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PDBsum entry 2dpm
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protein ligands metals links
Transferase PDB id
2dpm

 

 

 

 

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Contents
Protein chain
258 a.a. *
Ligands
SAM
Metals
_HG
Waters ×178
* Residue conservation analysis
PDB id:
2dpm
Name: Transferase
Title: Dpnm DNA adenine methyltransferase from streptoccocus pneumoniae complexed with s-adenosylmethionine
Structure: Protein (adenine-specific methyltransferase dpnii 1). Chain: a. Synonym: m.Dpnii 1. Engineered: yes. Other_details: s-adenosylmethionine
Source: Streptococcus pneumoniae. Organism_taxid: 1313. Strain: hb264. Gene: dpnm. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.238     R-free:   0.284
Authors: P.H.Tran,Z.R.Korszun,S.Cerritelli,S.S.Springhorn,S.A.Lacks
Key ref:
P.H.Tran et al. (1998). Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine. Structure, 6, 1563-1575. PubMed id: 9862809 DOI: 10.1016/S0969-2126(98)00154-3
Date:
03-Sep-98     Release date:   23-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04043  (MTD21_STREE) -  Type II methyltransferase M1.DpnII from Streptococcus pneumoniae
Seq:
Struc: 		284 a.a.
258 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.72  - site-specific DNA-methyltransferase (adenine-specific).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an N6-methyl- 2'-deoxyadenosine in DNA + S-adenosyl-L-homocysteine + H+
2'-deoxyadenosine in DNA
 +
S-adenosyl-L-methionine
Bound ligand (Het Group name = SAM)
corresponds exactly 		= N(6)-methyl- 2'-deoxyadenosine in DNA
 + S-adenosyl-L-homocysteine
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(98)00154-3 Structure 6:1563-1575 (1998)
PubMed id: 9862809  
 
 
Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine.
P.H.Tran, Z.R.Korszun, S.Cerritelli, S.S.Springhorn, S.A.Lacks.
 
  ABSTRACT  
 
Background:. Methyltransferases (Mtases) catalyze the transfer of methyl groups from S-adenosylmethionine (AdoMet) to a variety of small molecular and macromolecular substrates. These enzymes contain a characteristic alpha/beta structural fold. Four groups of DNA Mtases have been defined and representative structures have been determined for three groups. DpnM is a DNA Mtase that acts on adenine N6 in the sequence GATC; the enzyme represents group alpha DNA Mtases, for which no structures are known. Results:. The structure of DpnM in complex with AdoMet was determined at 1.80 A resolution. The protein comprises a consensus Mtase fold with a helical cluster insert. DpnM binds AdoMet in a similar manner to most other Mtases and the enzyme contains a hollow that can accommodate DNA. The helical cluster supports a shelf within the hollow that may recognize the target sequence. Modeling studies indicate a potential site for binding the target adenine, everted from the DNA helix. Comparison of the DpnM structure and sequences of group alpha DNA Mtases indicates that the group is a genetically related family. Structural comparisons show DpnM to be most similar to a small-molecule Mtase and then to macromolecular Mtases, although several dehydrogenases show greater similarity than one DNA Mtase. Conclusions:. DpnM, and by extension the DpnM family or group alpha Mtases, contains the consensus fold and AdoMet-binding motifs found in most Mtases. Structural considerations suggest that macromolecular Mtases evolved from small-molecule Mtases, with different groups of DNA Mtases evolving independently. Mtases may have evolved from dehydrogenases. Comparison of these enzymes indicates that in protein evolution, the structural fold is most highly conserved, then function and lastly sequence.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. The active site of DpnM showing the binding of AdoMet and the proposed binding mode of the target adenine in DNA. Atoms are shown in standard colors: C, black; N, blue; O, red (except water O, white); P, purple; S, yellow. The bonds are color coded: AdoMet, orange; adenylate residue of DNA, deep blue; protein, green. Dashed lines indicate hydrogen bonds. For Leu49, Phe43, Phe63 and Phe178, only mainchain atoms are shown; for Asp194 and Trp17, only terminal parts of the sidechain are indicated. Not all contacts are shown. (The figure was prepared using the program MOLSCRIPT [64].)
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1563-1575) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20939822 F.Xu, C.Mao, Y.Ding, C.Rui, L.Wu, A.Shi, H.Zhang, L.Zhang, and Z.Xu (2010).
Molecular and enzymatic profiles of mammalian DNA methyltransferases: structures and targets for drugs.
  Curr Med Chem, 17, 4052-4071.  
  19411852 L.M.Iyer, M.Tahiliani, A.Rao, and L.Aravind (2009).
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.
  Cell Cycle, 8, 1698-1710.  
17977734 F.H.Schmidt, M.Hüben, B.Gider, F.Renault, M.P.Teulade-Fichou, and E.Weinhold (2008).
Sequence-specific Methyltransferase-Induced Labelling (SMILing) of plasmid DNA for studying cell transfection.
  Bioorg Med Chem, 16, 40-48.  
16524590 J.R.Horton, K.Liebert, M.Bekes, A.Jeltsch, and X.Cheng (2006).
Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.
  J Mol Biol, 358, 559-570.
PDB code: 2g1p
15948708 S.Hattman (2005).
DNA-[adenine] methylation in lower eukaryotes.
  Biochemistry (Mosc), 70, 550-558.  
15195996 A.Dong, L.Zhou, X.Zhang, S.Stickel, R.J.Roberts, and X.Cheng (2004).
Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.
  Biol Chem, 385, 373-379.
PDB code: 1svu
15382231 A.R.Panchenko, and T.Madej (2004).
Analysis of protein homology by assessing the (dis)similarity in protein loop regions.
  Proteins, 57, 539-547.  
12732637 C.B.Thomas, R.D.Scavetta, R.I.Gumport, and M.E.Churchill (2003).
Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding.
  J Biol Chem, 278, 26094-26101.
PDB codes: 1nw5 1nw6 1nw7 1nw8
12893823 E.G.Malygin, W.M.Lindstrom, V.V.Zinoviev, A.A.Evdokimov, S.L.Schlagman, N.O.Reich, and S.Hattman (2003).
Bacteriophage T4Dam (DNA-(adenine-N6)-methyltransferase): evidence for two distinct stages of methylation under single turnover conditions.
  J Biol Chem, 278, 41749-41755.  
12954781 J.Osipiuk, M.A.Walsh, and A.Joachimiak (2003).
Crystal structure of MboIIA methyltransferase.
  Nucleic Acids Res, 31, 5440-5448.
PDB code: 1g60
12937411 Z.Yang, J.R.Horton, L.Zhou, X.J.Zhang, A.Dong, X.Zhang, S.L.Schlagman, V.Kossykh, S.Hattman, and X.Cheng (2003).
Structure of the bacteriophage T4 DNA adenine methyltransferase.
  Nat Struct Biol, 10, 849-855.
PDB codes: 1q0s 1q0t
11933228 A.Jeltsch (2002).
Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases.
  Chembiochem, 3, 274-293.  
11729191 C.P.Swaminathan, U.T.Sankpal, D.N.Rao, and A.Surolia (2002).
Water-assisted dual mode cofactor recognition by HhaI DNA methyltransferase.
  J Biol Chem, 277, 4042-4049.  
12056895 G.D.Markham, P.O.Norrby, and C.W.Bock (2002).
S-adenosylmethionine conformations in solution and in protein complexes: conformational influences of the sulfonium group.
  Biochemistry, 41, 7636-7646.  
11917015 G.Vilkaitis, A.Lubys, E.Merkiene, A.Timinskas, A.Janulaitis, and S.Klimasauskas (2002).
Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation.
  Nucleic Acids Res, 30, 1547-1557.  
11929612 J.M.Bujnicki, and L.Rychlewski (2002).
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.
  BMC Bioinformatics, 3, 10.  
12429089 J.P.Keller, P.M.Smith, J.Benach, D.Christendat, G.T.deTitta, and J.F.Hunt (2002).
The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase.
  Structure, 10, 1475-1487.
PDB codes: 1f38 1kxz 1l3b 1l3c 1l3i
12077432 O.Nureki, M.Shirouzu, K.Hashimoto, R.Ishitani, T.Terada, M.Tamakoshi, T.Oshima, M.Chijimatsu, K.Takio, D.G.Vassylyev, T.Shibata, Y.Inoue, S.Kuramitsu, and S.Yokoyama (2002).
An enzyme with a deep trefoil knot for the active-site architecture.
  Acta Crystallogr D Biol Crystallogr, 58, 1129-1137.
PDB code: 1ipa
11405235 A.Jeltsch (2001).
The cytosine N4-methyltransferase M.PvuII also modifies adenine residues.
  Biol Chem, 382, 707-710.  
11266551 A.V.Matveyev, K.T.Young, A.Meng, and J.Elhai (2001).
DNA methyltransferases of the cyanobacterium Anabaena PCC 7120.
  Nucleic Acids Res, 29, 1491-1506.  
11705888 D.A.Low, N.J.Weyand, and M.J.Mahan (2001).
Roles of DNA adenine methylation in regulating bacterial gene expression and virulence.
  Infect Immun, 69, 7197-7204.  
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.  
11179656 J.Eberhard, J.Oza, and N.O.Reich (2001).
Cloning, sequence analysis and heterologous expression of the DNA adenine-(N(6)) methyltransferase from the human pathogen Actinobacillus actinomycetemcomitans.
  FEMS Microbiol Lett, 195, 223-229.  
11746687 K.Lim, H.Zhang, A.Tempczyk, N.Bonander, J.Toedt, A.Howard, E.Eisenstein, and O.Herzberg (2001).
Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine.
  Proteins, 45, 397-407.
PDB code: 1im8
11435118 L.J.Baker, J.A.Dorocke, R.A.Harris, and D.E.Timm (2001).
The crystal structure of yeast thiamin pyrophosphokinase.
  Structure, 9, 539-546.
PDB code: 1ig0
11470870 M.Roth, and A.Jeltsch (2001).
Changing the target base specificity of the EcoRV DNA methyltransferase by rational de novo protein-design.
  Nucleic Acids Res, 29, 3137-3144.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
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
11024176 S.S.Szegedi, N.O.Reich, and R.I.Gumport (2000).
Substrate binding in vitro and kinetics of RsrI [N6-adenine] DNA methyltransferase.
  Nucleic Acids Res, 28, 3962-3971.  
11024177 S.S.Szegedi, and R.I.Gumport (2000).
DNA binding properties in vivo and target recognition domain sequence alignment analyses of wild-type and mutant RsrI [N6-adenine] DNA methyltransferases.
  Nucleic Acids Res, 28, 3972-3981.  
10391886 A.Jeltsch, F.Christ, M.Fatemi, and M.Roth (1999).
On the substrate specificity of DNA methyltransferases. adenine-N6 DNA methyltransferases also modify cytosine residues at position N4.
  J Biol Chem, 274, 19538-19544.  
10651285 M.Radlinska, J.M.Bujnicki, and A.Piekarowicz (1999).
Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P.
  Proteins, 37, 717-728.  
  10518300 U.Melcher, Y.Sha, F.Ye, and J.Fletcher (1999).
Mechanisms of spiroplasma genome variation associated with SpV1-like viral DNA inferred from sequence comparisons.
  Microb Comp Genomics, 4, 29-46.  
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.

 

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