5HP4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Direct observation of DNA threading in flap endonuclease complexes.

AlMalki, F.A.Flemming, C.S.Zhang, J.Feng, M.Sedelnikova, S.E.Ceska, T.Rafferty, J.B.Sayers, J.R.Artymiuk, P.J.

(2016) Nat.Struct.Mol.Biol. 23: 640-646

  • DOI: 10.1038/nsmb.3241
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Maintenance of genome integrity requires that branched nucleic acid molecules be accurately processed to produce double-helical DNA. Flap endonucleases are essential enzymes that trim such branched molecules generated by Okazaki-fragment synthesis du ...

    Maintenance of genome integrity requires that branched nucleic acid molecules be accurately processed to produce double-helical DNA. Flap endonucleases are essential enzymes that trim such branched molecules generated by Okazaki-fragment synthesis during replication. Here, we report crystal structures of bacteriophage T5 flap endonuclease in complexes with intact DNA substrates and products, at resolutions of 1.9-2.2 Å. They reveal single-stranded DNA threading through a hole in the enzyme, which is enclosed by an inverted V-shaped helical arch straddling the active site. Residues lining the hole induce an unusual barb-like conformation in the DNA substrate, thereby juxtaposing the scissile phosphate and essential catalytic metal ions. A series of complexes and biochemical analyses show how the substrate's single-stranded branch approaches, threads through and finally emerges on the far side of the enzyme. Our studies suggest that substrate recognition involves an unusual 'fly-casting, thread, bend and barb' mechanism.


    Organizational Affiliation

    Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exodeoxyribonuclease
A
272Escherichia phage T5Mutation(s): 1 
Gene Names: D15 (exo5)
EC: 3.1.11.-
Find proteins for P06229 (Escherichia phage T5)
Go to UniProtKB:  P06229
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3')X17synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
X
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
X
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.510α = 90.00
b = 67.510β = 90.00
c = 187.810γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Taif UniversitySaudi ArabiaSchoalrship
University of SheffieldUnited KingdomScholarship

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2016-06-22
    Type: Database references
  • Version 1.3: 2016-07-20
    Type: Database references