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Title: Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase

Abstract

Two divalent metal ions are required for primer-extension catalyzed by DNA polymerases. One metal ion brings the 3'-hydroxyl of the primer terminus and the {alpha}-phosphorus atom of incoming dNTP together for bond formation so that the catalytically relevant conformation of the triphosphate tail of the dNTP is in an {alpha},{beta},{gamma}-tridentate coordination complex with the second metal ion required for proper substrate alignment. A probable base selectivity mechanism derived from structural studies on Dpo4 suggests that the inability of mispaired dNTPs to form a substrate-aligned, tridentate coordination complex could effectively cause the mispaired dNTPs to be rejected before catalysis. Nevertheless, we found that mispaired dNTPs can actually form a properly aligned tridentate coordination complex. However, complementary dNTPs occasionally form misaligned complexes with mutant RB69 DNA polymerases (RB69pols) that are not in a tridentate coordination state. Here, we report finding a {beta},{gamma}-bidentate coordination complex that contained the complementary dUpNpp opposite dA in the structure of a ternary complex formed by the wild type RB69pol at 1.88 {angstrom} resolution. Our observations suggest that several distinct metal-ion coordination states can exist at the ground state in the polymerase active site and that base selectivity is unlikely to be based on metal-ion coordination alone.

Authors:
; ; ;  [1]
  1. Yale
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
FOREIGNNIH
OSTI Identifier:
1034949
Resource Type:
Journal Article
Journal Name:
Protein Science
Additional Journal Information:
Journal Volume: 21; Journal Issue: 3
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; ALIGNMENT; ATOMS; CATALYSIS; DNA POLYMERASES; GROUND STATES; MUTANTS; POLYMERASES; RESOLUTION; SUBSTRATES

Citation Formats

Xia, Shuangluo, Eom, Soo Hyun, Konigsberg, William H, Wang, Jimin, and Gwangju). Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase. United States: N. p., 2012. Web. doi:10.1002/pro.2026.
Xia, Shuangluo, Eom, Soo Hyun, Konigsberg, William H, Wang, Jimin, & Gwangju). Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase. United States. https://doi.org/10.1002/pro.2026
Xia, Shuangluo, Eom, Soo Hyun, Konigsberg, William H, Wang, Jimin, and Gwangju). 2012. "Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase". United States. https://doi.org/10.1002/pro.2026.
@article{osti_1034949,
title = {Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase},
author = {Xia, Shuangluo and Eom, Soo Hyun and Konigsberg, William H and Wang, Jimin and Gwangju)},
abstractNote = {Two divalent metal ions are required for primer-extension catalyzed by DNA polymerases. One metal ion brings the 3'-hydroxyl of the primer terminus and the {alpha}-phosphorus atom of incoming dNTP together for bond formation so that the catalytically relevant conformation of the triphosphate tail of the dNTP is in an {alpha},{beta},{gamma}-tridentate coordination complex with the second metal ion required for proper substrate alignment. A probable base selectivity mechanism derived from structural studies on Dpo4 suggests that the inability of mispaired dNTPs to form a substrate-aligned, tridentate coordination complex could effectively cause the mispaired dNTPs to be rejected before catalysis. Nevertheless, we found that mispaired dNTPs can actually form a properly aligned tridentate coordination complex. However, complementary dNTPs occasionally form misaligned complexes with mutant RB69 DNA polymerases (RB69pols) that are not in a tridentate coordination state. Here, we report finding a {beta},{gamma}-bidentate coordination complex that contained the complementary dUpNpp opposite dA in the structure of a ternary complex formed by the wild type RB69pol at 1.88 {angstrom} resolution. Our observations suggest that several distinct metal-ion coordination states can exist at the ground state in the polymerase active site and that base selectivity is unlikely to be based on metal-ion coordination alone.},
doi = {10.1002/pro.2026},
url = {https://www.osti.gov/biblio/1034949}, journal = {Protein Science},
number = 3,
volume = 21,
place = {United States},
year = {Tue Feb 21 00:00:00 EST 2012},
month = {Tue Feb 21 00:00:00 EST 2012}
}