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Transferase PDB id
1eg2
Jmol
Contents
Protein chain
270 a.a. *
Ligands
MTA
Waters ×227
* Residue conservation analysis
PDB id:
1eg2
Name: Transferase
Title: Crystal structure of rhodobacter spheroides (n6 adenosine) methyltransferase (m.Rsri)
Structure: Modification methylase rsri. Chain: a. Synonym: adenine-specific methyltransferase rsri, m.Rsri. Engineered: yes
Source: Rhodobacter sphaeroides. Organism_taxid: 1063.
Biol. unit: Dimer (from PQS)
Resolution:
1.75Å     R-factor:   0.214     R-free:   0.250
Authors: R.D.Scavetta,C.B.Thomas,M.A.Walsh,S.Szegedi,A.Joachimiak,R.I M.E.A.Churchill,Midwest Center For Structural Genomics (Mcs
Key ref: R.D.Scavetta et al. (2000). Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases. Nucleic Acids Res, 28, 3950-3961. PubMed id: 11024175 DOI: 10.1093/nar/28.20.3950
Date:
11-Feb-00     Release date:   18-Oct-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P14751  (MTR1_RHOSH) -  Modification methylase RsrI
Seq:
Struc: 		319 a.a.
270 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: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine
S-adenosyl-L-methionine
 + DNA adenine
 =
S-adenosyl-L-homocysteine
Bound ligand (Het Group name = MTA)
matches with 76.92% similarity 		+ DNA 6-methylaminopurine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     methylation   4 terms 
  Biochemical function     nucleic acid binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1093/nar/28.20.3950 Nucleic Acids Res 28:3950-3961 (2000)
PubMed id: 11024175  
 
 
Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.
R.D.Scavetta, C.B.Thomas, M.A.Walsh, S.Szegedi, A.Joachimiak, R.I.Gumport, M.E.Churchill.
 
  ABSTRACT  
 
DNA methylation is important in cellular, developmental and disease processes, as well as in bacterial restriction-modification systems. Methylation of DNA at the amino groups of cytosine and adenine is a common mode of protection against restriction endonucleases afforded by the bacterial methyltransferases. The first structure of an N:6-adenine methyltransferase belonging to the beta class of bacterial methyltransferases is described here. The structure of M. RSR:I from Rhodobacter sphaeroides, which methylates the second adenine of the GAATTC sequence, was determined to 1.75 A resolution using X-ray crystallography. Like other methyltransferases, the enzyme contains the methylase fold and has well-defined substrate binding pockets. The catalytic core most closely resembles the PVU:II methyltransferase, a cytosine amino methyltransferase of the same beta group. The larger nucleotide binding pocket observed in M. RSR:I is expected because it methylates adenine. However, the most striking difference between the RSR:I methyltransferase and the other bacterial enzymes is the structure of the putative DNA target recognition domain, which is formed in part by two helices on an extended arm of the protein on the face of the enzyme opposite the active site. This observation suggests that a dramatic conformational change or oligomerization may take place during DNA binding and methylation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21166890 N.Parveen, and K.A.Cornell (2011).
Methylthioadenosine/S-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism.
  Mol Microbiol, 79, 7.  
19453271 E.G.Malygin, A.A.Evdokimov, and S.Hattman (2009).
Dimeric/oligomeric DNA methyltransferases: an unfinished story.
  Biol Chem, 390, 835-844.  
18618709 R.Morita, H.Ishikawa, N.Nakagawa, S.Kuramitsu, and R.Masui (2008).
Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8.
  Proteins, 73, 259-264.
PDB codes: 2zie 2zif 2zig
17617640 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2007).
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
  Nucleic Acids Res, 35, 4792-4799.  
17369272 M.Y.Niv, D.R.Ripoll, J.A.Vila, A.Liwo, E.S.Vanamee, A.K.Aggarwal, H.Weinstein, and H.A.Scheraga (2007).
Topology of Type II REases revisited; structural classes and the common conserved core.
  Nucleic Acids Res, 35, 2227-2237.  
16464821 C.B.Thomas, and R.I.Gumport (2006).
Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase.
  Nucleic Acids Res, 34, 806-815.  
16740122 S.Bheemanaik, J.M.Bujnicki, V.Nagaraja, and D.N.Rao (2006).
Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase.
  Biol Chem, 387, 515-523.  
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
12826405 H.L.Schubert, R.M.Blumenthal, and X.Cheng (2003).
Many paths to methyltransfer: a chronicle of convergence.
  Trends Biochem Sci, 28, 329-335.  
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.  
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.  
11914127 J.M.Bujnicki (2002).
Sequence permutations in the molecular evolution of DNA methyltransferases.
  BMC Evol Biol, 2, 3.  
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.  
12384598 M.J.Clancy, M.E.Shambaugh, C.S.Timpte, and J.A.Bokar (2002).
Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene.
  Nucleic Acids Res, 30, 4509-4518.  
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
11731804 S.Korolev, Y.Ikeguchi, T.Skarina, S.Beasley, C.Arrowsmith, A.Edwards, A.Joachimiak, A.E.Pegg, and A.Savchenko (2002).
The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor.
  Nat Struct Biol, 9, 27-31.
PDB codes: 1inl 1jq3
11405235 A.Jeltsch (2001).
The cytosine N4-methyltransferase M.PvuII also modifies adenine residues.
  Biol Chem, 382, 707-710.  
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.  
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.  
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.  
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 codes are shown on the right.