PDBsum entry 10mh

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protein dna_rna ligands links
Transferase/DNA PDB id
Protein chain
327 a.a. *
Waters ×129
* Residue conservation analysis
PDB id:
Name: Transferase/DNA
Title: Ternary structure of hhai methyltransferase with adohcy and hemimethylated DNA containing 5,6-dihydro-5-azacytosine at the target
Structure: DNA (5'-d(p Cp Cp Ap Tp Gp (5Cm) p Gp Cp Tp Gp Ap C)-3'). Chain: b. Engineered: yes. DNA (5'- d(p Gp Tp Cp Ap Gp 5Ncp Gp Cp Ap Tp Gp G)-3'). Chain: c. Engineered: yes. Protein (cytosine-specific methyltransferase
Source: Synthetic: yes. Haemophilus haemolyticus. Organism_taxid: 726. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Nonamer (from PQS)
2.55Å     R-factor:   0.205    
Authors: G.Sheikhnejad,A.Brank,J.K.Christman,A.Goddard,E.Alvarez, H.Ford Junior,V.E.Marquez,C.J.Marasco,J.R.Sufrin,M.O'Gara, X.Cheng
Key ref:
G.Sheikhnejad et al. (1999). Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine. J Mol Biol, 285, 2021-2034. PubMed id: 9925782 DOI: 10.1006/jmbi.1998.2426
10-Aug-98     Release date:   09-Feb-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P05102  (MTH1_HAEPH) -  Modification methylase HhaI
327 a.a.
327 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dna (cytosine-5-)-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Bound ligand (Het Group name = SAH)
corresponds exactly
+ DNA containing 5-methylcytosine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     C-5 methylation of cytosine   4 terms 
  Biochemical function     transferase activity     4 terms  


DOI no: 10.1006/jmbi.1998.2426 J Mol Biol 285:2021-2034 (1999)
PubMed id: 9925782  
Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine.
G.Sheikhnejad, A.Brank, J.K.Christman, A.Goddard, E.Alvarez, H.Ford, V.E.Marquez, C.J.Marasco, J.R.Sufrin, M.O'gara, X.Cheng.
A key step in the predicted mechanism of enzymatic transfer of methyl groups from S-adenosyl-l-methionine (AdoMet) to cytosine residues in DNA is the transient formation of a dihydrocytosine intermediate covalently linked to cysteine in the active site of a DNA (cytosine C5)-methyltransferase (DNA C5-MTase). Crystallographic analysis of complexes formed by HhaI methyltransferase (M.HhaI), AdoMet and a target oligodeoxyribonucleotide containing 5-fluorocytosine confirmed the existence of this dihydrocytosine intermediate. Based on the premise that 5,6-dihydro-5-azacytosine (DZCyt), a cytosine analog with an sp3-hybridized carbon (CH2) at position 6 and an NH group at position 5, could mimic the non-aromatic character of the cytosine ring in this transition state, we synthesized a series of synthetic substrates for DNA C5-MTase containing DZCyt. Substitution of DZCyt for target cytosines in C-G dinucleotides of single-stranded or double-stranded oligodeoxyribonucleotide substrates led to complete inhibition of methylation by murine DNA C5-MTase. Substitution of DZCyt for the target cytosine in G-C-G-C sites in double-stranded oligodeoxyribonucleotides had a similar effect on methylation by M. HhaI. Oligodeoxyribonucleotides containing DZCyt formed a tight but reversible complex with M.HhaI, and were consistently more potent as inhibitors of DNA methylation than oligodeoxyribonucleotides identical in sequence containing 5-fluorocytosine. Crystallographic analysis of a ternary complex involving M.HhaI, S-adenosyl-l-homocysteine and a double-stranded 13-mer oligodeoxyribonucleotide containing DZCyt at the target position showed that the analog is flipped out of the DNA helix in the same manner as cytosine, 5-methylcytosine, and 5-fluorocytosine. However, no formation of a covalent bond was detected between the sulfur atom of the catalytic site nucleophile, cysteine 81, and the pyrimidine C6 carbon. These results indicate that DZCyt can occupy the active site of M.HhaI as a transition state mimic and, because of the high degree of affinity of its interaction with the enzyme, it can act as a potent inhibitor of methylation.
  Selected figure(s)  
Figure 1.
Figure 1. Chemical structures of 5-azacytidine (ZCyd,1a), 5-aza-2 -deoxycytidine (ZdCyd,1b), 5,6-dihy- dro-5azacytidine (DZCyd, 2a), 5,6-dihydro-5aza-20-de- oxycytidine (DZdCyd, 2b), and two phosphoramidites of DZdCyd, with R = CH3O (3a) and R = NCCH2CH2O (3b).
Figure 8.
Figure 8. Interaction between DZCyt and M.HhaI. (a) Difference electron density maps (Fo - Fc, ac) super- imposed on the refined coordinates with carbon atoms being colored black, oxygen atoms red, nitrogen atoms blue, and sulfur atoms green, respectively. The black electron density map contoured at 5.0s was computed with the DZCyt omitted from the atomic model. The gold electron density maps contoured above 5.5s were computed with the C6, N5, and N4 atoms of DZCyt omitted from the atomic model, respectively. (b) A view perpendicular to (a), looking edge-on the flipped DZCyt. Atomic bonds are depicted on green sticks for DNA and white sticks for protein. Nitrogen, oxygen, carbon, sulfur and phosphorus atoms are shown as cyan, red, white, yellow and magenta balls, respectively. Specific interactions are displayed as double broken lines labeled with the interatomic distances in Å . The oxygen atoms of water are labeled as H2O.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 2021-2034) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21198420 A.Tovy, and S.Ankri (2010).
Epigenetics in the unicellular parasite Entamoeba histolytica.
  Future Microbiol, 5, 1875-1884.  
19467223 D.M.van Bemmel, A.S.Brank, R.Eritja, V.E.Marquez, and J.K.Christman (2009).
DNA (Cytosine-C5) methyltransferase inhibition by oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone (zebularine aglycon) at the enzymatic target site.
  Biochem Pharmacol, 78, 633-641.  
19606500 M.Tyagi, A.Bornot, B.Offmann, and Brevern (2009).
Analysis of loop boundaries using different local structure assignment methods.
  Protein Sci, 18, 1869-1881.  
19916931 O.V.Kirsanova, N.A.Cherepanova, and E.S.Gromova (2009).
Inhibition of C5-cytosine-DNA-methyltransferases.
  Biochemistry (Mosc), 74, 1175-1186.  
18499340 H.M.Byun, S.H.Choi, P.W.Laird, B.Trinh, M.A.Siddiqui, V.E.Marquez, and A.S.Yang (2008).
2'-Deoxy-N4-[2-(4-nitrophenyl)ethoxycarbonyl]-5-azacytidine: a novel inhibitor of DNA methyltransferase that requires activation by human carboxylesterase 1.
  Cancer Lett, 266, 238-248.  
18334209 X.Cheng, and R.M.Blumenthal (2008).
Mammalian DNA methyltransferases: a structural perspective.
  Structure, 16, 341-350.  
16924670 A.R.Alexanian (2007).
Epigenetic modifiers promote efficient generation of neural-like cells from bone marrow-derived mesenchymal cells grown in neural environment.
  J Cell Biochem, 100, 362-371.  
16700050 C.Sasaki, I.Sugiura, A.Ebihara, T.Tamura, S.Sugio, and K.Inagaki (2006).
The crystal structure of hypothetical methyltransferase from Thermus thermophilus HB8.
  Proteins, 64, 552-558.  
12506195 N.Huang, N.K.Banavali, and A.D.MacKerell (2003).
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.
  Proc Natl Acad Sci U S A, 100, 68-73.  
14751833 V.E.Marquez, R.Eritja, J.A.Kelley, D.Vanbemmel, and J.K.Christman (2003).
Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (zebularine) at the GCGC recognition domain.
  Ann N Y Acad Sci, 1002, 154-164.  
12206775 L.Zhou, X.Cheng, B.A.Connolly, M.J.Dickman, P.J.Hurd, and D.P.Hornby (2002).
Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases.
  J Mol Biol, 321, 591-599.
PDB code: 1m0e
11376154 E.G.Malygin, A.A.Evdokimov, V.V.Zinoviev, L.G.Ovechkina, W.M.Lindstrom, N.O.Reich, S.L.Schlagman, and S.Hattman (2001).
A dual role for substrate S-adenosyl-L-methionine in the methylation reaction with bacteriophage T4 Dam DNA-[N6-adenine]-methyltransferase.
  Nucleic Acids Res, 29, 2361-2369.  
11838638 R.Güimil García, A.S.Brank, J.K.Christman, V.E.Marquez, and R.Eritja (2001).
Synthesis of oligonucleotide inhibitors of DNA (Cytosine-C5) methyltransferase containing 5-azacytosine residues at specific sites.
  Antisense Nucleic Acid Drug Dev, 11, 369-378.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
11087417 A.N.Sharath, E.Weinhold, and A.S.Bhagwat (2000).
Reviving a dead enzyme: cytosine deaminations promoted by an inactive DNA methyltransferase and an S-adenosylmethionine analogue.
  Biochemistry, 39, 14611-14616.  
11080641 M.M.Skinner, J.M.Puvathingal, R.L.Walter, and A.M.Friedman (2000).
Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.
  Structure, 8, 1189-1201.
PDB code: 1dl5
11024175 R.D.Scavetta, C.B.Thomas, M.A.Walsh, S.Szegedi, A.Joachimiak, R.I.Gumport, and M.E.Churchill (2000).
Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.
  Nucleic Acids Res, 28, 3950-3961.
PDB code: 1eg2
10671528 W.M.Lindstrom, J.Flynn, and N.O.Reich (2000).
Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase.
  J Biol Chem, 275, 4912-4919.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.