DB code: S00262

RLCP classification 3.747.6310.11 : Transfer
CATH domain 3.40.50.150 : Rossmann fold Catalytic domain
E.C. 2.1.1.113
CSA 1boo
M-CSA 1boo
MACiE

CATH domain Related DB codes (homologues)
3.40.50.150 : Rossmann fold S00637 S00639 S00261 S00291 S00412 D00075 D00076 D00079 D00080 D00082 D00083 D00823

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P11409 Modification methylase PvuII
M.PvuII
EC 2.1.1.113
N-4 cytosine-specific methyltransferase PvuII
PF01555 (N6_N4_Mtase)
[Graphical View]

KEGG enzyme name
site-specific DNA-methyltransferase (cytosine-N4-specific)
modification methylase
restriction-modification system
DNA[cytosine-N4]methyltransferase
m4C-forming MTase
S-adenosyl-L-methionine:DNA-cytosine 4-N-methyltransferase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P11409 MTP2_PROVU S-adenosyl-L-methionine + DNA cytosine = S- adenosyl-L-homocysteine + DNA N(4)-methylcytosine.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00019 C00856 C00021 C03110
E.C.
Compound S-Adenosyl-L-methionine DNA cytosine S-Adenosyl-L-homocysteine DNA N4-methylcytosine
Type amino acids,amine group,nucleoside,sulfonium ion amine group,nucleic acids amino acids,amine group,nucleoside,sulfide group amine group,nucleic acids
ChEBI 67040
16680
57856
PubChem 34755
25246222
439155
1booA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:SAH Unbound

Reference for Active-site residues
resource references E.C.
literature [2]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1booA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 53;ASP 96

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Figure 6a, p.2711 1

References
[1]
Resource
Comments
Medline ID
PubMed ID 2690017
Journal Nucleic Acids Res
Year 1989
Volume 17
Pages 10403-25
Authors Kaszubska W, Aiken C, O'Connor CD, Gumport RI
Title Purification, cloning and sequence analysis of RsrI DNA methyltransferase: lack of homology between two enzymes, RsrI and EcoRI, that methylate the same nucleotide in identical recognition sequences.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID 97351137
PubMed ID 9207015
Journal Nucleic Acids Res
Year 1997
Volume 25
Pages 2702-15
Authors Gong W, O'Gara M, Blumenthal RM, Cheng X
Title Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
Related PDB 1boo
Related UniProtKB P11409
[3]
Resource
Comments
Medline ID
PubMed ID 9288926
Journal Eur J Biochem
Year 1997
Volume 247
Pages 1009-18
Authors O'Gara M, Adams GM, Gong W, Kobayashi R, Blumenthal RM, Cheng X
Title Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9204874
Journal Biochemistry
Year 1997
Volume 36
Pages 8284-92
Authors Adams GM, Blumenthal RM
Title The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10651285
Journal Proteins
Year 1999
Volume 37
Pages 717-28
Authors Radlinska M, Bujnicki JM, Piekarowicz A
Title Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9927736
Journal Nucleic Acids Res
Year 1999
Volume 27
Pages 1032-8
Authors Rice MR, Koons MD, Blumenthal RM
Title Substrate recognition by the Pvu II endonuclease: binding and cleavage of CAG5mCTG sites.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10329711
Journal J Biol Chem
Year 1999
Volume 274
Pages 15066-72
Authors Holz B, Dank N, Eickhoff JE, Lipps G, Krauss G, Weinhold E
Title Identification of the binding site for the extrahelical target base in N6-adenine DNA methyltransferases by photo-cross-linking with duplex oligodeoxyribonucleotides containing 5-iodouracil at the target position.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9931007
Journal Biochemistry
Year 1999
Volume 38
Pages 1426-34
Authors Pues H, Bleimling N, Holz B, Wolcke J, Weinhold E
Title Functional roles of the conserved aromatic amino acid residues at position 108 (motif IV) and position 196 (motif VIII) in base flipping and catalysis by the N6-adenine DNA methyltransferase from Thermus aquaticus.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11024175
Journal Nucleic Acids Res
Year 2000
Volume 28
Pages 3950-61
Authors Scavetta RD, Thomas CB, Walsh MA, Szegedi S, Joachimiak A, Gumport RI, Churchill ME
Title Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 11405235
Journal Biol Chem
Year 2001
Volume 382
Pages 707-10
Authors Jeltsch A
Title The cytosine N4-methyltransferase M.PvuII also modifies adenine residues.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 12507474
Journal J Mol Biol
Year 2003
Volume 325
Pages 711-20
Authors Lindstrom WM Jr, Malygin EG, Ovechkina LG, Zinoviev VV, Reich NO
Title Functional analysis of BamHI DNA cytosine-N4 methyltransferase.
Related PDB
Related UniProtKB

Comments
According to the literature [2], the reaction proceeds as follows:
(1) Asp96 may act as a general base to activate the N4 amino group, the cytosine acceptor group through the Ser53 (as a proton shuttle). (Ser53 and Asp96 seem to belong to a charge relay system, which is analogous to that seen in the serine proteases.)
(2) At the next step, the activated cytosine N4 atom makes a nucleophilic attack on the AdoMet methyl group, resulting in the formation of the methylated cytosine product.

Created Updated
2002-11-22 2009-02-26