DB code: D00082

RLCP classification	3.797.810.4110 : Transfer
RLCP classification	5.1504.667700.4100 : Elimination
CATH domain	3.40.50.150 : Rossmann fold	Catalytic domain
CATH domain	3.90.120.10 : DNA Methylase; Chain A, domain 2
E.C.	2.1.1.37
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)
3.40.50.150 : Rossmann fold	S00637 S00639 S00262 S00261 S00291 S00412 D00075 D00076 D00079 D00080 D00083 D00823

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	Pfam
P20589	Modification methylase HaeIII	M.HaeIII EC 2.1.1.37 Cytosine-specific methyltransferase HaeIII	PF00145 (DNA_methylase) [Graphical View]

KEGG enzyme name
DNA (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)

KEGG enzyme name

DNA (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)

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P20589	MTH3_HAEAE	S-adenosyl-L-methionine + DNA = S-adenosyl-L- homocysteine + DNA containing 5-methylcytosine.

KEGG Pathways
Map code	Pathways	E.C.
MAP00271	Methionine metabolism

Compound table
	Substrates			Products			Intermediates
KEGG-id	C00019	C00856	C02026	C00021	C02967	C03592
E.C.
Compound	S-Adenosyl-L-methionine	DNA cytosine	Deoxycytosine	S-Adenosyl-L-homocysteine	DNA 5-methylcytosine	5-Methyl-2'-deoxycytidine
Type	amino acids,amine group,nucleoside,sulfonium ion	amine group,nucleic acids	amine group,aromatic ring (with nitrogen atoms)	amino acids,amine group,nucleoside,sulfide group	amine group,amide group,nucleic acids	amine group,nucleoside
ChEBI	67040 67040			16680 57856 16680 57856		47876 47876
PubChem	34755 34755			25246222 439155 25246222 439155		440055 440055

1dctA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-analogue:A-C-C-A-G-C-A-G-G-C49-C-A-C-C-A-G-T-G (chain F)
1dctB01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-analogue:C-A-G-C-A-G-G-C49-C-A-C-C-A-G-T-G (chain G)
1dctA02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1dctB02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
literature [4]

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1dctA01	CYS 71;GLU 109;ARG 155			GLY 68
1dctB01	CYS 71;GLU 109;ARG 155			GLY 68
1dctA02
1dctB02

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	Fig.1, p.11024	3
[2]	Fig.1, p.197-198	4
[3]	Fig.1, p.383-384	4
[4]	p.145-146

References
[1]
Resource
Comments
Medline ID
PubMed ID	1932026
Journal	Biochemistry
Year	1991
Volume	30
Pages	11018-11025
Authors	Chen L, McMillan AM, Chang W, Ezak-Nipkav K, Lane WS, Verdine GL
Title	Direct identification of the active site nucleophile in a DNA(cytosine-5)-methyltransferase.
Related PDB
Related UniProtKB	P20589
[2]
Resource
Comments
Medline ID
PubMed ID	8293456
Journal	Cell
Year	1994
Volume	76
Pages	197-200
Authors	Verdine GL
Title	The flip side of DNA methylation.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	7917329
Journal	Curr Opin Cell Biol
Year	1994
Volume	6
Pages	380-9
Authors	Bestor TH, Verdine GL
Title	DNA methyltransferases.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID	7606780
Journal	Cell
Year	1995
Volume	82(1)
Pages	143-53
Authors	Reinisch KM, Chen L, Verdine GL, Lipscomb WN
Title	The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
Related PDB	1dct
Related UniProtKB	P20589
[5]
Resource
Comments
Medline ID
PubMed ID	9427765
Journal	EMBO J
Year	1998
Volume	17
Pages	317-24
Authors	Klimasauskas S, Szyperski T, Serva S, Wuthrich K
Title	Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	9543000
Journal	Protein Eng
Year	1997
Volume	10
Pages	1385-93
Authors	Schroeder SG, Samudzi CT
Title	Structural studies of EcoRII methylase: exploring similarities among methylases.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	10828365
Journal	Int J Biol Macromol
Year	2000
Volume	27
Pages	195-204
Authors	Bujnicki JM
Title	Homology modelling of the DNA 5mC methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	11088571
Journal	Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics
Year	2000
Volume	62
Pages	1133-7
Authors	Chen YZ, Mohan V, Griffey RH
Title	Spontaneous base flipping in DNA and its possible role in methyltransferase binding.
Related PDB
Related UniProtKB

Comments
(B) Transfer of methyl group from SAM to C5 atom of the cytosine. (A4) Arg155 and Gly68 stabilize the cytosine covalently-bonded to Cys71 (see [4]). 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. (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.

Comments

(B) Transfer of methyl group from SAM to C5 atom of the cytosine.
(A4) Arg155 and Gly68 stabilize the cytosine covalently-bonded to Cys71 (see [4]).
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.
(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.

Created	Updated
2002-08-14	2009-02-26