5TXX

DNA Polymerase Mu Pre-Catalytic Ground State Ternary Complex, Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.948 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.

Jamsen, J.A.Beard, W.A.Pedersen, L.C.Shock, D.D.Moon, A.F.Krahn, J.M.Bebenek, K.Kunkel, T.A.Wilson, S.H.

(2017) Nat Commun 8: 253-253

  • DOI: 10.1038/s41467-017-00271-7
  • Primary Citation of Related Structures:  5TXZ, 5TYB, 5TYC, 5TYD, 5TYE, 5TYF, 5TYG, 5TYU, 5TYV, 5TYW, 5TYX, 5TYY, 5TYZ

  • PubMed Abstract: 
  • DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of cata ...

    DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PPi. The product metal is not observed during DNA synthesis in the presence of magnesium. Kinetic analyses indicate that manganese increases the rate constant for deoxynucleoside 5'-triphosphate insertion compared to magnesium. The likely product stabilization role of the manganese product metal in pol μ is discussed. These observations provide insight on structural attributes of this X-family double-strand break repair polymerase that impact its biological function in genome maintenance.DNA polymerase (pol) μ functions in DNA double-strand break repair. Here the authors use time-lapse X-ray crystallography to capture the states of pol µ during the conversion from pre-catalytic to product complex and observe a third transiently bound metal ion in the product state.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed DNA/RNA polymerase mu
A
356Homo sapiensGene 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')T9unidentified
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*A)-3')P4unidentified
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*CP*G)-3')D4unidentified
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
NA
Query on NA

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

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TTP
Query on TTP

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Download CCD File 
A
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.948 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.538α = 90.00
b = 68.243β = 90.00
c = 110.200γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesZ01-ES050158

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release