5TYF

DNA Polymerase Mu Product Complex, 10 mM Mg2+ (270 min)

Summary for 5TYF

• Entry DOI: 10.2210/pdb5tyf/pdb
• Related: 5TXX 5TXZ 5TYB 5TYC 5TYD 5TYF 5TYG 5TYU 5TYV 5TYW 5TYX 5TYY 5TYZ
• Descriptor: DNA-directed DNA/RNA polymerase mu, GLYCOLIC ACID, DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3'), ... (11 entities in total)
• Functional Keywords: time-lapse crystallography, product metal, dna polymerase mu, double strand break repair, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 46145.11

Authors

Jamsen, J.A.,Wilson, S.H. (deposition date: 2016-11-19, release date: 2017-08-30, Last modification date: 2023-11-15)

Primary citation

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.
Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.
Nat Commun, 8:253-253, 2017

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 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 PP. 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.

PubMed: 28811466
DOI: 10.1038/s41467-017-00271-7

Experimental method

X-RAY DIFFRACTION (1.971 Å)