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PDBsum entry 1yf3

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protein dna_rna ligands links
Transferase/DNA PDB id
1yf3
Jmol
Contents
Protein chains
259 a.a. *
DNA/RNA
Ligands
SAH ×2
GOL ×2
Waters ×204
* Residue conservation analysis
PDB id:
1yf3
Name: Transferase/DNA
Title: T4dam in complex with adohcy and 13-mer oligonucleotide maki and semi-specific (~1/4) contact
Structure: 5'-d( Ap Cp Cp Ap Tp Gp Ap Tp Cp Tp Gp Ap C)-3'. Chain: c. Engineered: yes. 5'-d( Tp Gp Tp Cp Ap Gp Ap Tp Cp Ap Tp Gp G)-3'. Chain: d. Engineered: yes. DNA adenine methylase. Chain: a, b. Synonym: deoxyadenosyl-methyltransferase, m.Ecot4dam.
Source: Synthetic: yes. Other_details: synthesized by new england biolabs. Enterobacteria phage t4. Organism_taxid: 10665. Gene: dam. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.29Å     R-factor:   0.214     R-free:   0.270
Authors: J.R.Horton,K.Liebert,S.Hattman,A.Jeltsch,X.Cheng
Key ref:
J.R.Horton et al. (2005). Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase. Cell, 121, 349-361. PubMed id: 15882618 DOI: 10.1016/j.cell.2005.02.021
Date:
30-Dec-04     Release date:   17-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04392  (DMA_BPT4) -  DNA adenine methylase
Seq:
Struc:
259 a.a.
259 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 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 = SAH)
corresponds exactly
+ 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   3 terms 
  Biochemical function     nucleic acid binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.cell.2005.02.021 Cell 121:349-361 (2005)
PubMed id: 15882618  
 
 
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.
J.R.Horton, K.Liebert, S.Hattman, A.Jeltsch, X.Cheng.
 
  ABSTRACT  
 
DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure of T4Dam-AdoHcy-15-mer DNA
Figure 7.
Figure 7. Snapshots of T4Dam-DNA Interactions Illustrated by Orientation of the Protein Hairpin Loop Relative to the DNA Axis
 
  The above figures are reprinted by permission from Cell Press: Cell (2005, 121, 349-361) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20375284 I.E.Sánchez, D.U.Ferreiro, M.Dellarole, and G.de Prat-Gay (2010).
Experimental snapshots of a protein-DNA binding landscape.
  Proc Natl Acad Sci U S A, 107, 7751-7756.  
20118257 R.Kaminska, and M.W.van der Woude (2010).
Establishing and maintaining sequestration of Dam target sites for phase variation of agn43 in Escherichia coli.
  J Bacteriol, 192, 1937-1945.  
20419059 R.Xiao, R.Roman-Sanchez, and D.D.Moore (2010).
DamIP: a novel method to identify DNA binding sites in vivo.
  Nucl Recept Signal, 8, e003.  
19453271 E.G.Malygin, A.A.Evdokimov, and S.Hattman (2009).
Dimeric/oligomeric DNA methyltransferases: an unfinished story.
  Biol Chem, 390, 835-844.  
19725089 H.Elsawy, S.Podobinschi, S.Chahar, and A.Jeltsch (2009).
Transition from EcoDam to T4Dam DNA recognition mechanism without loss of activity and specificity.
  Chembiochem, 10, 2488-2493.  
19740769 R.K.Neely, G.Tamulaitis, K.Chen, M.Kubala, V.Siksnys, and A.C.Jones (2009).
Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes.
  Nucleic Acids Res, 37, 6859-6870.  
19419959 S.R.Coffin, and N.O.Reich (2009).
Escherichia coli DNA Adenine Methyltransferase: THE STRUCTURAL BASIS OF PROCESSIVE CATALYSIS AND INDIRECT READ-OUT.
  J Biol Chem, 284, 18390-18400.  
18664582 D.U.Ferreiro, I.E.Sánchez, and G.de Prat Gay (2008).
Transition state for protein-DNA recognition.
  Proc Natl Acad Sci U S A, 105, 10797-10802.  
18772888 H.Hashimoto, J.R.Horton, X.Zhang, M.Bostick, S.E.Jacobsen, and X.Cheng (2008).
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
  Nature, 455, 826-829.
PDB codes: 2zo0 2zo1 2zo2
17630395 A.A.Evdokimov, B.Sclavi, V.V.Zinoviev, E.G.Malygin, S.Hattman, and M.Buckle (2007).
Study of bacteriophage T4-encoded Dam DNA (adenine-N6)-methyltransferase binding with substrates by rapid laser UV cross-linking.
  J Biol Chem, 282, 26067-26076.  
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.  
17284455 H.Tjong, and H.X.Zhou (2007).
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.
  Nucleic Acids Res, 35, 1465-1477.  
17545164 K.Liebert, J.R.Horton, S.Chahar, M.Orwick, X.Cheng, and A.Jeltsch (2007).
Two alternative conformations of S-adenosyl-L-homocysteine bound to Escherichia coli DNA adenine methyltransferase and the implication of conformational changes in regulating the catalytic cycle.
  J Biol Chem, 282, 22848-22855.
PDB code: 2ore
17437717 S.A.Townson, J.C.Samuelson, Y.Bao, S.Y.Xu, and A.K.Aggarwal (2007).
BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning.
  Structure, 15, 449-459.
PDB code: 2p0j
17932050 S.Zheng, S.Shuman, and B.Schwer (2007).
Sinefungin resistance of Saccharomyces cerevisiae arising from Sam3 mutations that inactivate the AdoMet transporter or from increased expression of AdoMet synthase plus mRNA cap guanine-N7 methyltransferase.
  Nucleic Acids Res, 35, 6895-6903.  
17977824 T.P.Jurkowski, N.Anspach, L.Kulishova, W.Nellen, and A.Jeltsch (2007).
The M.EcoRV DNA-(Adenine N6)-methyltransferase Uses DNA Bending for Recognition of an Expanded EcoDam Recognition Site.
  J Biol Chem, 282, 36942-36952.  
17976013 V.V.Zinoviev, A.A.Evdokimov, E.G.Malygin, B.Sclavi, M.Buckle, and S.Hattman (2007).
Differential methylation kinetics of individual target site strands by T4Dam DNA methyltransferase.
  Biol Chem, 388, 1199-1207.  
16845123 B.Youngblood, and N.O.Reich (2006).
Conformational transitions as determinants of specificity for the DNA methyltransferase EcoRI.
  J Biol Chem, 281, 26821-26831.  
16959970 J.Casadesús, and D.Low (2006).
Epigenetic gene regulation in the bacterial world.
  Microbiol Mol Biol Rev, 70, 830-856.  
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
17005571 R.A.Estabrook, and N.Reich (2006).
Observing an induced-fit mechanism during sequence-specific DNA methylation.
  J Biol Chem, 281, 37205-37214.  
17125150 R.L.Rich, and D.G.Myszka (2006).
Survey of the year 2005 commercial optical biosensor literature.
  J Mol Recognit, 19, 478-534.  
16971388 S.Zheng, S.Hausmann, Q.Liu, A.Ghosh, B.Schwer, C.D.Lima, and S.Shuman (2006).
Mutational analysis of Encephalitozoon cuniculi mRNA cap (guanine-N7) methyltransferase, structure of the enzyme bound to sinefungin, and evidence that cap methyltransferase is the target of sinefungin's antifungal activity.
  J Biol Chem, 281, 35904-35913.
PDB code: 2hv9
16287970 J.Widom (2005).
Target site localization by site-specific, DNA-binding proteins.
  Proc Natl Acad Sci U S A, 102, 16909-16910.  
15948708 S.Hattman (2005).
DNA-[adenine] methylation in lower eukaryotes.
  Biochemistry (Mosc), 70, 550-558.  
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.