Reviewed, UniProtKB/Swiss-Prot Q43125 (CRY1_ARATH)

Names and origin

Protein names

Recommended name:
    Cryptochrome-1
Alternative name(s):
    Blue light photoreceptor
    Protein OUT OF PHASE 2
      Short name=OOP2
    Protein BLUE LIGHT UNINHIBITED 1
    Protein ELONGATED HYPOCOTYL 4

Gene names

Name:	CRY1
Synonyms:	BLU1, HY4
Ordered Locus Names:	At4g08920
ORF Names:	T3H13.5, T3H13.14

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	681 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Mediates blue light-induced gene expression through the inhibition of COP1-mediated degradation of the transcription factor BIT1. Involved in blue light-dependent stomatal opening, CHS gene expression, inhibition of stem growth and increase of root growth. Ref.4 Ref.6 Ref.13 Ref.16 Ref.18
Cofactor	Binds 1 FAD per subunit. Ref.4 Binds 1 5,10-methenyltetrahydrofolate (MTHF) per subunit. Ref.4
Enzyme regulation	Light exposure induces a conformational change in the C-terminal domain CCT1 required for activity. Ref.14
Subunit structure	Homodimer. Interacts with ADO1, COP1 and PHYA. Ref.7 Ref.8 Ref.9 Ref.10 Ref.15
Subcellular location	Cytoplasm. Nucleus. Note: The nuclear pool is involved in hypocotyl and petiole growth inhibition and anthocyanin production, while the cytoplasmic pool is involved in root growth and cotyledon expansion. Ref.17
Tissue specificity	Widely expressed.
Domain	The N-terminal domain CNT1 (1-489) is sufficient for autophosphorylation and is required for dimerization. The C-terminal domain CCT1 (490-681) of the homodimer binds to COP1.
Post-translational modification	Autophosphorylated; in response to blue light. Ref.7 Ref.11 Ref.12
Disruption phenotype	Plants show reduced root elongation in blue light. Ref.16
Sequence similarities	Belongs to the DNA photolyase class-1 family. Contains 1 DNA photolyase domain.
Caution	Was originally (Ref.1) thought to be a DNA photolyase.
Sequence caution	The sequence AAB28725.2 differs from that shown. Reason: Frameshift at position 546. The sequence AAD17364.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence CAB78016.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Sensory transduction
Cellular component	Cytoplasm Nucleus
Ligand	ATP-binding Chromophore FAD Flavoprotein Nucleotide-binding
Molecular function	Photoreceptor protein Receptor
PTM	Disulfide bond Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: InterPro anthocyanin metabolic process Inferred from mutant phenotype. Source: TAIR blue light signaling pathway Traceable author statement. Source: TAIR circadian regulation of calcium ion oscillation Inferred from mutant phenotype. Source: TAIR oxidation reduction Inferred from mutant phenotype. Source: TAIR protein amino acid autophosphorylation Ref.12 Inferred from direct assay. Source: TAIR protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW regulation of meristem growth Inferred from genetic interaction. Source: TAIR response to water deprivation Ref.13 Inferred from genetic interaction. Source: TAIR singlet oxygen-mediated programmed cell death Inferred from mutant phenotype. Source: TAIR stomatal movement Ref.13 Inferred from genetic interaction. Source: TAIR
Cellular component	cytoplasm Ref.17 Inferred from direct assay. Source: TAIR nucleus Inferred from direct assay. Source: TAIR
Molecular function	ATP binding Ref.12 Inferred from direct assay. Source: TAIR DNA photolyase activity Inferred from electronic annotation. Source: InterPro blue light photoreceptor activity Ref.5 Inferred from mutant phenotype. Source: TAIR protein homodimerization activity Ref.15 Inferred from physical interaction. Source: TAIR protein kinase activity Ref.12 Inferred from direct assay. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		3	EBI-300703,EBI-300703
ADO1	Q94BT6	1	EBI-300703,EBI-300691

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 681

681

Cryptochrome-1

PRO_0000085121

Regions

Nucleotide binding

247 – 251

5

FAD

Sites

Binding site

235

1

FAD

Binding site

359

1

ATP

Binding site

359

1

FAD

Binding site

360

1

ATP

Binding site

390

1

FAD; via carbonyl oxygen

Binding site

392

1

FAD; via amide nitrogen

Binding site

409

1

ATP

Amino acid modifications

Disulfide bond

80 ↔ 190

Experimental info

Mutagenesis

66

1

S → N: Loss of dimerization and activity. Ref.15

Mutagenesis

340

1

G → E: Loss of activity. Ref.6

Mutagenesis

347

1

G → R: Loss of dimerization and activity. Ref.15

Mutagenesis

462

1

A → V: Loss of dimerization and activity. Ref.15

Sequence conflict

40

1

I → N in AAK32756. Ref.3

Sequence conflict

654

1

R → G in AAM70572. Ref.3

Secondary structure

1

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681

Helix Strand Turn

Details...

Beta strand

14 – 20

7

Helix

28 – 36

9

Beta strand

39 – 45

7

Helix

47 – 50

4

Helix

57 – 76

20

Beta strand

81 – 85

5

Helix

89 – 100

12

Beta strand

104 – 108

5

Helix

113 – 127

15

Turn

128 – 130

3

Beta strand

132 – 136

5

Helix

144 – 146

3

Beta strand

150 – 152

3

Helix

158 – 166

9

Helix

187 – 189

3

Helix

200 – 206

7

Helix

209 – 212

4

Helix

217 – 228

12

Helix

231 – 234

4

Turn

235 – 240

6

Beta strand

242 – 244

3

Helix

251 – 255

5

Helix

261 – 278

18

Helix

281 – 305

25

Turn

308 – 312

5

Turn

318 – 321

4

Helix

328 – 336

9

Helix

342 – 354

13

Helix

359 – 371

13

Helix

377 – 387

11

Helix

393 – 404

12

Helix

419 – 426

8

Helix

431 – 436

6

Helix

438 – 440

3

Helix

445 – 448

4

Turn

451 – 453

3

Helix

456 – 462

7

Turn

467 – 469

3

Helix

477 – 495

19

Sequences

	Sequence		Length	Mass (Da)
	Q43125-1 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 372A7E798D6FC076	FASTA	681	76,794
	10 20 30 40 50 60 MSGSVSGCGS GGCSIVWFRR DLRVEDNPAL AAAVRAGPVI ALFVWAPEEE GHYHPGRVSR 70 80 90 100 110 120 WWLKNSLAQL DSSLRSLGTC LITKRSTDSV ASLLDVVKST GASQIFFNHL YDPLSLVRDH 130 140 150 160 170 180 RAKDVLTAQG IAVRSFNADL LYEPWEVTDE LGRPFSMFAA FWERCLSMPY DPESPLLPPK 190 200 210 220 230 240 KIISGDVSKC VADPLVFEDD SEKGSNALLA RAWSPGWSNG DKALTTFING PLLEYSKNRR 250 260 270 280 290 300 KADSATTSFL SPHLHFGEVS VRKVFHLVRI KQVAWANEGN EAGEESVNLF LKSIGLREYS 310 320 330 340 350 360 RYISFNHPYS HERPLLGHLK FFPWAVDENY FKAWRQGRTG YPLVDAGMRE LWATGWLHDR 370 380 390 400 410 420 IRVVVSSFFV KVLQLPWRWG MKYFWDTLLD ADLESDALGW QYITGTLPDS REFDRIDNPQ 430 440 450 460 470 480 FEGYKFDPNG EYVRRWLPEL SRLPTDWIHH PWNAPESVLQ AAGIELGSNY PLPIVGLDEA 490 500 510 520 530 540 KARLHEALSQ MWQLEAASRA AIENGSEEGL GDSAEVEEAP IEFPRDITME ETEPTRLNPN 550 560 570 580 590 600 RRYEDQMVPS ITSSLIRPEE DEESSLNLRN SVGDSRAEVP RNMVNTNQAQ QRRAEPASNQ 610 620 630 640 650 660 VTAMIPEFNI RIVAESTEDS TAESSSSGRR ERSGGIVPEW SPGYSEQFPS EENRIGGGST 670 680 TSSYLQNHHE ILNWRRLSQT G

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor." Ahmad M., Cashmore A.R. Nature 366:162-166(1993) [PubMed: 8232555] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Columbia.
[2]	"Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana." Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B. , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R. Nature 402:769-777(1999) [PubMed: 10617198] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[4]	"Putative blue-light photoreceptors from Arabidopsis thaliana and Sinapis alba with a high degree of sequence homology to DNA photolyase contain the two photolyase cofactors but lack DNA repair activity." Malhotra K., Kim S.-T., Batschauer A., Dawut L., Sancar A. Biochemistry 34:6892-6899(1995) [PubMed: 7756321] [Abstract] Cited for: FUNCTION, COFACTOR.
[5]	"Arabidopsis cryptochrome 1 is a soluble protein mediating blue light-dependent regulation of plant growth and development." Lin C., Ahmad M., Cashmore A.R. Plant J. 10:893-902(1996) [PubMed: 8953250] [Abstract] Cited for: CHARACTERIZATION.
[6]	"Cryptochrome blue-light photoreceptors of Arabidopsis implicated in phototropism." Ahmad M., Jarillo J.A., Smirnova O., Cashmore A.R. Nature 392:720-723(1998) [PubMed: 9565033] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF GLY-340.
[7]	"The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in vitro." Ahmad M., Jarillo J.A., Smirnova O., Cashmore A.R. Mol. Cell 1:939-948(1998) [PubMed: 9651577] [Abstract] Cited for: INTERACTION WITH PHYA, PHOSPHORYLATION.
[8]	"An Arabidopsis circadian clock component interacts with both CRY1 and phyB." Jarillo J.A., Capel J., Tang R.-H., Yang H.-Q., Alonso J.M., Ecker J.R., Cashmore A.R. Nature 410:487-490(2001) [PubMed: 11260718] [Abstract] Cited for: INTERACTION WITH ADO1.
[9]	"Direct interaction of Arabidopsis cryptochromes with COP1 in light control development." Wang H., Ma L.-G., Li J.-M., Zhao H.-Y., Deng X.W. Science 294:154-158(2001) [PubMed: 11509693] [Abstract] Cited for: INTERACTION WITH COP1.
[10]	"The signaling mechanism of Arabidopsis CRY1 involves direct interaction with COP1." Yang H.-Q., Tang R.-H., Cashmore A.R. Plant Cell 13:2573-2587(2001) [PubMed: 11752373] [Abstract] Cited for: INTERACTION WITH COP1.
[11]	"Blue light-dependent in vivo and in vitro phosphorylation of Arabidopsis cryptochrome 1." Shalitin D., Yu X., Maymon M., Mockler T., Lin C. Plant Cell 15:2421-2429(2003) [PubMed: 14523249] [Abstract] Cited for: PHOSPHORYLATION.
[12]	"Novel ATP-binding and autophosphorylation activity associated with Arabidopsis and human cryptochrome-1." Bouly J.-P., Giovani B., Djamei A., Mueller M., Zeugner A., Dudkin E.A., Batschauer A., Ahmad M. Eur. J. Biochem. 270:2921-2928(2003) [PubMed: 12846824] [Abstract] Cited for: PHOSPHORYLATION.
[13]	"A role for Arabidopsis cryptochromes and COP1 in the regulation of stomatal opening." Mao J., Zhang Y.C., Sang Y., Li Q.H., Yang H.Q. Proc. Natl. Acad. Sci. U.S.A. 102:12270-12275(2005) [PubMed: 16093319] [Abstract] Cited for: FUNCTION.
[14]	"Role of structural plasticity in signal transduction by the cryptochrome blue-light photoreceptor." Partch C.L., Clarkson M.W., Ozgur S., Lee A.L., Sancar A. Biochemistry 44:3795-3805(2005) [PubMed: 15751956] [Abstract] Cited for: ENZYME REGULATION.
[15]	"N-terminal domain-mediated homodimerization is required for photoreceptor activity of Arabidopsis CRYPTOCHROME 1." Sang Y., Li Q.-H., Rubio V., Zhang Y.-C., Mao J., Deng X.-W., Yang H.-Q. Plant Cell 17:1569-1584(2005) [PubMed: 15805487] [Abstract] Cited for: SUBUNIT, MUTAGENESIS OF SER-66; GLY-347 AND ALA-462.
[16]	"Cryptochrome photoreceptors cry1 and cry2 antagonistically regulate primary root elongation in Arabidopsis thaliana." Canamero R.C., Bakrim N., Bouly J.-P., Garay A., Dudkin E.E., Habricot Y., Ahmad M. Planta 224:995-1003(2006) [PubMed: 16703358] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[17]	"Separate functions for nuclear and cytoplasmic cryptochrome 1 during photomorphogenesis of Arabidopsis seedlings." Wu G., Spalding E.P. Proc. Natl. Acad. Sci. U.S.A. 104:18813-18818(2007) [PubMed: 18003924] [Abstract] Cited for: SUBCELLULAR LOCATION.
[18]	"CRY1 inhibits COP1-mediated degradation of BIT1, a MYB transcription factor, to activate blue light-dependent gene expression in Arabidopsis." Hong S.H., Kim H.J., Ryu J.S., Choi H., Jeong S., Shin J., Choi G., Nam H.G. Plant J. 55:361-371(2008) [PubMed: 18397371] [Abstract] Cited for: FUNCTION.
[19]	"Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana." Brautigam C.A., Smith B.S., Ma Z., Palnitkar M., Tomchick D.R., Machius M., Deisenhofer J. Proc. Natl. Acad. Sci. U.S.A. 101:12142-12147(2004) [PubMed: 15299148] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 1-509 IN COMPLEX WITH FAD AND ATP, BINDING SITES.

Cross-references

Sequence databases

EMBLGenBankDDBJ

S66907 mRNA. Translation: AAB28724.1.
S66909 mRNA. Translation: AAB28725.2. Frameshift.
AF128396 Genomic DNA. Translation: AAD17364.1. Sequence problems.
AL161513 Genomic DNA. Translation: CAB78016.1. Sequence problems.
AF361588 mRNA. Translation: AAK32756.1.
AY124863 mRNA. Translation: AAM70572.1.

IPI

IPI00529765.

PIR

H85089.
S39058.

UniGene

At.27730
At.71242

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1U3C	X-ray	2.60	A	1-509	[»]
1U3D	X-ray	2.45	A	1-509	[»]

DisProt

DP00474.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q43125. 3 interactions.

Proteomic databases

PRIDE

Q43125.

Genome annotation databases

GenomeReviews

Gene locus AT4G08920 in contig CT486007_GR.

Organism-specific databases

TAIR

At4g08920.

Gene expression databases

ArrayExpress

Q43125.

GermOnline

AT4G08920. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR002081. Cryptochrome/DNA_photolyase_1.
IPR014134. Cryptochrome_pln.
IPR018394. DNA_photolyase_1_CS_C.
IPR006050. DNA_photolyase_N.
IPR005101. Photolyase_FAD-bd/Cryptochr_C.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]

Gene3D

G3DSA:3.40.50.620. Rossmann-like_a/b/a_fold. 1 hit.

Pfam

PF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 1 hit.
[Graphical view]

PRINTS

PR00147. DNAPHOTLYASE.

ProDom

PD004390. FAD_binding_N. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR02766. crypt_chrom_pln. 1 hit.

PROSITE

PS00394. DNA_PHOTOLYASES_1_1. 1 hit.
PS00691. DNA_PHOTOLYASES_1_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

CRY1_ARATH

Accession

Primary (citable) accession number: Q43125
Secondary accession number(s): Q43126 , Q8L7Y1, Q9ASZ2, Q9M0S9, Q9ZPF0

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	June 16, 2009
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)