5U9H

DNA polymerase beta product complex with inserted Sp-isomer of dCTP-alpha-S

Summary for 5U9H

• Entry DOI: 10.2210/pdb5u9h/pdb
• Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(C7R))-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... (8 entities in total)
• Functional Keywords: transferase, lyase, dna, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 48433.83

Authors

Freudenthal, B.D.,Wilson, S.H.,Beard, W.A. (deposition date: 2016-12-16, release date: 2017-02-08, Last modification date: 2023-10-04)

Primary citation

Perera, L.,Freudenthal, B.D.,Beard, W.A.,Pedersen, L.G.,Wilson, S.H.
Revealing the role of the product metal in DNA polymerase beta catalysis.
Nucleic Acids Res., 45:2736-2745, 2017

PubMed Abstract: DNA polymerases catalyze a metal-dependent nucleotidyl transferase reaction during extension of a DNA strand using the complementary strand as a template. The reaction has long been considered to require two magnesium ions. Recently, a third active site magnesium ion was identified in some DNA polymerase product crystallographic structures, but its role is not known. Using quantum mechanical/ molecular mechanical calculations of polymerase β, we find that a third magnesium ion positioned near the newly identified product metal site does not alter the activation barrier for the chemical reaction indicating that it does not have a role in the forward reaction. This is consistent with time-lapse crystallographic structures following insertion of Sp-dCTPαS. Although sulfur substitution deters product metal binding, this has only a minimal effect on the rate of the forward reaction. Surprisingly, monovalent sodium or ammonium ions, positioned in the product metal site, lowered the activation barrier. These calculations highlight the impact that an active site water network can have on the energetics of the forward reaction and how metals or enzyme side chains may interact with the network to modulate the reaction barrier. These results also are discussed in the context of earlier findings indicating that magnesium at the product metal position blocks the reverse pyrophosphorolysis reaction.

PubMed: 28108654
DOI: 10.1093/nar/gkw1363

Experimental method

X-RAY DIFFRACTION (1.85 Å)