Site-specific DNA-methyltransferase (cytosine-N4-specific)
This methylase recognizes the double-stranded sequence CAGCTG, causes specific methylation on C-4 on both strands, and protects the DNA from cleavage by the PvuII endonuclease.
Reference Protein and Structure
- Sequence
-
P11409
(2.1.1.113)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Proteus hauseri (Bacteria)
- PDB
-
1boo
- PVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC)
(2.8 Å)
- Catalytic CATH Domains
-
3.40.50.150
(see all for 1boo)
Enzyme Reaction (EC:2.1.1.113)
+
→
+
Alternative enzyme names: DNA(cytosine-N(4))methyltransferase, M4C-forming MTase, Modification methylase, Restriction-modification system, N(4)-cytosine-specific DNA methylase, S-adenosyl-L-methionine:DNA-cytosine 4-N-methyltransferase,
Enzyme Mechanism
Introduction
Asp96 abstracts the proton of the cytsosine base via a charge relay with Ser53. This step occurs first, followed by the nucleophilic attack of the activated amine on the methyl group of SAM.
Catalytic Residues Roles
| UniProt | PDB* (1boo) | ||
| Asp96 | Asp96(83)A | Forms a hydrogen bond with the Ser53 hydroxyl group, facilitating proton transfer from the cytosine amino group through the Ser and eventually to the Asp. | proton shuttle (general acid/base) |
| Ser53 | Ser53(40)A | Forms part of the charge relay system that is responsible for the abstraction of the proton from the cytosine group. | proton shuttle (general acid/base) |
| Pro54 (main-C) | Pro54(41)A (main-C) | Activates the cytosine group to proton abstraction. | modifies pKa, electrostatic stabiliser |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
References
- Gong W et al. (1997), Nucleic Acids Res, 25, 2702-2715. Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. DOI:10.1093/nar/25.14.2702. PMID:9207015.
- Aranda J et al. (2012), Org Biomol Chem, 10, 5395-5400. Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight. DOI:10.1039/c2ob07021a. PMID:22699309.
- Aranda J et al. (2010), J Phys Chem B, 114, 8467-8473. Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the BacteriumProteus vulgaris. DOI:10.1021/jp911036w. PMID:20524651.
- Jeltsch A (2001), Biol Chem, 382, 707-710. The Cytosine N4-Methyltransferase M.PvuII Also Modifies Adenine Residues. DOI:10.1515/bc.2001.084. PMID:11405235.
- Rice MR et al. (1999), Nucleic Acids Res, 27, 1032-1038. Substrate recognition by the Pvu II endonuclease: binding and cleavage of CAG5mCTG sites. PMID:9927736.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Ser53(40)A | proton shuttle (general acid/base) |
| Asp96(83)A | proton shuttle (general acid/base) |
| Pro54(41)A (main-C) | electrostatic stabiliser, modifies pKa |