EzCatDB: D00082
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DB codeD00082
RLCP classification3.797.810.4110 : Transfer
5.1504.667700.4100 : Elimination
CATH domainDomain 13.40.50.150 : Rossmann foldCatalytic domain
Domain 23.90.120.10 : DNA Methylase; Chain A, domain 2
E.C.2.1.1.37

CATH domainRelated DB codes (homologues)
3.40.50.150 : Rossmann foldS00637,S00639,S00262,S00261,S00291,S00412,D00075,D00076,D00079,D00080,D00083,D00823

Enzyme Name
UniProtKBKEGG

P20589
Protein nameModification methylase HaeIIIDNA (cytosine-5-)-methyltransferase
EcoRI methylase
DNA 5-cytosine methylase
DNA cytosine c5 methylase
DNA cytosine methylase
DNA methylase
DNA methyltransferase
DNA transmethylase
DNA-cytosine 5-methylase
DNA-cytosine methyltransferase
HpaII methylase
HpaII' methylase
M.BsuRIa
M.BsuRIb
Type II DNA methylase
cytosine 5-methyltransferase
cytosine DNA methylase
cytosine DNA methyltransferase
cytosine-specific DNA methyltransferase
deoxyribonucleate methylase
deoxyribonucleate methyltransferase
deoxyribonucleic (cytosine-5-)-methyltransferase
deoxyribonucleic acid (cytosine-5-)-methyltransferase
deoxyribonucleic acid methylase
deoxyribonucleic acid methyltransferase
deoxyribonucleic acid modification methylase
deoxyribonucleic methylase
methylphosphotriester-DNA methyltransferase
modification methylase
restriction-modification system
site-specific DNA-methyltransferase (cytosine-specific)
SynonymsM.HaeIII
EC 2.1.1.37
Cytosine-specific methyltransferase HaeIII
PfamPF00145 (DNA_methylase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00271Methionine metabolism

UniProtKB:Accession NumberP20589
Entry nameMTH3_HAEAE
ActivityS-adenosyl-L-methionine + DNA = S-adenosyl-L- homocysteine + DNA containing 5-methylcytosine.
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00019C00856C02026C00021C02967C03592
CompoundS-Adenosyl-L-methionineDNA cytosineDeoxycytosineS-Adenosyl-L-homocysteineDNA 5-methylcytosine5-Methyl-2'-deoxycytidine
Typeamino acids,amine group,nucleoside,sulfonium ionamine group,nucleic acidsamine group,aromatic ring (with nitrogen atoms)amino acids,amine group,nucleoside,sulfide groupamine group,amide group,nucleic acidsamine group,nucleoside
ChEBI67040


16680
57856

47876

PubChem34755


439155
25246222

440055

               
1dctA01UnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:A-C-C-A-G-C-A-G-G-C49-C-A-C-C-A-G-T-G(chain F)
1dctB01UnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:C-A-G-C-A-G-G-C49-C-A-C-C-A-G-T-G(chain G)
1dctA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1dctB02UnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [4]
pdbCatalytic residuesMain-chain involved in catalysis
          
1dctA01CYS 71;GLU 109;ARG 155
GLY 68
1dctB01CYS 71;GLU 109;ARG 155
GLY 68
1dctA02 
 
1dctB02 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.1, p.110243
[2]Fig.1, p.197-1984
[3]Fig.1, p.383-3844
[4]p.145-146

references
[1]
PubMed ID1932026
JournalBiochemistry
Year1991
Volume30
Pages11018-11025
AuthorsChen L, McMillan AM, Chang W, Ezak-Nipkav K, Lane WS, Verdine GL
TitleDirect identification of the active site nucleophile in a DNA(cytosine-5)-methyltransferase.
Related UniProtKBP20589
[2]
PubMed ID8293456
JournalCell
Year1994
Volume76
Pages197-200
AuthorsVerdine GL
TitleThe flip side of DNA methylation.
[3]
PubMed ID7917329
JournalCurr Opin Cell Biol
Year1994
Volume6
Pages380-9
AuthorsBestor TH, Verdine GL
TitleDNA methyltransferases.
[4]
PubMed ID7606780
JournalCell
Year1995
Volume82(1)
Pages143-53
AuthorsReinisch KM, Chen L, Verdine GL, Lipscomb WN
TitleThe crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
Related PDB1dct
Related UniProtKBP20589
[5]
PubMed ID9427765
JournalEMBO J
Year1998
Volume17
Pages317-24
AuthorsKlimasauskas S, Szyperski T, Serva S, Wuthrich K
TitleDynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.
[6]
PubMed ID9543000
JournalProtein Eng
Year1997
Volume10
Pages1385-93
AuthorsSchroeder SG, Samudzi CT
TitleStructural studies of EcoRII methylase: exploring similarities among methylases.
[7]
PubMed ID10828365
JournalInt J Biol Macromol
Year2000
Volume27
Pages195-204
AuthorsBujnicki JM
TitleHomology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?
[8]
PubMed ID11088571
JournalPhys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics
Year2000
Volume62
Pages1133-7
AuthorsChen YZ, Mohan V, Griffey RH
TitleSpontaneous base flipping in DNA and its possible role in methyltransferase binding.

comments
This enzyme recognizes the double-stranded sequence GGCC, methylates specifically C5 atom of Cytosine-3 (see [3] & [4]).
According to the literature [1], [2], [3] & [4], the reactions can be divided into three reactions:
(A) Addition of Cys71 to C6 atom of Cytosine substrate.
(B) Transfer of methyl group from SAM to C5 atom of the cytosine.
(C) Elimination of Cys71 from the cytosine.
Throughout the catalysis, Glu109 acts as general acid-base, modulating the proton at the N3 atom.
The reactions proceeds as follows:
(A) Addition of Cys71 to C6 atom of Cytosine substrate.
(A1) Cys71 acts as a nucleophile, whose sidechain thiolate attacks on C6 atom, adjacent to the acceptor atom, C5 of the substrate cytosine.
(A2) Simultanesouly, Glu109 acts as a general acid to protonate the N3 atom of the cytosine, which is 3-bonds away from the normally protonation site (C5).
(A3) An enamine intermediate, which is covalently-bonded to Cys71, is formed.
(A4) Arg155 and Gly68 stabilize the cytosine covalently-bonded to Cys71 (see [4]).
(B) Transfer of methyl group from SAM to C5 atom of the cytosine.
(B1) Glu109 acts as a general base to deprotonate the N3 atom of the cytosine, which is 3-bonds away from the normally protonation site (C5).
(B2) Arg155 and Gly68 stabilize the cytosine covalently-bonded to Cys71 (see [4]).
(B3) The C5 atom of the enamine intermediate, as a nucleophilic acceptor, attacks the methyl group of S-adenosyl-L-methionine (SAM), forming a covalent bond with it.
(B4) A general base might abstract the proton at C5, yielding an enamine intermediate again. Here, although there is no candidate for this general base, the thioether of Cys71 can play the role in the proximity of the proton at C5. Otherwise, a water molecule at the active site could act as the general base.
(C) Elimination of Cys71 from the cytosine.
(C1) Arg155 and Gly68 stabilize the cytosine covalently-bonded to Cys71 (see [4]).
(C2) Glu109 acts as a general base to deprotonate the N3 atom (2-bonds away from deprotonation site), leading to the elimination of Cys71 from the methylated product.

createdupdated
2002-08-142009-02-26


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