PDBsum entry 6aeh

Transferase

PDB id: 6aeh

Contents

Protein chain

329 a.a.

Ligands

UTP

SO4 ×7

Metals

_MN ×2

Waters ×391

PDB id:

6aeh

Name:

Transferase

Title:

Binary complex of human DNA polymerase mu with mnutp

Structure:

DNA-directed DNA/RNA polymerase mu. Chain: a. Synonym: pol mu,terminal transferase. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polm, polmu. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.64Å R-factor: 0.210 R-free: 0.245

Authors:

Y.K.Chang,W.J.Wu,M.D.Tsai

Key ref:

Y.K.Chang et al. (2019). Human DNA Polymerase μ Can Use a Noncanonical Mechanism for Multiple Mn²⁺-Mediated Functions. J Am Chem Soc, 141, 8489-8502. PubMed id: 31067051 DOI: 10.1021/jacs.9b01741

Date:

04-Aug-18 Release date: 29-May-19

Protein chain

Q9NP87  (DPOLM_HUMAN) -  DNA-directed DNA/RNA polymerase mu from Homo sapiens

Seq: 494 a.a.

Struc: 329 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/jacs.9b01741

J Am Chem Soc 141:8489-8502 (2019)

PubMed id: 31067051

Human DNA Polymerase μ Can Use a Noncanonical Mechanism for Multiple Mn²⁺-Mediated Functions.

Y.K.Chang, Y.P.Huang, X.X.Liu, T.P.Ko, Y.Bessho, Y.Kawano, M.Maestre-Reyna, W.J.Wu, M.D.Tsai.

ABSTRACT

Recent research on the structure and mechanism of DNA polymerases has continued to generate fundamentally important features, including a noncanonical pathway involving "prebinding" of metal-bound dNTP (MdNTP) in the absence of DNA. While this noncanonical mechanism was shown to be a possible subset for African swine fever DNA polymerase X (Pol X) and human Pol λ, it remains unknown whether it could be the primary pathway for a DNA polymerase. Pol μ is a unique member of the X-family with multiple functions and with unusual Mn²⁺ preference. Here we report that Pol μ not only prebinds MdNTP in a catalytically active conformation but also exerts a Mn²⁺ over Mg²⁺ preference at this early stage of catalysis, for various functions: incorporation of dNTP into a single nucleotide gapped DNA, incorporation of rNTP in the nonhomologous end joining (NHEJ) repair, incorporation of dNTP to an ssDNA, and incorporation of an 8-oxo-dGTP opposite template dA (mismatched) or dC (matched). The structural basis of this noncanonical mechanism and Mn²⁺ over Mg²⁺ preference in these functions was analyzed by solving 19 structures of prebinding binary complexes, precatalytic ternary complexes, and product complexes. The results suggest that the noncanonical pathway is functionally relevant for the multiple functions of Pol μ. Overall, this work provides the structural and mechanistic basis for the long-standing puzzle in the Mn²⁺ preference of Pol μ and expands the landscape of the possible mechanisms of DNA polymerases to include both mechanistic pathways.