6FN0

The animal-like Cryptochrome from Chlamydomonas reinhardtii in complex with 6-4 DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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Literature

Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii.

Franz, S., Ignatz, E., Wenzel, S., Zielosko, H., Putu, E.P.G.N., Maestre-Reyna, M., Tsai, M.D., Yamamoto, J., Mittag, M., Essen, L.O.

(2018) Nucleic Acids Res 46: 8010-8022

  • DOI: https://doi.org/10.1093/nar/gky621
  • Primary Citation of Related Structures:  
    5ZM0, 6FN0, 6FN2, 6FN3

  • PubMed Abstract: 

    • Photolyases and cryptochromes form an almost ubiquitous family of blue light photoreceptors involved in the repair and maintenance of DNA integrity or regulatory control. We found that one cryptochrome from the green alga Chlamydomonas reinhardtii (CraCRY) is capable of both, control of transcript levels and the sexual cycle of the alga in a positive (germination) and negative manner (mating ability), as well as catalyzing the repair of UV-DNA lesions ...

    Photolyases and cryptochromes form an almost ubiquitous family of blue light photoreceptors involved in the repair and maintenance of DNA integrity or regulatory control. We found that one cryptochrome from the green alga Chlamydomonas reinhardtii (CraCRY) is capable of both, control of transcript levels and the sexual cycle of the alga in a positive (germination) and negative manner (mating ability), as well as catalyzing the repair of UV-DNA lesions. Its 1.6 Å crystal structure shows besides the FAD chromophore an aromatic tetrad that is indispensable in animal-like type I cryptochromes for light-driven change of their signaling-active redox state and formation of a stable radical pair. Given CraCRY's catalytic activity as (6-4) photolyase in vivo and in vitro, we present the first co-crystal structure of a cryptochrome with duplex DNA comprising a (6-4) pyrimidine-pyrimidone lesion. This 2.9 Å structure reveals a distinct conformation for the catalytic histidine His1, H357, that challenges previous models of a single-photon driven (6-4) photolyase mechanism.

    Organizational Affiliation: 

    LOEWE Center of Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cryptochrome photoreceptorA499Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: UVR3, CHLREDRAFT_206002, CHLRE_06g278251v5
UniProt
Find proteins for A8J8W0 (Chlamydomonas reinhardtii)
Explore A8J8W0 
Go to UniProtKB:  A8J8W0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8J8W0
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*GP*CP*GP*GP*(64T)P*(5PY)P*GP*CP*CP*GP*TP*G)-3')B [auth C]14Chlamydomonas reinhardtii
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*CP*GP*GP*CP*AP*AP*CP*CP*GP*CP*TP*G)-3')C [auth D]14Chlamydomonas reinhardtii
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
D [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
1PE
Query on 1PE
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J [auth D]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
MES
Query on MES
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E [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
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F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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I [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
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G [auth C],
H [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.24α = 90
b = 146.24β = 90
c = 67.44γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR 1261-2

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references