› 6p1u

X-ray diffraction
1.75Å resolution

Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated CMP

Released:
DOI: 10.2210/pdb6p1u/pdb
PDB entry 6p1u coloured by chain, front view.
PDB entry 6p1u coloured by chain, side view.
PDB entry 6p1u coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC
Nucleic Acids Res 47 9410-9422 (2019)
PMID: 31435651

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113238 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct DNA/RNA hybrid molecule
Macromolecules (4 distinct):
DNA-directed DNA/RNA polymerase mu Chain: A
Molecule details ›
Chain: A
Length: 354 amino acids
Theoretical weight: 39.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NP87 (Residues: 134-397, 411-494; Coverage: 70%)
Gene names: POLM, polmu
Sequence domains:
DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 9 nucleotides
Theoretical weight: 2.77 KDa
DNA (5'-D(P*GP*CP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 5 nucleotides
Theoretical weight: 1.5 KDa

Ligands and Environments

7 bound ligands:
Ligand MN 1 x MN
Ligand NA 3 x NA
Ligand CL 4 x CL
Ligand PPV 1 x PPV
Ligand CTP 1 x CTP
Ligand EPE 1 x EPE
Ligand EDO 1 x EDO
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 59.864Å b: 68.825Å c: 110.594Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.193
Expression system: Escherichia coli

Quick links

Citations

2 review citations

DNA polymerase mu: An inflexible scaffold for substrate flexibility.
Kaminski et al. (2020)
1 more

2 mentions without citation

Structural Insights into the Specificity of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Family X DNA Polymerases.
Kaminski et al. (2021)
1 more