5KT6

Teranry complex of human DNA polymerase iota(1-445) inserting dCMPNPP opposite template G in the presence of Mg2+

Summary for 5KT6

• Entry DOI: 10.2210/pdb5kt6/pdb
• Related: 5KT2 5KT3 5KT4 5KT5 5KT7
• Descriptor: DNA (5'-D(P*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'), DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3'), DNA polymerase iota, ... (5 entities in total)
• Functional Keywords: dna polymerase, poli, magnesium, transferase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 55103.02

Authors

Choi, J.Y.,Patra, A.,Yeom, M.,Lee, Y.S.,Zhang, Q.,Egli, M.,Guengerich, F.P. (deposition date: 2016-07-11, release date: 2016-08-31, Last modification date: 2024-03-06)

Primary citation

Choi, J.Y.,Patra, A.,Yeom, M.,Lee, Y.S.,Zhang, Q.,Egli, M.,Guengerich, F.P.
Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota.
J.Biol.Chem., 291:21063-21073, 2016

PubMed Abstract: DNA polymerase (pol) ι is a Y-family polymerase involved in translesion synthesis, exhibiting higher catalytic activity with Mn than Mg The human germline R96G variant impairs both Mn-dependent and Mg-dependent activities of pol ι, whereas the Δ1-25 variant selectively enhances its Mg-dependent activity. We analyzed pre-steady-state kinetic and structural effects of these two metal ions and genetic variations on pol ι using pol ι core (residues 1-445) proteins. The presence of Mn (0.15 mm) instead of Mg (2 mm) caused a 770-fold increase in efficiency (k/K) of pol ι for dCTP insertion opposite G, mainly due to a 450-fold decrease in K The R96G and Δ1-25 variants displayed a 53-fold decrease and a 3-fold increase, respectively, in k/K for dCTP insertion opposite G with Mg when compared with wild type, substantially attenuated by substitution with Mn Crystal structures of pol ι ternary complexes, including the primer terminus 3'-OH and a non-hydrolyzable dCTP analogue opposite G with the active-site Mg or Mn, revealed that Mn achieves more optimal octahedral coordination geometry than Mg, with lower values in average coordination distance geometry in the catalytic metal A-site. Crystal structures of R96G revealed the loss of three H-bonds of residues Gly-96 and Tyr-93 with an incoming dNTP, due to the lack of an arginine, as well as a destabilized Tyr-93 side chain secondary to the loss of a cation-π interaction between both side chains. These results provide a mechanistic basis for alteration in pol ι catalytic function with coordinating metals and genetic variation.

PubMed: 27555320
DOI: 10.1074/jbc.M116.748285

Experimental method

X-RAY DIFFRACTION (3.54 Å)