Limits...
Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding.

Xu S, Wu J, Sun B, Zhong C, Ding J - Nucleic Acids Res. (2011)

Bottom Line: Our data demonstrate the important roles of both TPR and post-SET domains in the histone lysine methyltransferase (HKMT) activity of Smyd3, and show that the hydroxyl group of Tyr239 is critical for the enzymatic activity.The characteristic MYND domain is located nearby to the substrate binding pocket and exhibits a largely positively charged surface.Further biochemical assays show that DNA binding of Smyd3 can stimulate its HKMT activity and the process may be mediated via the MYND domain through direct DNA binding.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

ABSTRACT
The SET- and MYND-domain containing (Smyd) proteins constitute a special subfamily of the SET-containing lysine methyltransferases. Here we present the structure of full-length human Smyd3 in complex with S-adenosyl-L-homocysteine at 2.8 Å resolution. Smyd3 affords the first example that other region(s) besides the SET domain and its flanking regions participate in the formation of the active site. Structural analysis shows that the previously uncharacterized C-terminal domain of Smyd3 contains a tetratrico-peptide repeat (TPR) domain which together with the SET and post-SET domains forms a deep, narrow substrate binding pocket. Our data demonstrate the important roles of both TPR and post-SET domains in the histone lysine methyltransferase (HKMT) activity of Smyd3, and show that the hydroxyl group of Tyr239 is critical for the enzymatic activity. The characteristic MYND domain is located nearby to the substrate binding pocket and exhibits a largely positively charged surface. Further biochemical assays show that DNA binding of Smyd3 can stimulate its HKMT activity and the process may be mediated via the MYND domain through direct DNA binding.

Show MeSH

Related in: MedlinePlus

Structure of the lysine channel. (A) Comparison of the lysine channels of Smyd3 and SET7/9 (PDB code 1O9S). Superposition of the active sites of Smyd3 and SET7/9 reveals a narrow channel in Smyd3 which is similar to the lysine channel of SET7/9. The key residues forming the lysine channel are shown with ball-and-stick models. The color coding is the same as in Figure 1A. (B) Superposition of the active sites of Smyd3 and pea Rubisco LSMT (PDB code 1P0Y). The residues are shown with ball-and-stick models, and for clarity, the side chains of Asn181 of Smyd3 and Arg222 of Rubisco LSMT are hidden. The color coding for Smyd3 is the same as in Figure 1A, and Rubisco LSMT is colored in light gray. (C) HKMT activity of the wild-type Smyd3 and the mutants carrying point mutations at the lysine channel.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3105404&req=5

Figure 4: Structure of the lysine channel. (A) Comparison of the lysine channels of Smyd3 and SET7/9 (PDB code 1O9S). Superposition of the active sites of Smyd3 and SET7/9 reveals a narrow channel in Smyd3 which is similar to the lysine channel of SET7/9. The key residues forming the lysine channel are shown with ball-and-stick models. The color coding is the same as in Figure 1A. (B) Superposition of the active sites of Smyd3 and pea Rubisco LSMT (PDB code 1P0Y). The residues are shown with ball-and-stick models, and for clarity, the side chains of Asn181 of Smyd3 and Arg222 of Rubisco LSMT are hidden. The color coding for Smyd3 is the same as in Figure 1A, and Rubisco LSMT is colored in light gray. (C) HKMT activity of the wild-type Smyd3 and the mutants carrying point mutations at the lysine channel.

Mentions: Besides the residues that interact directly with AdoHcy, residue Asp262 of the post-SET domain might contribute to the cofactor binding as it forms a salt bridge with Arg14 to stabilize the positions of Arg14 and the β1–β2 loop where Arg14 is located, and perhaps interacts with the N1 and N6 atoms of the adenine moiety via a water molecule not seen at this resolution of diffraction data (Figure 3B). In addition, similar to its equivalent (Tyr335) in SET7/9 (25), Tyr239 may also make van der Waals interactions with the O4′ atom of the ribose ring (Figure 4A).Figure 4.


Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding.

Xu S, Wu J, Sun B, Zhong C, Ding J - Nucleic Acids Res. (2011)

Structure of the lysine channel. (A) Comparison of the lysine channels of Smyd3 and SET7/9 (PDB code 1O9S). Superposition of the active sites of Smyd3 and SET7/9 reveals a narrow channel in Smyd3 which is similar to the lysine channel of SET7/9. The key residues forming the lysine channel are shown with ball-and-stick models. The color coding is the same as in Figure 1A. (B) Superposition of the active sites of Smyd3 and pea Rubisco LSMT (PDB code 1P0Y). The residues are shown with ball-and-stick models, and for clarity, the side chains of Asn181 of Smyd3 and Arg222 of Rubisco LSMT are hidden. The color coding for Smyd3 is the same as in Figure 1A, and Rubisco LSMT is colored in light gray. (C) HKMT activity of the wild-type Smyd3 and the mutants carrying point mutations at the lysine channel.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105404&req=5

Figure 4: Structure of the lysine channel. (A) Comparison of the lysine channels of Smyd3 and SET7/9 (PDB code 1O9S). Superposition of the active sites of Smyd3 and SET7/9 reveals a narrow channel in Smyd3 which is similar to the lysine channel of SET7/9. The key residues forming the lysine channel are shown with ball-and-stick models. The color coding is the same as in Figure 1A. (B) Superposition of the active sites of Smyd3 and pea Rubisco LSMT (PDB code 1P0Y). The residues are shown with ball-and-stick models, and for clarity, the side chains of Asn181 of Smyd3 and Arg222 of Rubisco LSMT are hidden. The color coding for Smyd3 is the same as in Figure 1A, and Rubisco LSMT is colored in light gray. (C) HKMT activity of the wild-type Smyd3 and the mutants carrying point mutations at the lysine channel.
Mentions: Besides the residues that interact directly with AdoHcy, residue Asp262 of the post-SET domain might contribute to the cofactor binding as it forms a salt bridge with Arg14 to stabilize the positions of Arg14 and the β1–β2 loop where Arg14 is located, and perhaps interacts with the N1 and N6 atoms of the adenine moiety via a water molecule not seen at this resolution of diffraction data (Figure 3B). In addition, similar to its equivalent (Tyr335) in SET7/9 (25), Tyr239 may also make van der Waals interactions with the O4′ atom of the ribose ring (Figure 4A).Figure 4.

Bottom Line: Our data demonstrate the important roles of both TPR and post-SET domains in the histone lysine methyltransferase (HKMT) activity of Smyd3, and show that the hydroxyl group of Tyr239 is critical for the enzymatic activity.The characteristic MYND domain is located nearby to the substrate binding pocket and exhibits a largely positively charged surface.Further biochemical assays show that DNA binding of Smyd3 can stimulate its HKMT activity and the process may be mediated via the MYND domain through direct DNA binding.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

ABSTRACT
The SET- and MYND-domain containing (Smyd) proteins constitute a special subfamily of the SET-containing lysine methyltransferases. Here we present the structure of full-length human Smyd3 in complex with S-adenosyl-L-homocysteine at 2.8 Å resolution. Smyd3 affords the first example that other region(s) besides the SET domain and its flanking regions participate in the formation of the active site. Structural analysis shows that the previously uncharacterized C-terminal domain of Smyd3 contains a tetratrico-peptide repeat (TPR) domain which together with the SET and post-SET domains forms a deep, narrow substrate binding pocket. Our data demonstrate the important roles of both TPR and post-SET domains in the histone lysine methyltransferase (HKMT) activity of Smyd3, and show that the hydroxyl group of Tyr239 is critical for the enzymatic activity. The characteristic MYND domain is located nearby to the substrate binding pocket and exhibits a largely positively charged surface. Further biochemical assays show that DNA binding of Smyd3 can stimulate its HKMT activity and the process may be mediated via the MYND domain through direct DNA binding.

Show MeSH
Related in: MedlinePlus