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PDBsum entry 3pta

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
3pta
Jmol
Contents
Protein chain
904 a.a. *
DNA/RNA
Ligands
SAH
Metals
_ZN ×4
* Residue conservation analysis
PDB id:
3pta
Name: Transferase/DNA
Title: Crystal structure of human dnmt1(646-1600) in complex with d
Structure: DNA (cytosine-5)-methyltransferase 1. Chain: a. Fragment: unp residues 646-1600. Synonym: dnmt1, cxxc-type zinc finger protein 9, DNA methyltransferase hsai, DNA mtase hsai, m.Hsai, mcmt. Engineered: yes. DNA (5'- d( Tp Cp Cp Cp Gp Tp Gp Ap Gp Cp Cp Tp Cp Cp Gp Cp Ap Gp G) chain: b.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: dnmt1, aim, cxxc9, dnmt. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
3.60Å     R-factor:   0.257     R-free:   0.291
Authors: J.Song,D.J.Patel
Key ref: J.Song et al. (2011). Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science, 331, 1036-1040. PubMed id: 21163962
Date:
02-Dec-10     Release date:   29-Dec-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26358  (DNMT1_HUMAN) -  DNA (cytosine-5)-methyltransferase 1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1616 a.a.
904 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.37  - Dna (cytosine-5-)-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
S-adenosyl-L-methionine
+ DNA
=
S-adenosyl-L-homocysteine
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     DNA methylation   1 term 
  Biochemical function     chromatin binding     4 terms  

 

 
    reference    
 
 
Science 331:1036-1040 (2011)
PubMed id: 21163962  
 
 
Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
J.Song, O.Rechkoblit, T.H.Bestor, D.J.Patel.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23400093 Z.D.Smith, and A.Meissner (2013).
DNA methylation: roles in mammalian development.
  Nat Rev Genet, 14, 204-220.  
23064413 G.Landan, N.M.Cohen, Z.Mukamel, A.Bar, A.Molchadsky, R.Brosh, S.Horn-Saban, D.A.Zalcenstein, N.Goldfinger, A.Zundelevich, E.N.Gal-Yam, V.Rotter, and A.Tanay (2012).
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues.
  Nat Genet, 44, 1207-1214.  
21350155 L.A.Godley, and A.Mondragón (2011).
Molecular biology. Preference by exclusion.
  Science, 331, 1017-1018.  
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.