DB code: D00082

RLCP classification 5.1504.667700.4100 : Elimination
3.797.810.4110 : Transfer
CATH domain 3.40.50.150 : Rossmann fold Catalytic 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)

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
16680
57856
47876
PubChem 34755
25246222
439155
440055
1dctA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dctB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 71;GLU 109;ARG 155 GLY 68
1dctB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 71;GLU 109;ARG 155 GLY 68
1dctA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dctB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

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
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.

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