PDBsum entry 4ny8

Go to PDB code: 
protein dna_rna ligands metals links
Transferase, lyase/DNA PDB id
Jmol PyMol
Protein chain
323 a.a.
_MN ×2
_NA ×2
Waters ×120
PDB id:
Name: Transferase, lyase/DNA
Title: DNA polymerase beta with o6mg in the template base opposite incoming non-hydrolyzable ctp with manganese in the active
Structure: DNA polymerase beta. Chain: a. Fragment: unp residues 10-335. Engineered: yes. 5'-d( Cp Cp Gp Ap Cp (6Og)p Tp Cp Gp Cp Ap Tp Cp 3'. Chain: t. Engineered: yes. Other_details: template.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
2.25Å     R-factor:   0.209     R-free:   0.265
Authors: M.-C.Koag,K.Min,A.F.Monzingo,S.Lee
Key ref: M.C.Koag and S.Lee (2014). Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase β. J Am Chem Soc, 136, 5709-5721. PubMed id: 24694247 DOI: 10.1021/ja500172d
10-Dec-13     Release date:   16-Apr-14    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
335 a.a.
323 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   6 terms 
  Biological process     immunoglobulin heavy chain V-D-J recombination   27 terms 
  Biochemical function     protein binding     12 terms  


DOI no: 10.1021/ja500172d J Am Chem Soc 136:5709-5721 (2014)
PubMed id: 24694247  
Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase β.
M.C.Koag, S.Lee.
Human DNA polymerase β (polβ) inserts, albeit slowly, T opposite the carcinogenic lesion O6-methylguanine (O6MeG) ∼30-fold more frequently than C. To gain insight into this promutagenic process, we solved four ternary structures of polβ with an incoming dCTP or dTTP analogue base-paired with O6MeG in the presence of active-site Mg(2+) or Mn(2+). The Mg(2+)-bound structures show that both the O6MeG·dCTP/dTTP-Mg(2+) complexes adopt an open protein conformation, staggered base pair, and one active-site metal ion. The Mn(2+)-bound structures reveal that, whereas the O6Me·dCTP-Mn(2+) complex assumes the similar altered conformation, the O6MeG·dTTP-Mn(2+) complex adopts a catalytically competent state with a closed protein conformation and pseudo-Watson-Crick base pair. On the basis of these observations, we conclude that polβ slows nucleotide incorporation opposite O6MeG by inducing an altered conformation suboptimal for catalysis and promotes mutagenic replication by allowing Watson-Crick-mode for O6MeG·T but not for O6MeG·C in the enzyme active site. The O6MeG·dTTP-Mn(2+) ternary structure, which represents the first structure of mismatched polβ ternary complex with a closed protein conformation and coplanar base pair, the first structure of pseudo-Watson-Crick O6MeG·T formed in the active site of a DNA polymerase, and a rare, if not the first, example of metal-dependent conformational activation of a DNA polymerase, indicate that catalytic metal-ion coordination is utilized as a kinetic checkpoint by polβ and is crucial for the conformational activation of polβ. Overall, our structural studies not only explain the promutagenic polβ catalysis across O6MeG but also provide new insights into the replication fidelity of polβ.