Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase
- PMID: 10671528
- DOI: 10.1074/jbc.275.7.4912
Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase
Abstract
Pre-steady state partitioning analysis of the HhaI DNA methyltransferase directly demonstrates the catalytic competence of the enzyme.DNA complex and the lack of catalytic competence of the enzyme.S-adenosyl-L-methionine (AdoMet) complex. The enzyme.AdoMet complex does form, albeit with a 50-fold decrease in affinity compared with the ternary enzyme.AdoMet.DNA complex. These findings reconcile the distinct binding orientations previously observed within the binary enzyme.AdoMet and ternary enzyme. S-adenosyl-L-homocysteine.DNA crystal structures. The affinity of the enzyme for DNA is increased 900-fold in the presence of its cofactor, and the preference for hemimethylated DNA is increased to 12-fold over unmethylated DNA. We suggest that this preference is partially due to the energetic cost of retaining a cavity in place of the 5-methyl moiety in the ternary complex with the unmethylated DNA, as revealed by the corresponding crystal structures. The hemi- and unmethylated substrates alter the fates and lifetimes of discrete enzyme.substrate intermediates during the catalytic cycle. Hemimethylated substrates partition toward product formation versus dissociation significantly more than unmethylated substrates. The mammalian DNA cytosine-C-5 methyltransferase Dnmt1 shows an even more pronounced partitioning toward product formation.
Similar articles
-
The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of Hhai methyltransferase.J Biol Chem. 2001 Jun 15;276(24):20924-34. doi: 10.1074/jbc.M101429200. Epub 2001 Mar 29. J Biol Chem. 2001. PMID: 11283006
-
S-adenosyl-L-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine methylation.Biochemistry. 2007 Jul 31;46(30):8766-75. doi: 10.1021/bi7005948. Epub 2007 Jul 7. Biochemistry. 2007. PMID: 17616174
-
Water-assisted dual mode cofactor recognition by HhaI DNA methyltransferase.J Biol Chem. 2002 Feb 8;277(6):4042-9. doi: 10.1074/jbc.M109237200. Epub 2001 Nov 29. J Biol Chem. 2002. PMID: 11729191
-
Structure, function, and mechanism of HhaI DNA methyltransferases.Crit Rev Biochem Mol Biol. 2002;37(3):167-97. doi: 10.1080/10409230290771492. Crit Rev Biochem Mol Biol. 2002. PMID: 12139442 Review.
-
Structure and function of DNA methyltransferases.Annu Rev Biophys Biomol Struct. 1995;24:293-318. doi: 10.1146/annurev.bb.24.060195.001453. Annu Rev Biophys Biomol Struct. 1995. PMID: 7663118 Review.
Cited by
-
Control of catalytic cycle by a pair of analogous tRNA modification enzymes.J Mol Biol. 2010 Jul 9;400(2):204-17. doi: 10.1016/j.jmb.2010.05.003. Epub 2010 May 7. J Mol Biol. 2010. PMID: 20452364 Free PMC article.
-
A dual role for substrate S-adenosyl-L-methionine in the methylation reaction with bacteriophage T4 Dam DNA-[N6-adenine]-methyltransferase.Nucleic Acids Res. 2001 Jun 1;29(11):2361-9. doi: 10.1093/nar/29.11.2361. Nucleic Acids Res. 2001. PMID: 11376154 Free PMC article.
-
Transient kinetics of the reaction catalysed by magnesium protoporphyrin IX methyltransferase.Biochem J. 2004 Sep 15;382(Pt 3):1009-13. doi: 10.1042/BJ20040661. Biochem J. 2004. PMID: 15239672 Free PMC article.
-
DNA cytosine methylation: structural and thermodynamic characterization of the epigenetic marking mechanism.Biochemistry. 2013 Apr 23;52(16):2828-38. doi: 10.1021/bi400163k. Epub 2013 Apr 12. Biochemistry. 2013. PMID: 23528166 Free PMC article.
-
Cavitation as a mechanism of substrate discrimination by adenylosuccinate synthetases.Biochemistry. 2006 Sep 26;45(38):11703-11. doi: 10.1021/bi0607498. Biochemistry. 2006. PMID: 16981730 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Molecular Biology Databases
