› 5hp4

X-ray diffraction
1.86Å resolution

Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product complex with DNA and metal ions

Released:
DOI: 10.2210/pdb5hp4/pdb
PDB entry 5hp4 coloured by chain, front view.
PDB entry 5hp4 coloured by chain, side view.
PDB entry 5hp4 coloured by chain, top view.
Source organisms:
Primary publication:
Direct observation of DNA threading in flap endonuclease complexes.
AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ
Nat Struct Mol Biol 23 640-6 (2016)
PMID: 27273516

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118750 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Flap endonuclease Chain: A
Molecule details ›
Chain: A
Length: 272 amino acids
Theoretical weight: 31.28 KDa
Source organism: Escherichia virus T5
Expression system: Escherichia coli
UniProt:
  • Canonical: P06229 (Residues: 20-291; Coverage: 94%)
Gene names: D15, T5.130, T5p128, exo5
Sequence domains:
Structure domains:
DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3') Chain: X
Molecule details ›
Chain: X
Length: 17 nucleotides
Theoretical weight: 5.2 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand CA 2 x CA
Ligand NA 1 x NA
Ligand K 1 x K
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P43212
Unit cell:
a: 67.51Å b: 67.51Å c: 187.81Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.158 0.188
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria.
McLean et al. (2022)
20 other articles

2 mentions without citation

Direct observation of DNA threading in flap endonuclease complexes.
AlMalki et al. (2016)
1 more