6AKH

Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Adenine and Incoming Mn-dUMPNPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

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

(2019) J.Am.Chem.Soc. 141: 8489-8502

  • DOI: 10.1021/jacs.9b01741
  • Primary Citation of Related Structures:  

  • PubMed 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 noncan ...

    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 Mn 2+ preference. Here we report that Pol μ not only prebinds MdNTP in a catalytically active conformation but also exerts a Mn 2+ over Mg 2+ 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 Mn 2+ over Mg 2+ 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 Mn 2+ preference of Pol μ and expands the landscape of the possible mechanisms of DNA polymerases to include both mechanistic pathways.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica , 128 Academia Road Sec. 2 , Nankang, Taipei 115 , Taiwan.,Institute of Biochemical Sciences , National Taiwan University , Taipei 106 , Taiwan.,RIKEN SPring-8 Center , 1-1-1 Kouto , Sayo , Hyogo 679-5148 , Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed DNA/RNA polymerase mu
A
356Homo sapiensMutation(s): 0 
Gene Names: POLM (polmu)
EC: 2.7.7.7
Find proteins for Q9NP87 (Homo sapiens)
Go to Gene View: POLM
Go to UniProtKB:  Q9NP87
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')T9synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*A)-3')P4synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*CP*G)-3')D4synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP

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Download CCD File 
A
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
 Ligand Interaction
EPE
Query on EPE

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Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, T
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.838α = 90.00
b = 68.800β = 90.00
c = 109.680γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-12
    Type: Data collection, Database references