4YD2

Nicked complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.471 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Creative template-dependent synthesis by human polymerase mu.

Moon, A.F.Gosavi, R.A.Kunkel, T.A.Pedersen, L.C.Bebenek, K.

(2015) Proc.Natl.Acad.Sci.USA 112: E4530-E4536

  • DOI: 10.1073/pnas.1505798112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Among the many proteins used to repair DNA double-strand breaks by nonhomologous end joining (NHEJ) are two related family X DNA polymerases, Pol λ and Pol µ. Which of these two polymerases is preferentially used for filling DNA gaps during NHEJ part ...

    Among the many proteins used to repair DNA double-strand breaks by nonhomologous end joining (NHEJ) are two related family X DNA polymerases, Pol λ and Pol µ. Which of these two polymerases is preferentially used for filling DNA gaps during NHEJ partly depends on sequence complementarity at the break, with Pol λ and Pol µ repairing complementary and noncomplementary ends, respectively. To better understand these substrate preferences, we present crystal structures of Pol µ on a 2-nt gapped DNA substrate, representing three steps of the catalytic cycle. In striking contrast to Pol λ, Pol µ "skips" the first available template nucleotide, instead using the template base at the 5' end of the gap to direct nucleotide binding and incorporation. This remarkable divergence from canonical 3'-end gap filling is consistent with data on end-joining substrate specificity in cells, and provides insights into polymerase substrate choices during NHEJ.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709.,Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709 pederse2@niehs.nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed DNA/RNA polymerase mu
A
354Homo 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*AP*T)-3')T10Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*AP*T)-3')P5Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*CP*G)-3')D4Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PPV
Query on PPV

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.471 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.083α = 90.00
b = 68.700β = 90.00
c = 114.977γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
Cootmodel building
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIA ES102645-03
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01 ES065070

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references
  • Version 1.2: 2015-08-26
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-18
    Type: Author supporting evidence