PDBsum entry 4j2a

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
Protein chain
901 a.a.
_CA ×7
Waters ×858
PDB id:
Name: Transferase/DNA
Title: Rb69 DNA polymerase l415a ternary complex
Structure: DNA polymerase. Chain: a. Synonym: gp43. Engineered: yes. Mutation: yes. DNA (5'- d( Tp Cp Gp Ap Gp Tp Ap Ap Gp Cp Ap Gp Tp Cp Cp Gp Cp G)-3' chain: t. Engineered: yes.
Source: Enterobacteria phage rb69. Organism_taxid: 12353. Gene: 43. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
1.80Å     R-factor:   0.180     R-free:   0.211
Authors: S.Xia,J.Wang,W.H.Konigsberg
Key ref: S.Xia et al. (2013). Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics. Nucleic Acids Res, 41, 9077-9089. PubMed id: 23921641 DOI: 10.1093/nar/gkt674
04-Feb-13     Release date:   19-Feb-14    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q38087  (DPOL_BPR69) -  DNA polymerase
903 a.a.
901 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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
Bound ligand (Het Group name = TTP)
matches with 66.67% similarity
+ 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!
  Biological process     DNA biosynthetic process   4 terms 
  Biochemical function     nucleotide binding     9 terms  


DOI no: 10.1093/nar/gkt674 Nucleic Acids Res 41:9077-9089 (2013)
PubMed id: 23921641  
Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.
S.Xia, M.Wood, M.J.Bradley, E.M.De La Cruz, W.H.Konigsberg.
Internal cavities are a common feature of many proteins, often having profound effects on the dynamics of their interactions with substrate and binding partners. RB69 DNA polymerase (pol) has a hydrophobic cavity right below the nucleotide binding pocket at the tip of highly conserved L415 side chain. Replacement of this residue with Gly or Met in other B family pols resulted in higher mutation rates. When similar substitutions for L415 were introduced into RB69pol, only L415A and L415G had dramatic effects on pre-steady-state kinetic parameters, reducing base selectivity by several hundred fold. On the other hand, the L415M variant behaved like the wild-type. Using a novel tC(o)-tCnitro Förster Resonance Energy Transfer (FRET) assay, we were able to show that the partition of the primer terminus between pol and exonuclease (exo) domains was compromised with the L415A and L415G mutants, but not with the L415M variant. These results could be rationalized by changes in their structures as determined by high resolution X-ray crystallography.