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PDBsum entry 4i9q

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
4i9q
Jmol
Contents
Protein chains
846 a.a.
DNA/RNA
Ligands
XG4 ×4
Metals
_NA ×2
_CA ×2
Waters ×398
PDB id:
4i9q
Name: Transferase/DNA
Title: Crystal structure of the ternary complex of the d714a mutant DNA polymerase
Structure: DNA polymerase. Chain: a, b. Synonym: gp43. Engineered: yes. Mutation: yes. DNA (5'- d( Tp Cp Ap Cp Gp Tp Ap Ap Gp Cp Ap Gp Tp Cp Cp Gp Cp G)-3' chain: t, d. Engineered: yes.
Source: Enterobacteria phage rb69. Organism_taxid: 12353. Gene: 43. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630
Resolution:
2.30Å     R-factor:   0.254     R-free:   0.287
Authors: K.E.Guja,A.Jacewicz,A.Trzemecka,D.Plochocka,E.Yakubovskaya,A M.Garcia-Diaz
Key ref: A.Jacewicz et al. (2013). A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site. PLoS One, 8, e76700. PubMed id: 24116139 DOI: 10.1371/journal.pone.0076700
Date:
05-Dec-12     Release date:   09-Oct-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q38087  (DPOL_BPR69) -  DNA polymerase
Seq:
Struc:
 
Seq:
Struc:
903 a.a.
846 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.2.7.7.7  - 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!
  Biological process     nucleic acid phosphodiester bond hydrolysis   4 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
DOI no: 10.1371/journal.pone.0076700 PLoS One 8:e76700 (2013)
PubMed id: 24116139  
 
 
A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.
A.Jacewicz, A.Trzemecka, K.E.Guja, D.Plochocka, E.Yakubovskaya, A.Bebenek, M.Garcia-Diaz.
 
  ABSTRACT  
 
Non-conserved amino acids that are far removed from the active site can sometimes have an unexpected effect on enzyme catalysis. We have investigated the effects of alanine replacement of residues distant from the active site of the replicative RB69 DNA polymerase, and identified a substitution in a weakly conserved palm residue (D714A), that renders the enzyme incapable of sustaining phage replication in vivo. D714, located several angstroms away from the active site, does not contact the DNA or the incoming dNTP, and our apoenzyme and ternary crystal structures of the Pol(D714A) mutant demonstrate that D714A does not affect the overall structure of the protein. The structures reveal a conformational change of several amino acid side chains, which cascade out from the site of the substitution towards the catalytic center, substantially perturbing the geometry of the active site. Consistent with these structural observations, the mutant has a significantly reduced k pol for correct incorporation. We propose that the observed structural changes underlie the severe polymerization defect and thus D714 is a remote, non-catalytic residue that is nevertheless critical for maintaining an optimal active site conformation. This represents a striking example of an action-at-a-distance interaction.