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Probable chlorophyll(ide) b reductase NYC1, chloroplastic (EC 1.1.1.294) (Protein NON-YELLOW COLORING 1) (OsNYC1)

 NYC1_ORYSJ              Reviewed;         504 AA.
Q5N800; A0A0P0V014;
09-FEB-2010, integrated into UniProtKB/Swiss-Prot.
01-FEB-2005, sequence version 1.
23-MAY-2018, entry version 94.
RecName: Full=Probable chlorophyll(ide) b reductase NYC1, chloroplastic;
EC=1.1.1.294;
AltName: Full=Protein NON-YELLOW COLORING 1;
Short=OsNYC1;
Flags: Precursor;
Name=NYC1; OrderedLocusNames=Os01g0227100, LOC_Os01g12710;
ORFNames=OsJ_00960, P0443E07.35, P0452F10.6;
Oryza sativa subsp. japonica (Rice).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BOP clade;
Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
NCBI_TaxID=39947;
[1]
NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
DEVELOPMENTAL STAGE, INDUCTION, AND DISRUPTION PHENOTYPE.
PubMed=17416733; DOI=10.1105/tpc.106.042911;
Kusaba M., Ito H., Morita R., Iida S., Sato Y., Fujimoto M.,
Kawasaki S., Tanaka R., Hirochika H., Nishimura M., Tanaka A.;
"Rice NON-YELLOW COLORING1 is involved in light-harvesting complex II
and grana degradation during leaf senescence.";
Plant Cell 19:1362-1375(2007).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Nipponbare;
PubMed=12447438; DOI=10.1038/nature01184;
Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M.,
Okamoto M., Ando T., Aoki H., Arita K., Hamada M., Harada C.,
Hijishita S., Honda M., Ichikawa Y., Idonuma A., Iijima M., Ikeda M.,
Ikeno M., Ito S., Ito T., Ito Y., Ito Y., Iwabuchi A., Kamiya K.,
Karasawa W., Katagiri S., Kikuta A., Kobayashi N., Kono I.,
Machita K., Maehara T., Mizuno H., Mizubayashi T., Mukai Y.,
Nagasaki H., Nakashima M., Nakama Y., Nakamichi Y., Nakamura M.,
Namiki N., Negishi M., Ohta I., Ono N., Saji S., Sakai K., Shibata M.,
Shimokawa T., Shomura A., Song J., Takazaki Y., Terasawa K., Tsuji K.,
Waki K., Yamagata H., Yamane H., Yoshiki S., Yoshihara R., Yukawa K.,
Zhong H., Iwama H., Endo T., Ito H., Hahn J.H., Kim H.-I., Eun M.-Y.,
Yano M., Jiang J., Gojobori T.;
"The genome sequence and structure of rice chromosome 1.";
Nature 420:312-316(2002).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Nipponbare;
PubMed=16100779; DOI=10.1038/nature03895;
International rice genome sequencing project (IRGSP);
"The map-based sequence of the rice genome.";
Nature 436:793-800(2005).
[4]
GENOME REANNOTATION.
STRAIN=cv. Nipponbare;
PubMed=18089549; DOI=10.1093/nar/gkm978;
The rice annotation project (RAP);
"The rice annotation project database (RAP-DB): 2008 update.";
Nucleic Acids Res. 36:D1028-D1033(2008).
[5]
GENOME REANNOTATION.
STRAIN=cv. Nipponbare;
PubMed=24280374; DOI=10.1186/1939-8433-6-4;
Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H.,
McCombie W.R., Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S.,
Childs K.L., Davidson R.M., Lin H., Quesada-Ocampo L.,
Vaillancourt B., Sakai H., Lee S.S., Kim J., Numa H., Itoh T.,
Buell C.R., Matsumoto T.;
"Improvement of the Oryza sativa Nipponbare reference genome using
next generation sequence and optical map data.";
Rice 6:4-4(2013).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Nipponbare;
PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H.,
Cong L., Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J.,
Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X.,
Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y.,
Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J.,
Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y.,
Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y.,
Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z.,
Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T.,
Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H.,
Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W.,
Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L.,
Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J.,
Samudrala R., Wang J., Wong G.K.-S., Yang H.;
"The genomes of Oryza sativa: a history of duplications.";
PLoS Biol. 3:266-281(2005).
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Nipponbare;
PubMed=12869764; DOI=10.1126/science.1081288;
The rice full-length cDNA consortium;
"Collection, mapping, and annotation of over 28,000 cDNA clones from
japonica rice.";
Science 301:376-379(2003).
[8]
INTERACTION WITH NOL.
PubMed=18778405; DOI=10.1111/j.1365-313X.2008.03670.x;
Sato Y., Morita R., Katsuma S., Nishimura M., Tanaka A., Kusaba M.;
"Two short-chain dehydrogenase/reductases, NON-YELLOW COLORING 1 and
NYC1-LIKE, are required for chlorophyll b and light-harvesting complex
II degradation during senescence in rice.";
Plant J. 57:120-131(2009).
-!- FUNCTION: Required for proper chloroplast degradation. Involved in
chlorophyll b degradation.
-!- CATALYTIC ACTIVITY: 7(1)-hydroxychlorophyllide a + NAD(P)(+) =
chlorophyllide b + NAD(P)H.
-!- SUBUNIT: Interacts with NOL to form a complex that acts as a
chlorophyll b reductase. {ECO:0000269|PubMed:18778405}.
-!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
{ECO:0000305|PubMed:17416733}; Multi-pass membrane protein
{ECO:0000305|PubMed:17416733}.
-!- TISSUE SPECIFICITY: Expressed in leaves and stems. Also detected
in non-photosynthetic tissues such as roots.
{ECO:0000269|PubMed:17416733}.
-!- DEVELOPMENTAL STAGE: Strongly expressed in late-senescing leaves.
{ECO:0000269|PubMed:17416733}.
-!- INDUCTION: Up-regulated by dark treatment, abscisic acid and
methyl jasmonate. {ECO:0000269|PubMed:17416733}.
-!- DISRUPTION PHENOTYPE: Stay-green phenotype during senescence.
Grana stacks fused into large stable stacks during semescence.
{ECO:0000269|PubMed:17416733}.
-!- MISCELLANEOUS: No chlorophyll b reductase activity detected in
vitro with a recombinant protein produced in a heterologous
system.
-!- SIMILARITY: Belongs to the short-chain dehydrogenases/reductases
(SDR) family. {ECO:0000305}.
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EMBL; AB255025; BAF49740.1; -; mRNA.
EMBL; AP002900; BAD81513.1; -; Genomic_DNA.
EMBL; AP003434; BAD82407.1; -; Genomic_DNA.
EMBL; AP008207; BAF04382.1; -; Genomic_DNA.
EMBL; AP014957; BAS71128.1; -; Genomic_DNA.
EMBL; CM000138; EEE54154.1; -; Genomic_DNA.
EMBL; AK068523; BAG90942.1; -; mRNA.
RefSeq; XP_015621887.1; XM_015766401.1.
UniGene; Os.18818; -.
ProteinModelPortal; Q5N800; -.
SMR; Q5N800; -.
STRING; 39947.LOC_Os01g12710.1; -.
PaxDb; Q5N800; -.
EnsemblPlants; Os01t0227100-01; Os01t0227100-01; Os01g0227100.
GeneID; 4327178; -.
Gramene; Os01t0227100-01; Os01t0227100-01; Os01g0227100.
KEGG; osa:4327178; -.
eggNOG; KOG0725; Eukaryota.
eggNOG; COG1028; LUCA.
InParanoid; Q5N800; -.
KO; K13606; -.
OMA; GRWFDDE; -.
OrthoDB; EOG0936099K; -.
BRENDA; 1.1.1.294; 4460.
Proteomes; UP000059680; Chromosome 1.
ExpressionAtlas; Q5N800; differential.
Genevisible; Q5N800; OS.
GO; GO:0009535; C:chloroplast thylakoid membrane; IEA:UniProtKB-SubCell.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0009536; C:plastid; IDA:Gramene.
GO; GO:0034256; F:chlorophyll(ide) b reductase activity; IBA:GO_Central.
GO; GO:0016491; F:oxidoreductase activity; IDA:Gramene.
GO; GO:0015996; P:chlorophyll catabolic process; IMP:Gramene.
GO; GO:0010304; P:PSII associated light-harvesting complex II catabolic process; IMP:Gramene.
InterPro; IPR036291; NAD(P)-bd_dom_sf.
InterPro; IPR002347; SDR_fam.
Pfam; PF00106; adh_short; 1.
PRINTS; PR00081; GDHRDH.
SUPFAM; SSF51735; SSF51735; 1.
1: Evidence at protein level;
Chlorophyll catabolism; Chloroplast; Complete proteome; Membrane; NAD;
Oxidoreductase; Plastid; Reference proteome; Thylakoid;
Transit peptide; Transmembrane; Transmembrane helix.
TRANSIT 1 33 Chloroplast. {ECO:0000255}.
CHAIN 34 504 Probable chlorophyll(ide) b reductase
NYC1, chloroplastic.
/FTId=PRO_0000391413.
TRANSMEM 114 134 Helical. {ECO:0000255}.
TRANSMEM 141 161 Helical. {ECO:0000255}.
TRANSMEM 479 499 Helical. {ECO:0000255}.
NP_BIND 175 199 NAD. {ECO:0000250}.
COMPBIAS 52 55 Poly-Pro.
COMPBIAS 61 64 Poly-Arg.
ACT_SITE 339 339 Proton acceptor. {ECO:0000250}.
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


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