4i9q

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4i9q, resolution 2.30Å ()
Ligands: , ,
Gene: 43 (Enterobacteria phage RB69)
Activity: DNA-directed DNA polymerase, with EC number 2.7.7.7
Related: 4i9l, 4khn


Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

Publication Abstract from PubMed

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.

A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site., Jacewicz A, Trzemecka A, Guja KE, Plochocka D, Yakubovskaya E, Bebenek A, Garcia-Diaz M, PLoS One. 2013 Oct 7;8(10):e76700. doi: 10.1371/journal.pone.0076700. PMID:24116139

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Function

[DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.

About this Structure

4i9q is a 6 chain structure with sequence from Enterobacteria phage rb69. Full crystallographic information is available from OCA.

Reference

  • Jacewicz A, Trzemecka A, Guja KE, Plochocka D, Yakubovskaya E, Bebenek A, Garcia-Diaz M. A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site. PLoS One. 2013 Oct 7;8(10):e76700. doi: 10.1371/journal.pone.0076700. PMID:24116139 doi:http://dx.doi.org/10.1371/journal.pone.0076700

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