(6-4) Photolyase Crystal Structure

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 

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Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes.

Hitomi, K.DiTacchio, L.Arvai, A.S.Yamamoto, J.Kim, S.T.Todo, T.Tainer, J.A.Iwai, S.Panda, S.Getzoff, E.D.

(2009) Proc Natl Acad Sci U S A 106: 6962-6967

  • DOI: https://doi.org/10.1073/pnas.0809180106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Homologous flavoproteins from the photolyase (PHR)/cryptochrome (CRY) family use the FAD cofactor in PHRs to catalyze DNA repair and in CRYs to tune the circadian clock and control development. To help address how PHR/CRY members achieve these diverse functions, we determined the crystallographic structure of Arabidopsis thaliana (6-4) PHR (UVR3), which is strikingly (>65%) similar in sequence to human circadian clock CRYs. The structure reveals a substrate-binding cavity specific for the UV-induced DNA lesion, (6-4) photoproduct, and cofactor binding sites different from those of bacterial PHRs and consistent with distinct mechanisms for activities and regulation. Mutational analyses were combined with this prototypic structure for the (6-4) PHR/clock CRY cluster to identify structural and functional motifs: phosphate-binding and Pro-Lys-Leu protrusion motifs constricting access to the substrate-binding cavity above FAD, sulfur loop near the external end of the Trp electron-transfer pathway, and previously undefined C-terminal helix. Our results provide a detailed, unified framework for investigations of (6-4) PHRs and the mammalian CRYs. Conservation of key residues and motifs controlling FAD access and activities suggests that regulation of FAD redox properties and radical stability is essential not only for (6-4) photoproduct DNA repair, but also for circadian clock-regulating CRY functions. The structural and functional results reported here elucidate archetypal relationships within this flavoprotein family and suggest how PHRs and CRYs use local residue and cofactor tuning, rather than larger structural modifications, to achieve their diverse functions encompassing DNA repair, plant growth and development, and circadian clock regulation.

  • Organizational Affiliation

    Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-4 photolyase
A, B, C
537Arabidopsis thalianaMutation(s): 0 
Gene Names: 6-4 PHOTOLYASEUVR3At3g15620SJ11.2
Find proteins for O48652 (Arabidopsis thaliana)
Explore O48652 
Go to UniProtKB:  O48652
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO48652
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth B],
V [auth C]
C27 H33 N9 O15 P2
Query on MES

Download Ideal Coordinates CCD File 
G [auth A],
O [auth B],
T [auth C]
C6 H13 N O4 S
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A],
P [auth B],
U [auth C]
O4 P
Query on IMD

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
J [auth B]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
R [auth C],
S [auth C]
C3 H5 N2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.447α = 90
b = 139.033β = 90
c = 143.118γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance