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PDBsum entry 2j4d
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protein ligands Protein-protein interface(s) links
DNA binding protein PDB id
2j4d

 

 

 

 

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Contents
Protein chains
496 a.a. *
Ligands
FAD ×2
MHF ×2
Waters ×747
* Residue conservation analysis
PDB id:
2j4d
Name: DNA binding protein
Title: Cryptochrome 3 from arabidopsis thaliana
Structure: Cryptochrome dash. Chain: a, b. Fragment: mature protein without plastid import sequence, residues 45-569. Synonym: cryptochrome 3. Engineered: yes
Source: Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.189     R-free:   0.221
Authors: T.Klar,R.Pokorny,A.Batschauer,L.-O.Essen
Key ref:
T.Klar et al. (2007). Cryptochrome 3 from Arabidopsis thaliana: structural and functional analysis of its complex with a folate light antenna. J Mol Biol, 366, 954-964. PubMed id: 17188299 DOI: 10.1016/j.jmb.2006.11.066
Date:
28-Aug-06     Release date:   19-Jun-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q84KJ5  (CRYD_ARATH) -  Cryptochrome DASH, chloroplastic/mitochondrial from Arabidopsis thaliana
Seq:
Struc: 		 
Seq:
Struc: 		569 a.a.
496 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/j.jmb.2006.11.066 J Mol Biol 366:954-964 (2007)
PubMed id: 17188299  
 
 
Cryptochrome 3 from Arabidopsis thaliana: structural and functional analysis of its complex with a folate light antenna.
T.Klar, R.Pokorny, J.Moldt, A.Batschauer, L.O.Essen.
 
  ABSTRACT  
 
Cryptochromes are almost ubiquitous blue-light receptors and act in several species as central components of the circadian clock. Despite being evolutionary and structurally related with DNA photolyases, a class of light-driven DNA-repair enzymes, and having similar cofactor compositions, cryptochromes lack DNA-repair activity. Cryptochrome 3 from the plant Arabidopsis thaliana belongs to the DASH-type subfamily. Its crystal structure determined at 1.9 Angstroms resolution shows cryptochrome 3 in a dimeric state with the antenna cofactor 5,10-methenyltetrahydrofolate (MTHF) bound in a distance of 15.2 Angstroms to the U-shaped FAD chromophore. Spectroscopic studies on a mutant where a residue crucial for MTHF-binding, E149, was replaced by site-directed mutagenesis demonstrate that MTHF acts in cryptochrome 3 as a functional antenna for the photoreduction of FAD.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Overall structure of Arabidopsis cry3. The N-terminal antenna domain is shown in green, the FAD-binding domain in grey. The dimeric organisation is shown on the left. (b) Structural comparison of A. thaliana cry3 with CryDASH from S. sp. (magenta, 1NP7), A. thaliana cry1 (orange, 1U3D), E. coli DNA photolyase (blue, 1DNP) and A. nidulans photolyase (cyan, 1TEZ). The MTHF (orange), FAD (yellow) and 8-HDF chromophores (blue, from the A. nidulans DNA photolyase) are shown with their molecular surfaces. The N-terminal extension that is a unique feature of cry3 is coloured in red. (c) Chromophore arrangement in the E. coli DNA photolyase. This Figure and Figures 2, 3, 4 were prepared by PyMOL [http://www.pymol.org].
Figure 4.
Figure 4. The MTHF binding site of A. thaliana cry3. Stereo diagrams showing the MTHF binding site of (a) A. thaliana cry3 and (c) E. coli DNA photolyase. (b) Schematic diagram of MTHF–cry3 interactions.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 366, 954-964) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21526969 I.Chaves, R.Pokorny, M.Byrdin, N.Hoang, T.Ritz, K.Brettel, L.O.Essen, G.T.van der Horst, A.Batschauer, and M.Ahmad (2011).
The cryptochromes: blue light photoreceptors in plants and animals.
  Annu Rev Plant Biol, 62, 335-364.  
20192744 A.Möglich, X.Yang, R.A.Ayers, and K.Moffat (2010).
Structure and function of plant photoreceptors.
  Annu Rev Plant Biol, 61, 21-47.  
20418333 Y.J.Moon, E.M.Lee, Y.M.Park, Y.S.Park, W.I.Chung, and Y.H.Chung (2010).
The role of cyanopterin in UV/blue light signal transduction of cyanobacterium Synechocystis sp. PCC 6803 phototaxis.
  Plant Cell Physiol, 51, 969-980.  
19570997 A.F.Glas, M.J.Maul, M.Cryle, T.R.Barends, S.Schneider, E.Kaya, I.Schlichting, and T.Carell (2009).
The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes.
  Proc Natl Acad Sci U S A, 106, 11540-11545.
PDB code: 3cvv
19508644 A.K.Hendrischk, J.Moldt, S.W.Frühwirth, and G.Klug (2009).
Characterization of an unusual LOV domain protein in the alpha-proteobacterium Rhodobacter sphaeroides.
  Photochem Photobiol, 85, 1254-1259.  
19624734 E.Schleicher, R.Bittl, and S.Weber (2009).
New roles of flavoproteins in molecular cell biology: blue-light active flavoproteins studied by electron paramagnetic resonance.
  FEBS J, 276, 4290-4303.  
19531478 J.Moldt, R.Pokorny, C.Orth, U.Linne, Y.Geisselbrecht, M.A.Marahiel, L.O.Essen, and A.Batschauer (2009).
Photoreduction of the folate cofactor in members of the photolyase family.
  J Biol Chem, 284, 21670-21683.  
19487120 M.Müller, and T.Carell (2009).
Structural biology of DNA photolyases and cryptochromes.
  Curr Opin Struct Biol, 19, 277-285.  
19074258 R.Pokorny, T.Klar, U.Hennecke, T.Carell, A.Batschauer, and L.O.Essen (2008).
Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome.
  Proc Natl Acad Sci U S A, 105, 21023-21027.
PDB code: 2vtb
18028200 A.Losi (2007).
Flavin-based Blue-Light photosensors: a photobiophysics update.
  Photochem Photobiol, 83, 1283-1300.  
17355959 R.Banerjee, E.Schleicher, S.Meier, R.M.Viana, R.Pokorny, M.Ahmad, R.Bittl, and A.Batschauer (2007).
The signaling state of Arabidopsis cryptochrome 2 contains flavin semiquinone.
  J Biol Chem, 282, 14916-14922.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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