PDBsum entry 5tyc

Transferase/DNA

PDB id: 5tyc

Contents

Protein chain

327 a.a.

DNA/RNA

Ligands

PPV

TTP

EPE

DTT

EDO

Metals

_CA

_MG ×2

_NA

Waters ×323

PDB id:

5tyc

Name:

Transferase/DNA

Title:

DNA polymerase mu reactant complex, 10mm mg2+ (15 min)

Structure:

DNA-directed DNA/RNA polymerase mu. Chain: a. Fragment: unp residues 132-494. Synonym: pol mu,terminal transferase. Engineered: yes. DNA (5'-d( Cp Gp Gp Cp Ap Tp Ap Cp G)-3'). Chain: t. Engineered: yes. DNA (5'-d( Cp Gp Tp Ap T)-3').

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polm, polmu. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: codonplus-ril. Synthetic: yes. Unidentified.

Resolution:

2.10Å R-factor: 0.198 R-free: 0.237

Authors:

J.A.Jamsen,S.H.Wilson

Key ref:

J.A.Jamsen et al. (2017). Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Nat Commun, 8, 253. PubMed id: 28811466

Date:

19-Nov-16 Release date: 30-Aug-17

Protein chain

Q9NP87  (DPOLM_HUMAN) -  DNA-directed DNA/RNA polymerase mu from Homo sapiens

Seq: 494 a.a.

Struc: 327 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-G-G-C-A-T-A-C-G 9 bases

C-G-T-A-T 5 bases

G-C-C-G 4 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PPV) corresponds exactly) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Nat Commun 8:253 (2017)

PubMed id: 28811466

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

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

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_i. 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.