CRYD_ARATH
ID CRYD_ARATH Reviewed; 569 AA.
AC Q84KJ5; F4KIJ6; Q8VZD8;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Cryptochrome DASH, chloroplastic/mitochondrial;
DE AltName: Full=Cryptochrome-3;
DE Flags: Precursor;
GN Name=CRYD; Synonyms=CRY3; OrderedLocusNames=At5g24850; ORFNames=F6A4.60;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 14-569.
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 45-569.
RX PubMed=12535521; DOI=10.1016/s1097-2765(03)00008-x;
RA Brudler R., Hitomi K., Daiyasu H., Toh H., Kucho K., Ishiura M.,
RA Kanehisa M., Roberts V.A., Todo T., Tainer J.A., Getzoff E.D.;
RT "Identification of a new cryptochrome class. Structure, function, and
RT evolution.";
RL Mol. Cell 11:59-67(2003).
RN [5]
RP COFACTOR, SUBCELLULAR LOCATION, LACK OF PHOTOLYASE ACTIVITY, AND BINDING TO
RP SINGLE-STRANDED AND DOUBLE-STRANDED DNA.
RX PubMed=12834405; DOI=10.1046/j.1365-313x.2003.01787.x;
RA Kleine T., Lockhart P., Batschauer A.;
RT "An Arabidopsis protein closely related to Synechocystis cryptochrome is
RT targeted to organelles.";
RL Plant J. 35:93-103(2003).
RN [6]
RP FUNCTION.
RX PubMed=17062752; DOI=10.1073/pnas.0607993103;
RA Selby C.P., Sancar A.;
RT "A cryptochrome/photolyase class of enzymes with single-stranded DNA-
RT specific photolyase activity.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:17696-17700(2006).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 44-569.
RX PubMed=17101984; DOI=10.1073/pnas.0608554103;
RA Huang Y., Baxter R., Smith B.S., Partch C.L., Colbert C.L., Deisenhofer J.;
RT "Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its
RT implications for photolyase activity.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:17701-17706(2006).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 45-569, SUBUNIT, AND MUTAGENESIS
RP OF GLU-193.
RX PubMed=17188299; DOI=10.1016/j.jmb.2006.11.066;
RA Klar T., Pokorny R., Moldt J., Batschauer A., Essen L.-O.;
RT "Cryptochrome 3 from Arabidopsis thaliana: structural and functional
RT analysis of its complex with a folate light antenna.";
RL J. Mol. Biol. 366:954-964(2007).
CC -!- FUNCTION: May have a photoreceptor function. Binds ss- and ds-DNA in a
CC sequence non-specific manner. Has a photolyase activity specific for
CC cyclobutane pyrimidine dimers in ssDNA. {ECO:0000269|PubMed:17062752}.
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:12834405};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:12834405};
CC -!- COFACTOR:
CC Name=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate;
CC Xref=ChEBI:CHEBI:15636; Evidence={ECO:0000269|PubMed:12834405};
CC Note=Binds 1 5,10-methenyltetrahydrofolate (MTHF) per subunit.
CC {ECO:0000269|PubMed:12834405};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17188299}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:12834405}. Mitochondrion
CC {ECO:0000269|PubMed:12834405}.
CC -!- MISCELLANEOUS: 5,10-methenyltetrahydrofolate (MTHF) acts as a
CC functional antenna for the photoreduction of FAD.
CC -!- SIMILARITY: Belongs to the DNA photolyase class-1 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAL57669.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AF069716; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED93369.2; -; Genomic_DNA.
DR EMBL; AY065032; AAL57669.1; ALT_INIT; mRNA.
DR EMBL; AY102138; AAM26705.1; -; mRNA.
DR EMBL; AB062926; BAC65244.1; -; mRNA.
DR RefSeq; NP_568461.3; NM_122394.4.
DR PDB; 2IJG; X-ray; 2.10 A; X=44-569.
DR PDB; 2J4D; X-ray; 1.90 A; A/B=45-569.
DR PDB; 2VTB; X-ray; 2.01 A; A/B/C/D/E/F=44-569.
DR PDBsum; 2IJG; -.
DR PDBsum; 2J4D; -.
DR PDBsum; 2VTB; -.
DR AlphaFoldDB; Q84KJ5; -.
DR SMR; Q84KJ5; -.
DR BioGRID; 17829; 1.
DR DIP; DIP-48661N; -.
DR STRING; 3702.AT5G24850.1; -.
DR PaxDb; Q84KJ5; -.
DR PRIDE; Q84KJ5; -.
DR ProteomicsDB; 220350; -.
DR EnsemblPlants; AT5G24850.1; AT5G24850.1; AT5G24850.
DR GeneID; 832554; -.
DR Gramene; AT5G24850.1; AT5G24850.1; AT5G24850.
DR KEGG; ath:AT5G24850; -.
DR Araport; AT5G24850; -.
DR eggNOG; KOG0133; Eukaryota.
DR HOGENOM; CLU_010348_6_2_1; -.
DR InParanoid; Q84KJ5; -.
DR OMA; FLMECLV; -.
DR OrthoDB; 378952at2759; -.
DR PhylomeDB; Q84KJ5; -.
DR BRENDA; 4.1.99.3; 399.
DR EvolutionaryTrace; Q84KJ5; -.
DR PRO; PR:Q84KJ5; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q84KJ5; baseline and differential.
DR Genevisible; Q84KJ5; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0003913; F:DNA photolyase activity; IEA:InterPro.
DR GO; GO:0071949; F:FAD binding; IBA:GO_Central.
DR GO; GO:0009881; F:photoreceptor activity; IEA:UniProtKB-KW.
DR GO; GO:0000719; P:photoreactive repair; IMP:CACAO.
DR Gene3D; 3.40.50.620; -; 1.
DR InterPro; IPR014133; Cry_DASH.
DR InterPro; IPR036134; Crypto/Photolyase_FAD-like_sf.
DR InterPro; IPR036155; Crypto/Photolyase_N_sf.
DR InterPro; IPR005101; Cryptochr/Photolyase_FAD-bd.
DR InterPro; IPR002081; Cryptochrome/DNA_photolyase_1.
DR InterPro; IPR006050; DNA_photolyase_N.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR PANTHER; PTHR11455; PTHR11455; 1.
DR Pfam; PF00875; DNA_photolyase; 1.
DR Pfam; PF03441; FAD_binding_7; 1.
DR PRINTS; PR00147; DNAPHOTLYASE.
DR SUPFAM; SSF48173; SSF48173; 1.
DR SUPFAM; SSF52425; SSF52425; 1.
DR TIGRFAMs; TIGR02765; crypto_DASH; 1.
DR PROSITE; PS51645; PHR_CRY_ALPHA_BETA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Chloroplast; Chromophore; DNA-binding; FAD;
KW Flavoprotein; Mitochondrion; Nucleotide-binding; Photoreceptor protein;
KW Plastid; Receptor; Reference proteome; Sensory transduction;
KW Transit peptide.
FT TRANSIT 1..?
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN ?..569
FT /note="Cryptochrome DASH, chloroplastic/mitochondrial"
FT /id="PRO_0000235318"
FT DOMAIN 84..221
FT /note="Photolyase/cryptochrome alpha/beta"
FT REGION 541..569
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 316
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 329..333
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 436
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 466
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 468
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 485
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MUTAGEN 193
FT /note="E->A: Loss of binding of the MTHF cofactor."
FT /evidence="ECO:0000269|PubMed:17188299"
FT STRAND 48..52
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 56..70
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:2VTB"
FT STRAND 85..92
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 100..107
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 110..118
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:2J4D"
FT TURN 127..129
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 136..155
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 161..165
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 167..178
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 181..186
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 191..205
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 212..216
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 219..222
FT /evidence="ECO:0007829|PDB:2IJG"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 231..233
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 238..248
FT /evidence="ECO:0007829|PDB:2J4D"
FT TURN 276..280
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 288..292
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 296..307
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 313..315
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 316..319
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 324..326
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 333..337
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 343..356
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 361..383
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 384..387
FT /evidence="ECO:0007829|PDB:2J4D"
FT TURN 390..395
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 404..411
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 418..430
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 435..447
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 453..463
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 469..479
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 483..485
FT /evidence="ECO:0007829|PDB:2VTB"
FT HELIX 486..488
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 494..501
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 506..511
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 513..515
FT /evidence="ECO:0007829|PDB:2J4D"
FT TURN 520..524
FT /evidence="ECO:0007829|PDB:2J4D"
FT HELIX 527..530
FT /evidence="ECO:0007829|PDB:2J4D"
FT STRAND 539..541
FT /evidence="ECO:0007829|PDB:2VTB"
SQ SEQUENCE 569 AA; 64983 MW; 5C4E4BD9B45D22C6 CRC64;
MAASSLSLSS PLSNPLRRFT LHHLHLSKKP LSSSSLFLCS AAKMNDHIHR VPALTEEEID
SVAIKTFERY ALPSSSSVKR KGKGVTILWF RNDLRVLDND ALYKAWSSSD TILPVYCLDP
RLFHTTHFFN FPKTGALRGG FLMECLVDLR KNLMKRGLNL LIRSGKPEEI LPSLAKDFGA
RTVFAHKETC SEEVDVERLV NQGLKRVGNS TKLELIWGST MYHKDDLPFD VFDLPDVYTQ
FRKSVEAKCS IRSSTRIPLS LGPTPSVDDW GDVPTLEKLG VEPQEVTRGM RFVGGESAGV
GRVFEYFWKK DLLKVYKETR NGMLGPDYST KFSPWLAFGC ISPRFIYEEV QRYEKERVAN
NSTYWVLFEL IWRDYFRFLS IKCGNSLFHL GGPRNVQGKW SQDQKLFESW RDAKTGYPLI
DANMKELSTT GFMSNRGRQI VCSFLVRDMG LDWRMGAEWF ETCLLDYDPC SNYGNWTYGA
GVGNDPREDR YFSIPKQAQN YDPEGEYVAF WLQQLRRLPK EKRHWPGRLM YMDTVVPLKH
GNGPMAGGSK SGGGFRGSHS GRRSRHNGP
