3CVV

Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion and F0 cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes.

Glas, A.F.Maul, M.J.Cryle, M.Barends, T.R.Schneider, S.Kaya, E.Schlichting, I.Carell, T.

(2009) Proc.Natl.Acad.Sci.USA 106: 11540-11545

  • DOI: 10.1073/pnas.0812665106

  • PubMed Abstract: 
  • Archae possess unique biochemical systems quite distinct from the pathways present in eukaryotes and eubacteria. 7,8-Dimethyl-8-hydroxy-5deazaflavin (F(0)) and F(420) are unique deazaflavin-containing coenzyme and methanogenic signature molecules, es ...

    Archae possess unique biochemical systems quite distinct from the pathways present in eukaryotes and eubacteria. 7,8-Dimethyl-8-hydroxy-5deazaflavin (F(0)) and F(420) are unique deazaflavin-containing coenzyme and methanogenic signature molecules, essential for a variety of biochemical transformations associated with methane biosynthesis and light-dependent DNA repair. The deazaflavin cofactor system functions during methane biosynthesis as a low-potential hydrid shuttle F(420)/F(420)H(2). In DNA photolyase repair proteins, the deazaflavin cofactor is in the deprotonated state active as a light-collecting energy transfer pigment. As such, it converts blue sunlight into energy used by the proteins to drive an essential repair process. Analysis of a eukaryotic (6-4) DNA photolyase from Drosophila melanogaster revealed a binding pocket, which tightly binds F(0). Residues in the pocket activate the cofactor by deprotonation so that light absorption and energy transfer are switched on. The crystal structure of F(0) in complex with the D. melanogaster protein shows the atomic details of F(0) binding and activation, allowing characterization of the residues involved in F(0) activation. The results show that the F(0)/F(420) coenzyme system, so far believed to be strictly limited to the archael kingdom of life, is far more widespread than anticipated. Analysis of a D. melanogaster extract and of a DNA photolyase from the primitive eukaryote Ostreococcus tauri provided direct proof for the presence of the F(0) cofactor also in higher eukaryotes.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, Centre for Integrative Protein Science, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RE11660p
A
543Drosophila melanogasterMutation(s): 0 
Gene Names: phr6-4
Find proteins for Q8SXK5 (Drosophila melanogaster)
Go to UniProtKB:  Q8SXK5
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DGP*DGP*(64T)P*(5PY)P*DGP*DCP*DAP*DGP*DGP*DT)-3')C15N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DAP*DCP*DCP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DTP*DG)-3')D15N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FO1
Query on FO1

Download SDF File 
Download CCD File 
A
1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol
7,8-didemethyl-8-hydroxy-5-deazariboflavin
C16 H17 N3 O7
AUEILLWDYUBWCM-XQQFMLRXSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
64T
Query on 64T
C
DNA LINKINGC10 H17 N2 O9 PDT
5PY
Query on 5PY
C
DNA LINKINGC10 H15 N2 O7 PDT
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FO1Kd: 8600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.590α = 90.00
b = 91.070β = 90.00
c = 88.260γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description