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PDBsum entry 1u3c
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Signaling protein PDB id
1u3c

 

 

 

 

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Contents
Protein chain
485 a.a. *
Ligands
FAD
NDS
HEZ
Metals
_MG ×3
_CL
Waters ×68
* Residue conservation analysis
PDB id:
1u3c
Name: Signaling protein
Title: Crystal structure of the phr domain of cryptochrome 1 from arabidopsis thaliana
Structure: Cryptochrome 1 apoprotein. Chain: a. Fragment: phr domain, residues 1-509. Synonym: blue light photoreceptor. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: cry1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
2.60Å     R-factor:   0.205     R-free:   0.254
Authors: C.A.Brautigam,B.S.Smith,Z.Ma,M.Palnitkar,D.R.Tomchick,M.Machius, J.Deisenhofer
Key ref:
C.A.Brautigam et al. (2004). Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana. Proc Natl Acad Sci U S A, 101, 12142-12147. PubMed id: 15299148 DOI: 10.1073/pnas.0404851101
Date:
21-Jul-04     Release date:   24-Aug-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q43125  (CRY1_ARATH) -  Cryptochrome-1 from Arabidopsis thaliana
Seq:
Struc: 		 
Seq:
Struc: 		681 a.a.
485 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1073/pnas.0404851101 Proc Natl Acad Sci U S A 101:12142-12147 (2004)
PubMed id: 15299148  
 
 
Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana.
C.A.Brautigam, B.S.Smith, Z.Ma, M.Palnitkar, D.R.Tomchick, M.Machius, J.Deisenhofer.
 
  ABSTRACT  
 
Signals generated by cryptochrome (CRY) blue-light photoreceptors are responsible for a variety of developmental and circadian responses in plants. The CRYs are also identified as circadian blue-light photoreceptors in Drosophila and components of the mammalian circadian clock. These flavoproteins all have an N-terminal domain that is similar to photolyase, and most have an additional C-terminal domain of variable length. We present here the crystal structure of the photolyase-like domain of CRY-1 from Arabidopsis thaliana. The structure reveals a fold that is very similar to photolyase, with a single molecule of FAD noncovalently bound to the protein. The surface features of the protein and the dissimilarity of a surface cavity to that of photolyase account for its lack of DNA-repair activity. Previous in vitro experiments established that the photolyase-like domain of CRY-1 can bind Mg.ATP, and we observe a single molecule of an ATP analog bound in the aforementioned surface cavity, near the bound FAD cofactor. The structure has implications for the signaling mechanism of CRY blue-light photoreceptors.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structure of CRY1-PHR and its disulfide bond. (A) The structure of CRY1-PHR. Green, helices; purple, -strands; dark blue, loop regions; orange, FAD cofactor; light blue, AMP-PNP, which is not bound in the native structure. (B) The disulfide bond in CRY1-PHR. The side chains of Cys-80 and Cys-190 are shown, with the carbons in dark blue and the sulfurs in yellow. Superimposed is a simulated-annealing omit map (F[o] - F[c], contoured at 3 ) (28). Figs. 1 and 3 were generated by using PYMOL. 		Figure 2.
Fig. 2. Surface features near to the FAD-access cavity. Shown are the surfaces of CRY1-PHR (A) and photolyase (B). The electrostatic potential is color-coded on the surface, with red and blue representing areas of negative and positive electrostatic potential, respectively. White line, boundary of the FAD-access cavities in both parts. Figs. 2 and 5C were generated by using GRASP (29).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22388820 D.Wu, Q.Hu, Z.Yan, W.Chen, C.Yan, X.Huang, J.Zhang, P.Yang, H.Deng, J.Wang, X.Deng, and Y.Shi (2012).
Structural basis of ultraviolet-B perception by UVR8.
  Nature, 484, 214-219.
PDB codes: 4dnu 4dnv 4dnw
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.  
21187431 N.Ozturk, C.P.Selby, Y.Annayev, D.Zhong, and A.Sancar (2011).
Reaction mechanism of Drosophila cryptochrome.
  Proc Natl Acad Sci U S A, 108, 516-521.  
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.  
20821290 D.Chao, and H.Lin (2010).
The tricks plants use to reach appropriate light.
  Sci China Life Sci, 53, 916-926.  
20840750 N.Ozber, I.Baris, G.Tatlici, I.Gur, S.Kilinc, E.B.Unal, and I.H.Kavakli (2010).
Identification of two amino acids in the C-terminal domain of mouse CRY2 essential for PER2 interaction.
  BMC Mol Biol, 11, 69.  
20529902 R.Yang, and Z.Su (2010).
Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation.
  Bioinformatics, 26, i168-i174.  
20926618 V.Exner, C.Alexandre, G.Rosenfeldt, P.Alfarano, M.Nater, A.Caflisch, W.Gruissem, A.Batschauer, and L.Hennig (2010).
A gain-of-function mutation of Arabidopsis cryptochrome1 promotes flowering.
  Plant Physiol, 154, 1633-1645.  
19129499 C.T.Rodgers, and P.J.Hore (2009).
Chemical magnetoreception in birds: the radical pair mechanism.
  Proc Natl Acad Sci U S A, 106, 353-360.  
19527640 I.A.Solov'yov, and K.Schulten (2009).
Magnetoreception through cryptochrome may involve superoxide.
  Biophys J, 96, 4804-4813.  
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.  
19359474 K.Hitomi, L.DiTacchio, A.S.Arvai, J.Yamamoto, S.T.Kim, T.Todo, J.A.Tainer, S.Iwai, S.Panda, and E.D.Getzoff (2009).
Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes.
  Proc Natl Acad Sci U S A, 106, 6962-6967.
PDB code: 3fy4
19487120 M.Müller, and T.Carell (2009).
Structural biology of DNA photolyases and cryptochromes.
  Curr Opin Struct Biol, 19, 277-285.  
19243237 T.Senda, M.Senda, S.Kimura, and T.Ishida (2009).
Redox control of protein conformation in flavoproteins.
  Antioxid Redox Signal, 11, 1741-1766.  
18682397 A.Sancar (2008).
Structure and function of photolyase and in vivo enzymology: 50th anniversary.
  J Biol Chem, 283, 32153-32157.  
18988809 H.Liu, X.Yu, K.Li, J.Klejnot, H.Yang, D.Lisiero, and C.Lin (2008).
Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis.
  Science, 322, 1535-1539.  
18494763 K.Zikihara, T.Ishikawa, T.Todo, and S.Tokutomi (2008).
Involvement of electron transfer in the photoreaction of zebrafish Cryptochrome-DASH.
  Photochem Photobiol, 84, 1016-1023.  
18597555 N.Hoang, E.Schleicher, S.Kacprzak, J.P.Bouly, M.Picot, W.Wu, A.Berndt, E.Wolf, R.Bittl, and M.Ahmad (2008).
Human and Drosophila cryptochromes are light activated by flavin photoreduction in living cells.
  PLoS Biol, 6, e160.  
17981903 O.Efimova, and P.J.Hore (2008).
Role of exchange and dipolar interactions in the radical pair model of the avian magnetic compass.
  Biophys J, 94, 1565-1574.  
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
18500802 Y.T.Kao, C.Tan, S.H.Song, N.Oztürk, J.Li, L.Wang, A.Sancar, and D.Zhong (2008).
Ultrafast dynamics and anionic active states of the flavin cofactor in cryptochrome and photolyase.
  J Am Chem Soc, 130, 7695-7701.  
18028200 A.Losi (2007).
Flavin-based Blue-Light photosensors: a photobiophysics update.
  Photochem Photobiol, 83, 1283-1300.  
17259272 I.A.Solov'yov, D.E.Chandler, and K.Schulten (2007).
Magnetic field effects in Arabidopsis thaliana cryptochrome-1.
  Biophys J, 92, 2711-2726.  
17971869 M.Liedvogel, K.Maeda, K.Henbest, E.Schleicher, T.Simon, C.R.Timmel, P.J.Hore, and H.Mouritsen (2007).
Chemical magnetoreception: bird cryptochrome 1a is excited by blue light and forms long-lived radical-pairs.
  PLoS ONE, 2, e1106.  
18419269 N.Oztürk, S.H.Song, S.Ozgür, C.P.Selby, L.Morrison, C.Partch, D.Zhong, and A.Sancar (2007).
Structure and function of animal cryptochromes.
  Cold Spring Harb Symp Quant Biol, 72, 119-131.  
17438275 X.Yu, D.Shalitin, X.Liu, M.Maymon, J.Klejnot, H.Yang, J.Lopez, X.Zhao, K.T.Bendehakkalu, and C.Lin (2007).
Derepression of the NC80 motif is critical for the photoactivation of Arabidopsis CRY2.
  Proc Natl Acad Sci U S A, 104, 7289-7294.  
17018288 A.G.Ladurner (2006).
Rheostat control of gene expression by metabolites.
  Mol Cell, 24, 1.  
17073458 S.Ozgür, and A.Sancar (2006).
Analysis of autophosphorylating kinase activities of Arabidopsis and human cryptochromes.
  Biochemistry, 45, 13369-13374.  
17101984 Y.Huang, R.Baxter, B.S.Smith, C.L.Partch, C.L.Colbert, and J.Deisenhofer (2006).
Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity.
  Proc Natl Acad Sci U S A, 103, 17701-17706.
PDB code: 2ijg
16686694 Y.Kubo, M.Akiyama, Y.Fukada, and T.Okano (2006).
Molecular cloning, mRNA expression, and immunocytochemical localization of a putative blue-light photoreceptor CRY4 in the chicken pineal gland.
  J Neurochem, 97, 1155-1165.  
16164372 C.L.Partch, and A.Sancar (2005).
Photochemistry and photobiology of cryptochrome blue-light photopigments: the search for a photocycle.
  Photochem Photobiol, 81, 1291-1304.  
15892880 C.Lin, and T.Todo (2005).
The cryptochromes.
  Genome Biol, 6, 220.  
16010344 M.Fischer, and A.Bacher (2005).
Biosynthesis of flavocoenzymes.
  Nat Prod Rep, 22, 324-350.  
15924418 S.Anderson, V.Dragnea, S.Masuda, J.Ybe, K.Moffat, and C.Bauer (2005).
Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides.
  Biochemistry, 44, 7998-8005.
PDB code: 1yrx
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 codes are shown on the right.

 

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