ID CKX3_ORYSJ Reviewed; 527 AA.
AC Q8LNV6; A0A0P0XVJ7; A3CF07;
DT 18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 24-JAN-2024, entry version 125.
DE RecName: Full=Cytokinin dehydrogenase 3 {ECO:0000303|PubMed:15976269};
DE EC=1.5.99.12 {ECO:0000269|PubMed:36031806};
DE AltName: Full=Cytokinin oxidase 3 {ECO:0000303|PubMed:15976269};
DE Short=OsCKX3 {ECO:0000303|PubMed:15976269};
DE Flags: Precursor;
GN Name=CKX3 {ECO:0000303|PubMed:15976269};
GN OrderedLocusNames=Os10g0483500 {ECO:0000312|EMBL:BAT11359.1},
GN LOC_Os10g34230 {ECO:0000312|EMBL:AAP54326.1};
GN ORFNames=OsJ_31929, OsJ_35246,
GN OSJNBa0012L23.33 {ECO:0000312|EMBL:AAM91887.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
RP REVIEW.
RX PubMed=12721786; DOI=10.1007/s10265-003-0096-4;
RA Schmuelling T., Werner T., Riefler M., Krupkova E., Bartrina y Manns I.;
RT "Structure and function of cytokinin oxidase/dehydrogenase genes of maize,
RT rice, Arabidopsis and other species.";
RL J. Plant Res. 116:241-252(2003).
RN [8]
RP TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
RC STRAIN=cv. Koshihikari;
RX PubMed=15976269; DOI=10.1126/science.1113373;
RA Ashikari M., Sakakibara H., Lin S., Yamamoto T., Takashi T., Nishimura A.,
RA Angeles E.R., Qian Q., Kitano H., Matsuoka M.;
RT "Cytokinin oxidase regulates rice grain production.";
RL Science 309:741-745(2005).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP TISSUE SPECIFICITY, INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=36031806; DOI=10.1093/plphys/kiac401;
RA Huang P., Zhao J., Hong J., Zhu B., Xia S., Engao Z., Han P., Zhang K.;
RT "Cytokinins regulate rice lamina joint development and leaf angle.";
RL Plant Physiol. 0:0-0(2022).
CC -!- FUNCTION: Catalyzes the oxidation of cytokinins, a family of N(6)-
CC substituted adenine derivatives, where the substituent is an
CC isopentenyl group (Probable). Cytokinins are plant hormones essential
CC for plant growth, development, and stress responses (Probable).
CC Exhibits specific activities toward trans-zeatin (tZ) and
CC isopentenyladenine (iP) (PubMed:36031806). Plays a role in lamina joint
CC inclination (PubMed:36031806). Regulates cell proliferation and
CC vascular bundle number on the abaxial side of lamina joint
CC (PubMed:36031806). {ECO:0000269|PubMed:36031806,
CC ECO:0000305|PubMed:36031806}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=A + H2O + N(6)-dimethylallyladenine = 3-methyl-2-butenal +
CC adenine + AH2; Xref=Rhea:RHEA:13625, ChEBI:CHEBI:13193,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15825, ChEBI:CHEBI:16708,
CC ChEBI:CHEBI:17499, ChEBI:CHEBI:17660; EC=1.5.99.12;
CC Evidence={ECO:0000269|PubMed:36031806};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:36031806};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.74 uM for trans-zeatin {ECO:0000269|PubMed:36031806};
CC KM=2.61 uM for isopentenyladenine {ECO:0000269|PubMed:36031806};
CC Vmax=2.6 nmol/min/mg enzyme with trans-zeatin as substrate
CC {ECO:0000269|PubMed:36031806};
CC Vmax=0.54 nmol/min/mg enzyme with isopentenyladenine as substrate
CC {ECO:0000269|PubMed:36031806};
CC -!- SUBUNIT: Monomer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum
CC {ECO:0000269|PubMed:36031806}.
CC -!- TISSUE SPECIFICITY: Expressed in inflorescence meristems
CC (PubMed:15976269). Highly expressed in lamina joints, and mainly in the
CC parenchyma cells and vascular bundles on the abaxial side of the lamina
CC joint (PubMed:36031806). Expressed in roots, stems, leaves and young
CC panicles (PubMed:36031806). {ECO:0000269|PubMed:15976269,
CC ECO:0000269|PubMed:36031806}.
CC -!- INDUCTION: Induced by isopentenyladenine, trans-zeatin and 24-
CC epibrassinolide. {ECO:0000269|PubMed:36031806}.
CC -!- DISRUPTION PHENOTYPE: Increased leaf erectness, asymmetric growth and
CC development of lamina joint. {ECO:0000269|PubMed:36031806}.
CC -!- MISCELLANEOUS: Plants over-expressing CKX3 exhibit decreased leaf
CC erectness. {ECO:0000269|PubMed:36031806}.
CC -!- SIMILARITY: Belongs to the oxygen-dependent FAD-linked oxidoreductase
CC family. {ECO:0000305}.
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DR EMBL; AC051632; AAM91887.1; -; Genomic_DNA.
DR EMBL; DP000086; AAP54326.1; -; Genomic_DNA.
DR EMBL; AP008216; BAF26800.1; -; Genomic_DNA.
DR EMBL; AP014966; BAT11359.1; -; Genomic_DNA.
DR EMBL; CM000147; EAZ16460.1; -; Genomic_DNA.
DR EMBL; CM000149; EAZ19670.1; -; Genomic_DNA.
DR EMBL; AK103272; BAG95988.1; -; mRNA.
DR RefSeq; XP_015613042.1; XM_015757556.1.
DR RefSeq; XP_015613043.1; XM_015757557.1.
DR RefSeq; XP_015613045.1; XM_015757559.1.
DR RefSeq; XP_015613046.1; XM_015757560.1.
DR AlphaFoldDB; Q8LNV6; -.
DR SMR; Q8LNV6; -.
DR STRING; 39947.Q8LNV6; -.
DR GlyCosmos; Q8LNV6; 1 site, No reported glycans.
DR PaxDb; 39947-Q8LNV6; -.
DR EnsemblPlants; Os10t0483500-01; Os10t0483500-01; Os10g0483500.
DR GeneID; 4348932; -.
DR Gramene; Os10t0483500-01; Os10t0483500-01; Os10g0483500.
DR KEGG; osa:4348932; -.
DR eggNOG; KOG1231; Eukaryota.
DR HOGENOM; CLU_024955_1_0_1; -.
DR InParanoid; Q8LNV6; -.
DR OMA; RNSGLWE; -.
DR OrthoDB; 455805at2759; -.
DR PlantReactome; R-OSA-9828944; Regulation of lemma joints development and leaf angle by cytokinin.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000007752; Chromosome 10.
DR Proteomes; UP000007752; Chromosome 12.
DR Proteomes; UP000059680; Chromosome 10.
DR Genevisible; Q8LNV6; OS.
DR GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
DR GO; GO:0019139; F:cytokinin dehydrogenase activity; IC:Gramene.
DR GO; GO:0071949; F:FAD binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0009690; P:cytokinin metabolic process; IEA:InterPro.
DR Gene3D; 3.30.465.10; -; 1.
DR Gene3D; 3.40.462.10; FAD-linked oxidases, C-terminal domain; 1.
DR Gene3D; 3.30.43.10; Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2; 1.
DR InterPro; IPR016170; Cytok_DH_C_sf.
DR InterPro; IPR015345; Cytokinin_DH_FAD/cytokin-bd.
DR InterPro; IPR016166; FAD-bd_PCMH.
DR InterPro; IPR036318; FAD-bd_PCMH-like_sf.
DR InterPro; IPR016167; FAD-bd_PCMH_sub1.
DR InterPro; IPR016169; FAD-bd_PCMH_sub2.
DR InterPro; IPR016164; FAD-linked_Oxase-like_C.
DR InterPro; IPR006094; Oxid_FAD_bind_N.
DR PANTHER; PTHR13878:SF107; CYTOKININ DEHYDROGENASE 3; 1.
DR PANTHER; PTHR13878; GULONOLACTONE OXIDASE; 1.
DR Pfam; PF09265; Cytokin-bind; 1.
DR Pfam; PF01565; FAD_binding_4; 1.
DR SUPFAM; SSF56176; FAD-binding/transporter-associated domain-like; 1.
DR SUPFAM; SSF55103; FAD-linked oxidases, C-terminal domain; 1.
DR PROSITE; PS51387; FAD_PCMH; 1.
PE 1: Evidence at protein level;
KW Endoplasmic reticulum; FAD; Flavoprotein; Glycoprotein; Oxidoreductase;
KW Reference proteome; Signal.
FT SIGNAL 1..22
FT /evidence="ECO:0000255"
FT CHAIN 23..527
FT /note="Cytokinin dehydrogenase 3"
FT /id="PRO_0000394206"
FT DOMAIN 52..231
FT /note="FAD-binding PCMH-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00718"
FT BINDING 87
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9FUJ1"
FT BINDING 89
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 91
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 93
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 97
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 155
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 160
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 166
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 170
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 221
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 471
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT BINDING 509
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT MOD_RES 92
FT /note="Pros-8alpha-FAD histidine"
FT /evidence="ECO:0000250|UniProtKB:Q9T0N8"
FT CARBOHYD 413
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
SQ SEQUENCE 527 AA; 58429 MW; 9EB8175695F49265 CRC64;
MEVAMVCTRV NLLILILSLC SPYKFIQSPM DFGPLNLLPT TTTASSDFGR ILFHSPSAVL
KPQAPRDISL LLSFLSASPL GKVTVAARGA GHSIHGQAQA LDGIVVEMSS LPSEIEFYRR
GEGDVSYADV GGGIMWIELL EQSLKLGLAP RSWTDYLYLT IGGTLSNAGI SGQTFKHGPQ
ISNVLQLEVV TGRGEIVTCS PTKDAELFNA VLGGLGQFGI ITRARILLQE APQKVKWVRA
FYDDFATFTK DQELLVSMPV LVDYVEGFIV LNEQSLHSSS IAFPTNVDFN PDFGTKNNPK
IYYCIEFAVH DYQNKNINVE QVVEVISRQM SHIASHLYSV EVSYFDFLNR VRMEEMSLRN
SGLWEVHHPW LNMFVPSAGI SDFRDLLMDS ISPDNFEGLI LIYPLLRHKW DTNTSVVLPD
SGSTDQVMYA VGILRSANPD DGCSHHCLQE LLLRHRRLAG AAASGLGAKQ YLAHHPTPAG
WRRHFGRRWE RFADRKARFD PRCILGPGQG IFPRDSSSSN GAFASYS
//
