EzCatDB: S00262

DB codeS00262
RLCP classification3.747.6310.11
CATH domainDomain 13.40.50.150Catalytic domain
E.C.2.1.1.113
CSA1boo

CATH domainRelated DB codes (homologues)
3.40.50.150S00637,S00639,S00261,S00291,S00412,D00075,D00076,D00079,D00080,D00082,D00083,D00823

Enzyme Name
Swiss-protKEGG

P11409
Protein nameModification methylase PvuIIsite-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
SynonymsM.PvuII
EC 2.1.1.113
N-4 cytosine-specific methyltransferase PvuII


Swiss-prot:Accession NumberP11409
Entry nameMTP2_PROVU
ActivityS-adenosyl-L-methionine + DNA cytosine = S- adenosyl-L-homocysteine + DNA N(4)-methylcytosine.
Subunit
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC00019C00856C00021C03110
CompoundS-Adenosyl-L-methionineDNA cytosineS-Adenosyl-L-homocysteineDNA N4-methylcytosine
Typeamino acids,amine group,nucleoside,sulfonium ionamine group,nucleic acidsamino acids,amine group,nucleoside,sulfide groupamine group,nucleic acids
1booAUnboundUnboundBound:SAHUnbound

Active-site residues
resource
literature [2]
pdbCatalytic residues
1booASER 53;ASP 96

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Figure 6a, p.27111

references
[1]
PubMed ID2690017
JournalNucleic Acids Res
Year1989
Volume17
Pages10403-25
AuthorsKaszubska W, Aiken C, O'Connor CD, Gumport RI
TitlePurification, 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.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID97351137
PubMed ID9207015
JournalNucleic Acids Res
Year1997
Volume25
Pages2702-15
AuthorsGong W, O'Gara M, Blumenthal RM, Cheng X
TitleStructure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
Related PDB1boo
Related Swiss-protP11409
[3]
PubMed ID9288926
JournalEur J Biochem
Year1997
Volume247
Pages1009-18
AuthorsO'Gara M, Adams GM, Gong W, Kobayashi R, Blumenthal RM, Cheng X
TitleExpression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).
[4]
PubMed ID9204874
JournalBiochemistry
Year1997
Volume36
Pages8284-92
AuthorsAdams GM, Blumenthal RM
TitleThe PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine.
[5]
PubMed ID10651285
JournalProteins
Year1999
Volume37
Pages717-28
AuthorsRadlinska M, Bujnicki JM, Piekarowicz A
TitleStructural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P.
[6]
PubMed ID9927736
JournalNucleic Acids Res
Year1999
Volume27
Pages1032-8
AuthorsRice MR, Koons MD, Blumenthal RM
TitleSubstrate recognition by the Pvu II endonuclease: binding and cleavage of CAG5mCTG sites.
[7]
PubMed ID10329711
JournalJ Biol Chem
Year1999
Volume274
Pages15066-72
AuthorsHolz B, Dank N, Eickhoff JE, Lipps G, Krauss G, Weinhold E
TitleIdentification 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.
[8]
PubMed ID9931007
JournalBiochemistry
Year1999
Volume38
Pages1426-34
AuthorsPues H, Bleimling N, Holz B, Wolcke J, Weinhold E
TitleFunctional 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.
[9]
PubMed ID11024175
JournalNucleic Acids Res
Year2000
Volume28
Pages3950-61
AuthorsScavetta RD, Thomas CB, Walsh MA, Szegedi S, Joachimiak A, Gumport RI, Churchill ME
TitleStructure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.
[10]
PubMed ID11405235
JournalBiol Chem
Year2001
Volume382
Pages707-10
AuthorsJeltsch A
TitleThe cytosine N4-methyltransferase M.PvuII also modifies adenine residues.
[11]
PubMed ID12507474
JournalJ Mol Biol
Year2003
Volume325
Pages711-20
AuthorsLindstrom WM Jr, Malygin EG, Ovechkina LG, Zinoviev VV, Reich NO
TitleFunctional analysis of BamHI DNA cytosine-N4 methyltransferase.

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.

createdupdated
2002-11-222009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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