking methyl-lysine forming very few contacts [1].Please note that a web plugin is required to access this enhanced functionality.Instructions for the installation and use of the web plugin are available in Text S1.

View Article: PubMed Central - PubMed

Affiliation: Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

ABSTRACT

Background: The Polycomb group (PcG) of proteins is a family of important developmental regulators. The respective members function as large protein complexes involved in establishment and maintenance of transcriptional repression of developmental control genes. MBTD1, Malignant Brain Tumor domain-containing protein 1, is one such PcG protein. MBTD1 contains four MBT repeats.

Methodology/principal findings: We have determined the crystal structure of MBTD1 (residues 130-566aa covering the 4 MBT repeats) at 2.5 A resolution by X-ray crystallography. The crystal structure of MBTD1 reveals its similarity to another four-MBT-repeat protein L3MBTL2, which binds lower methylated lysine histones. Fluorescence polarization experiments confirmed that MBTD1 preferentially binds mono- and di-methyllysine histone peptides, like L3MBTL1 and L3MBTL2. All known MBT-peptide complex structures characterized to date do not exhibit strong histone peptide sequence selectivity, and use a "cavity insertion recognition mode" to recognize the methylated lysine with the deeply buried methyl-lysine forming extensive interactions with the protein while the peptide residues flanking methyl-lysine forming very few contacts [1]. Nevertheless, our mutagenesis data based on L3MBTL1 suggested that the histone peptides could not bind to MBT repeats in any orientation.

Conclusions: The four MBT repeats in MBTD1 exhibits an asymmetric rhomboid architecture. Like other MBT repeat proteins characterized so far, MBTD1 binds mono- or dimethylated lysine histones through one of its four MBT repeats utilizing a semi-aromatic cage.

Enhanced version: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Show MeSH
Related in: MedlinePlus