› 5c51

X-ray diffraction
3.43Å resolution

Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma

Released:
DOI: 10.2210/pdb5c51/pdb
PDB entry 5c51 coloured by chain, front view.
PDB entry 5c51 coloured by chain, side view.
PDB entry 5c51 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase γ.
Sohl CD, Szymanski MR, Mislak AC, Shumate CK, Amiralaei S, Schinazi RF, Anderson KS, Yin YW
Proc Natl Acad Sci U S A 112 8596-601 (2015)
PMID: 26124101

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 pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118459 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase subunit gamma-1 Chain: A
Molecule details ›
Chain: A
Length: 1205 amino acids
Theoretical weight: 136.03 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: P54098 (Residues: 25-1239; Coverage: 97%)
Gene names: MDP1, POLG, POLG1, POLGA
Sequence domains: DNA mitochondrial polymerase exonuclease domain
DNA polymerase subunit gamma-2 Chains: B, C
Molecule details ›
Chains: B, C
Length: 485 amino acids
Theoretical weight: 54.99 KDa
Source organism: Homo sapiens
Expression system: Insect cell expression vector pTIE1
UniProt:
  • Canonical: Q9UHN1 (Residues: 1-485; Coverage: 100%)
Gene names: MTPOLB, POLG2
Sequence domains: Anticodon binding domain
Structure domains:
DNA (5'-D(*(AD)P*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 22 nucleotides
Theoretical weight: 6.78 KDa
DNA Chain: T
Molecule details ›
Chain: T
Length: 25 nucleotides
Theoretical weight: 7.67 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand 1RY 1 x 1RY
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P41212
Unit cell:
a: 215.049Å b: 215.049Å c: 161.692Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.316 0.315 0.345
Expression system: Insect cell expression vector pTIE1

Quick links

Citations

10 review citations

Mammalian Mitochondria and Aging: An Update.
Kauppila et al. (2017)
9 more

4 mentions without citation

Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase γ.
Sohl et al. (2015)
3 more