CCD4_ARATH
ID CCD4_ARATH Reviewed; 595 AA.
AC O49675;
DT 01-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Probable carotenoid cleavage dioxygenase 4, chloroplastic {ECO:0000305};
DE Short=AtCCD4 {ECO:0000305};
DE EC=1.14.99.- {ECO:0000250|UniProtKB:O65572};
DE AltName: Full=AtNCED4 {ECO:0000303|PubMed:11532178, ECO:0000303|PubMed:15340011};
DE Flags: Precursor;
GN Name=CCD4;
GN Synonyms=NCED4 {ECO:0000303|PubMed:11532178, ECO:0000303|PubMed:15340011};
GN OrderedLocusNames=At4g19170 {ECO:0000312|Araport:AT4G19170};
GN ORFNames=T18B16.140 {ECO:0000312|EMBL:CAA16706.1};
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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].
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 [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP LACK OF INDUCTION BY DROUGHT STRESS.
RX PubMed=11532178; DOI=10.1046/j.1365-313x.2001.01096.x;
RA Iuchi S., Kobayashi M., Taji T., Naramoto M., Seki M., Kato T., Tabata S.,
RA Kakubari Y., Yamaguchi-Shinozaki K., Shinozaki K.;
RT "Regulation of drought tolerance by gene manipulation of 9-cis-
RT epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in
RT Arabidopsis.";
RL Plant J. 27:325-333(2001).
RN [6]
RP SUBCELLULAR LOCATION, AND INTERACTION WITH VAR3.
RX PubMed=15340011; DOI=10.1242/jcs.01360;
RA Naested H., Holm A., Jenkins T., Nielsen H.B., Harris C.A., Beale M.H.,
RA Andersen M., Mant A., Scheller H., Camara B., Mattsson O., Mundy J.;
RT "Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger
RT protein required for chloroplast and palisade cell development.";
RL J. Cell Sci. 117:4807-4818(2004).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=16461379; DOI=10.1104/pp.105.076083;
RA Ytterberg A.J., Peltier J.-B., van Wijk K.J.;
RT "Protein profiling of plastoglobules in chloroplasts and chromoplasts. A
RT surprising site for differential accumulation of metabolic enzymes.";
RL Plant Physiol. 140:984-997(2006).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=22274653; DOI=10.1104/pp.111.193144;
RA Lundquist P.K., Poliakov A., Bhuiyan N.H., Zybailov B., Sun Q.,
RA van Wijk K.J.;
RT "The functional network of the Arabidopsis plastoglobule proteome based on
RT quantitative proteomics and genome-wide coexpression analysis.";
RL Plant Physiol. 158:1172-1192(2012).
RN [9]
RP INTERACTION WITH PGM48.
RX PubMed=27895226; DOI=10.1105/tpc.16.00745;
RA Bhuiyan N.H., Friso G., Rowland E., Majsec K., van Wijk K.J.;
RT "The plastoglobule-localized metallopeptidase PGM48 is a positive regulator
RT of senescence in Arabidopsis thaliana.";
RL Plant Cell 28:3020-3037(2016).
RN [10]
RP TISSUE SPECIFICITY, AND DEGRADATION BY PGM48.
RX PubMed=28534654; DOI=10.1080/15592324.2017.1331197;
RA Bhuiyan N.H., van Wijk K.J.;
RT "Functions and substrates of plastoglobule-localized metallopeptidase
RT PGM48.";
RL Plant Signal. Behav. 12:e1331197-e1331197(2017).
CC -!- FUNCTION: May be involved in carotenoid cleavage.
CC {ECO:0000250|UniProtKB:O24592}.
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q28175};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q28175};
CC -!- SUBUNIT: Interacts with VAR3 (PubMed:15340011). Interacts with PGM48
CC (PubMed:27895226). {ECO:0000269|PubMed:15340011,
CC ECO:0000269|PubMed:27895226}.
CC -!- INTERACTION:
CC O49675; Q8S9K3: VAR3; NbExp=2; IntAct=EBI-632411, EBI-632401;
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast, plastoglobule
CC {ECO:0000269|PubMed:15340011, ECO:0000269|PubMed:16461379,
CC ECO:0000269|PubMed:22274653}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in flowers (e.g. sepals and
CC petals), siliques, seeds, leaves and cotyledons.
CC {ECO:0000269|PubMed:28534654}.
CC -!- INDUCTION: Probably proteolytically degraded by PGM48 during leaves
CC senescence (PubMed:28534654). Not induced by drought stress.
CC {ECO:0000269|PubMed:28534654}.
CC -!- SIMILARITY: Belongs to the carotenoid oxygenase family. {ECO:0000305}.
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DR EMBL; AL021687; CAA16706.1; -; Genomic_DNA.
DR EMBL; AL161550; CAB78919.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84154.1; -; Genomic_DNA.
DR EMBL; AY136353; AAM97019.1; -; mRNA.
DR EMBL; BT008785; AAP68224.1; -; mRNA.
DR EMBL; AY056789; AAL10480.1; -; mRNA.
DR EMBL; AK227175; BAE99215.1; -; mRNA.
DR PIR; T04438; T04438.
DR RefSeq; NP_193652.1; NM_118036.3.
DR AlphaFoldDB; O49675; -.
DR SMR; O49675; -.
DR BioGRID; 12948; 2.
DR IntAct; O49675; 2.
DR STRING; 3702.AT4G19170.1; -.
DR PaxDb; O49675; -.
DR PRIDE; O49675; -.
DR ProteomicsDB; 223960; -.
DR EnsemblPlants; AT4G19170.1; AT4G19170.1; AT4G19170.
DR GeneID; 827655; -.
DR Gramene; AT4G19170.1; AT4G19170.1; AT4G19170.
DR KEGG; ath:AT4G19170; -.
DR Araport; AT4G19170; -.
DR TAIR; locus:2134796; AT4G19170.
DR eggNOG; KOG1285; Eukaryota.
DR HOGENOM; CLU_016472_0_0_1; -.
DR InParanoid; O49675; -.
DR OMA; SGFMKPC; -.
DR OrthoDB; 524712at2759; -.
DR PhylomeDB; O49675; -.
DR BioCyc; ARA:AT4G19170-MON; -.
DR PRO; PR:O49675; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O49675; baseline and differential.
DR Genevisible; O49675; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0010287; C:plastoglobule; HDA:TAIR.
DR GO; GO:0010436; F:carotenoid dioxygenase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:1901811; P:beta-carotene catabolic process; IMP:TAIR.
DR GO; GO:0016121; P:carotene catabolic process; IBA:GO_Central.
DR InterPro; IPR004294; Carotenoid_Oase.
DR PANTHER; PTHR10543; PTHR10543; 1.
DR Pfam; PF03055; RPE65; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Dioxygenase; Iron; Metal-binding; Oxidoreductase; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..34
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 35..595
FT /note="Probable carotenoid cleavage dioxygenase 4,
FT chloroplastic"
FT /id="PRO_0000285993"
FT REGION 41..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 287
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:O24592"
FT BINDING 336
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:O24592"
FT BINDING 404
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:O24592"
FT BINDING 583
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:O24592"
SQ SEQUENCE 595 AA; 65602 MW; 711EDC4AF59920B9 CRC64;
MDSVSSSSFL SSTFSLHHSL LRRRSSSPTL LRINSAVVEE RSPITNPSDN NDRRNKPKTL
HNRTNHTLVS SPPKLRPEMT LATALFTTVE DVINTFIDPP SRPSVDPKHV LSDNFAPVLD
ELPPTDCEII HGTLPLSLNG AYIRNGPNPQ FLPRGPYHLF DGDGMLHAIK IHNGKATLCS
RYVKTYKYNV EKQTGAPVMP NVFSGFNGVT ASVARGALTA ARVLTGQYNP VNGIGLANTS
LAFFSNRLFA LGESDLPYAV RLTESGDIET IGRYDFDGKL AMSMTAHPKT DPITGETFAF
RYGPVPPFLT YFRFDSAGKK QRDVPIFSMT SPSFLHDFAI TKRHAIFAEI QLGMRMNMLD
LVLEGGSPVG TDNGKTPRLG VIPKYAGDES EMKWFEVPGF NIIHAINAWD EDDGNSVVLI
APNIMSIEHT LERMDLVHAL VEKVKIDLVT GIVRRHPISA RNLDFAVINP AFLGRCSRYV
YAAIGDPMPK ISGVVKLDVS KGDRDDCTVA RRMYGSGCYG GEPFFVARDP GNPEAEEDDG
YVVTYVHDEV TGESKFLVMD AKSPELEIVA AVRLPRRVPY GFHGLFVKES DLNKL
