NYC1_ORYSJ
ID NYC1_ORYSJ Reviewed; 504 AA.
AC Q5N800; A0A0P0V014;
DT 09-FEB-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Probable chlorophyll(ide) b reductase NYC1, chloroplastic;
DE EC=1.1.1.294;
DE AltName: Full=Protein NON-YELLOW COLORING 1;
DE Short=OsNYC1;
DE Flags: Precursor;
GN Name=NYC1; OrderedLocusNames=Os01g0227100, LOC_Os01g12710;
GN ORFNames=OsJ_00960, P0443E07.35, P0452F10.6;
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 [MRNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17416733; DOI=10.1105/tpc.106.042911;
RA Kusaba M., Ito H., Morita R., Iida S., Sato Y., Fujimoto M., Kawasaki S.,
RA Tanaka R., Hirochika H., Nishimura M., Tanaka A.;
RT "Rice NON-YELLOW COLORING1 is involved in light-harvesting complex II and
RT grana degradation during leaf senescence.";
RL Plant Cell 19:1362-1375(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [3]
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 [4]
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 [5]
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 [6]
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 [7]
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 [8]
RP INTERACTION WITH NOL.
RX PubMed=18778405; DOI=10.1111/j.1365-313x.2008.03670.x;
RA Sato Y., Morita R., Katsuma S., Nishimura M., Tanaka A., Kusaba M.;
RT "Two short-chain dehydrogenase/reductases, NON-YELLOW COLORING 1 and NYC1-
RT LIKE, are required for chlorophyll b and light-harvesting complex II
RT degradation during senescence in rice.";
RL Plant J. 57:120-131(2009).
CC -!- FUNCTION: Required for proper chloroplast degradation. Involved in
CC chlorophyll b degradation.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7(1)-hydroxychlorophyllide a + NAD(+) = chlorophyllide b +
CC H(+) + NADH; Xref=Rhea:RHEA:24768, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:83356,
CC ChEBI:CHEBI:83357; EC=1.1.1.294;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7(1)-hydroxychlorophyllide a + NADP(+) = chlorophyllide b +
CC H(+) + NADPH; Xref=Rhea:RHEA:24772, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349, ChEBI:CHEBI:83356,
CC ChEBI:CHEBI:83357; EC=1.1.1.294;
CC -!- SUBUNIT: Interacts with NOL to form a complex that acts as a
CC chlorophyll b reductase. {ECO:0000269|PubMed:18778405}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
CC {ECO:0000305|PubMed:17416733}; Multi-pass membrane protein
CC {ECO:0000305|PubMed:17416733}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves and stems. Also detected in
CC non-photosynthetic tissues such as roots.
CC {ECO:0000269|PubMed:17416733}.
CC -!- DEVELOPMENTAL STAGE: Strongly expressed in late-senescing leaves.
CC {ECO:0000269|PubMed:17416733}.
CC -!- INDUCTION: Up-regulated by dark treatment, abscisic acid and methyl
CC jasmonate. {ECO:0000269|PubMed:17416733}.
CC -!- DISRUPTION PHENOTYPE: Stay-green phenotype during senescence. Grana
CC stacks fused into large stable stacks during semescence.
CC {ECO:0000269|PubMed:17416733}.
CC -!- MISCELLANEOUS: No chlorophyll b reductase activity detected in vitro
CC with a recombinant protein produced in a heterologous system.
CC -!- SIMILARITY: Belongs to the short-chain dehydrogenases/reductases (SDR)
CC family. {ECO:0000305}.
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DR EMBL; AB255025; BAF49740.1; -; mRNA.
DR EMBL; AP002900; BAD81513.1; -; Genomic_DNA.
DR EMBL; AP003434; BAD82407.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF04382.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS71128.1; -; Genomic_DNA.
DR EMBL; CM000138; EEE54154.1; -; Genomic_DNA.
DR EMBL; AK068523; BAG90942.1; -; mRNA.
DR RefSeq; XP_015621887.1; XM_015766401.1.
DR AlphaFoldDB; Q5N800; -.
DR SMR; Q5N800; -.
DR STRING; 4530.OS01T0227100-01; -.
DR PaxDb; Q5N800; -.
DR PRIDE; Q5N800; -.
DR EnsemblPlants; Os01t0227100-01; Os01t0227100-01; Os01g0227100.
DR GeneID; 4327178; -.
DR Gramene; Os01t0227100-01; Os01t0227100-01; Os01g0227100.
DR KEGG; osa:4327178; -.
DR eggNOG; KOG0725; Eukaryota.
DR InParanoid; Q5N800; -.
DR OMA; ANKGFRP; -.
DR OrthoDB; 1190834at2759; -.
DR BRENDA; 1.1.1.294; 4460.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR ExpressionAtlas; Q5N800; baseline and differential.
DR Genevisible; Q5N800; OS.
DR GO; GO:0009535; C:chloroplast thylakoid membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0009536; C:plastid; IDA:Gramene.
DR GO; GO:0034256; F:chlorophyll(ide) b reductase activity; IBA:GO_Central.
DR GO; GO:0016491; F:oxidoreductase activity; IDA:Gramene.
DR GO; GO:0015996; P:chlorophyll catabolic process; IMP:Gramene.
DR GO; GO:0010304; P:PSII associated light-harvesting complex II catabolic process; IMP:Gramene.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR002347; SDR_fam.
DR Pfam; PF00106; adh_short; 1.
DR PRINTS; PR00081; GDHRDH.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW Chlorophyll catabolism; Chloroplast; Membrane; NAD; Oxidoreductase;
KW Plastid; Reference proteome; Thylakoid; Transit peptide; Transmembrane;
KW Transmembrane helix.
FT TRANSIT 1..33
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 34..504
FT /note="Probable chlorophyll(ide) b reductase NYC1,
FT chloroplastic"
FT /id="PRO_0000391413"
FT TRANSMEM 114..134
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 141..161
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 479..499
FT /note="Helical"
FT /evidence="ECO:0000255"
FT REGION 41..63
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 339
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 175..199
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
SQ SEQUENCE 504 AA; 54716 MW; 68AAC7043496F95D CRC64;
MAAAAVVHLS VHGRLRRSPE LHARPYHRPS LLRCRAFKQE ADNGGEEASS SPPPPTTAEA
RRRRKGPLYK LKAAIQGLAG SRSAAAEAYG GEYQRAVEKA EEIFFSVATQ VGRYVITMMS
SGVVLGVGFQ LSGGDSQMNT LIWYSWLGGV IIGTMIGANS VLEEHCKAGP RNVVITGSTR
GLGKALAREF LLSGDRVVIA SRSPESVLQT INELEENIQE GLSVAKKKQR EILLHAKVVG
TSCDVCKPED VKKLVNFAKD ELGSIDIWIN NAGTNKGFRP LVNFSDEDIS QIVSTNLVGS
LLCTREAMNV MQHQQKGGHV FNMDGAGSGG SSTPLTAVYG STKCGLRQFQ ASLLKESRRS
KVGVHTASPG MVLTDLLLSG SSLRNKQMFN LICELPETVA RTLVPRMRVV KGSGKAINYL
TPPRILLALV TAWVRRGRWF DEEGRAVYAA EADRIRNWAE SRARFSFTDA MEMYTENTWV
SVFSLSVVCA FIILSSSGGP LPGT
