6IPD | pdb_00006ipd

Post-catalytic Complex of Human DNA Polymerase Mu with Templating Adenine and Mn-8oxodGMP

• PDB DOI: https://doi.org/10.2210/pdb6IPD/pdb
• NAKB: 6IPD

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-03 Released: 2019-05-29 
• Deposition Author(s): Chang, Y.K., Wu, W.J., Tsai, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.218 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

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

• PubMed: 31067051 
• DOI: https://doi.org/10.1021/jacs.9b01741
• Primary Citation Related Structures: 
  5ZLC, 6AEC, 6AEH, 6AK5, 6AK6, 6AK8, 6AK9, 6AKH, 6IPD, 6IPE, 6IPF, 6IPG, 6IPH, 6IPI, 6IPJ, 6IPK, 6IPL, 6IPM, 6IPN


• 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 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.19 kDa 
• Atom Count: 3,605 
• Modeled Residue Count: 344 
• Deposited Residue Count: 374 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed DNA/RNA polymerase mu	A	356	Homo sapiens	Mutation(s): 0  Gene Names: POLM, polmu EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP87 (Homo sapiens) Explore Q9NP87  Go to UniProtKB:  Q9NP87
PHAROS:  Q9NP87 GTEx:  ENSG00000122678

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')	B [auth T]	9	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')	C [auth P]	5	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*CP*G)-3')	D	4	synthetic construct

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	J [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
OXD	I [auth A]	OXALIC ACID C2 H2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-N
EDO	K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.218 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.68	α = 90
b = 68.671	β = 90
c = 109.576	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Chang, Y.K., Wu, W.J., Tsai, M.D.

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Derived calculations