ID NYC1_ARATH Reviewed; 496 AA.
AC Q93ZA0; Q9SVQ2;
DT 09-FEB-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 27-MAR-2024, entry version 135.
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=AtNYC1;
DE Flags: Precursor;
GN Name=NYC1; OrderedLocusNames=At4g13250; ORFNames=F17N18.140;
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 [MRNA].
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. 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 [3]
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 [4]
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 [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=19403948; DOI=10.1074/jbc.m109.008912;
RA Horie Y., Ito H., Kusaba M., Tanaka R., Tanaka A.;
RT "Participation of chlorophyll b reductase in the initial step of the
RT degradation of light-harvesting chlorophyll a/b-protein complexes in
RT Arabidopsis.";
RL J. Biol. Chem. 284:17449-17456(2009).
RN [6]
RP SUBCELLULAR LOCATION, AND INTERACTION WITH SGR1; RCCR; NOL AND LHCII
RP COMPLEX.
RX PubMed=22366162; DOI=10.1105/tpc.111.089474;
RA Sakuraba Y., Schelbert S., Park S.Y., Han S.H., Lee B.D., Andres C.B.,
RA Kessler F., Hortensteiner S., Paek N.C.;
RT "STAY-GREEN and chlorophyll catabolic enzymes interact at light-harvesting
RT complex II for chlorophyll detoxification during leaf senescence in
RT Arabidopsis.";
RL Plant Cell 24:507-518(2012).
RN [7]
RP INTERACTION WITH HCAR, AND DEVELOPMENTAL STAGE.
RX PubMed=23200839; DOI=10.1016/j.bbrc.2012.11.050;
RA Sakuraba Y., Kim Y.S., Yoo S.C., Hortensteiner S., Paek N.C.;
RT "7-Hydroxymethyl chlorophyll a reductase functions in metabolic channeling
RT of chlorophyll breakdown intermediates during leaf senescence.";
RL Biochem. Biophys. Res. Commun. 430:32-37(2013).
CC -!- FUNCTION: Involved in chlorophyll b degradation. Belongs to the
CC chlorophyll catabolic enzymes (CCEs). {ECO:0000269|PubMed:19403948}.
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. Interacts with HCAR, RCCR, SGR1 and the LHCII
CC complex. Part of a SGR1-CCE-LHCII complex, which acts in chlorophyll
CC breakdown. {ECO:0000269|PubMed:22366162, ECO:0000269|PubMed:23200839}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
CC {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q93ZA0-1; Sequence=Displayed;
CC -!- DEVELOPMENTAL STAGE: Up-regulated during senescence.
CC {ECO:0000269|PubMed:23200839}.
CC -!- DISRUPTION PHENOTYPE: Decrease in chlorophyll b during dark incubation
CC substantially suppressed. {ECO:0000269|PubMed:19403948}.
CC -!- SIMILARITY: Belongs to the short-chain dehydrogenases/reductases (SDR)
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB41935.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78367.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB255028; BAF49743.1; -; mRNA.
DR EMBL; AL049751; CAB41935.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161535; CAB78367.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83251.1; -; Genomic_DNA.
DR EMBL; AY057697; AAL15327.1; -; mRNA.
DR PIR; T07705; T07705.
DR RefSeq; NP_567400.1; NM_117396.4. [Q93ZA0-1]
DR AlphaFoldDB; Q93ZA0; -.
DR SMR; Q93ZA0; -.
DR BioGRID; 12239; 7.
DR IntAct; Q93ZA0; 2.
DR MINT; Q93ZA0; -.
DR STRING; 3702.Q93ZA0; -.
DR PaxDb; 3702-AT4G13250-1; -.
DR ProteomicsDB; 249354; -. [Q93ZA0-1]
DR EnsemblPlants; AT4G13250.1; AT4G13250.1; AT4G13250. [Q93ZA0-1]
DR GeneID; 826942; -.
DR Gramene; AT4G13250.1; AT4G13250.1; AT4G13250. [Q93ZA0-1]
DR KEGG; ath:AT4G13250; -.
DR Araport; AT4G13250; -.
DR TAIR; AT4G13250; NYC1.
DR eggNOG; KOG0725; Eukaryota.
DR HOGENOM; CLU_010194_46_1_1; -.
DR InParanoid; Q93ZA0; -.
DR OMA; MNKGFRP; -.
DR OrthoDB; 1078218at2759; -.
DR PhylomeDB; Q93ZA0; -.
DR BioCyc; ARA:AT4G13250-MONOMER; -.
DR BioCyc; MetaCyc:AT4G13250-MONOMER; -.
DR BRENDA; 1.1.1.294; 399.
DR PRO; PR:Q93ZA0; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q93ZA0; baseline and differential.
DR Genevisible; Q93ZA0; AT.
DR GO; GO:0009507; C:chloroplast; IC:TAIR.
DR GO; GO:0009535; C:chloroplast thylakoid membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0034256; F:chlorophyll(ide) b reductase activity; IMP:TAIR.
DR GO; GO:0015996; P:chlorophyll catabolic process; IMP:TAIR.
DR GO; GO:0010304; P:PSII associated light-harvesting complex II catabolic process; IMP:TAIR.
DR CDD; cd05233; SDR_c; 1.
DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR002347; SDR_fam.
DR PANTHER; PTHR24314:SF21; CHLOROPHYLL(IDE) B REDUCTASE NYC1, CHLOROPLASTIC-RELATED; 1.
DR PANTHER; PTHR24314; NON-SPECIFIC LIPID TRANSFER PROTEIN-RELATED; 1.
DR Pfam; PF00106; adh_short; 1.
DR PRINTS; PR00081; GDHRDH.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chlorophyll catabolism; Chloroplast; Coiled coil;
KW Membrane; NAD; Oxidoreductase; Plastid; Reference proteome; Thylakoid;
KW Transit peptide; Transmembrane; Transmembrane helix.
FT TRANSIT 1..43
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 44..496
FT /note="Probable chlorophyll(ide) b reductase NYC1,
FT chloroplastic"
FT /id="PRO_0000391415"
FT TRANSMEM 105..125
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 132..152
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 470..490
FT /note="Helical"
FT /evidence="ECO:0000255"
FT COILED 195..224
FT /evidence="ECO:0000255"
FT ACT_SITE 330
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 166..190
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
SQ SEQUENCE 496 AA; 54845 MW; 9174A2DF927565BF CRC64;
MTTLTKIQVY PQVLEHRLFF RDPIRVGSRL TCRERSNRVY VHRCEKKVER KRKVEKFKGN
GSWDSLKSGF LGFSKLGFLS KDEYNQKVEN LEMVFSSVAV QIARYIVTMT STGAILLIGF
QLSGGDSSMN SLVWYSWLGG IIIGTMTGAN MVLEDHYRAG PRNVVITGST RGLGKALARE
FLLSGDRVIV TSRSSESVDM TVKELEQNLK EIMSNASESA RKKLSDAKVV GIACDVCKPE
DVEKLSNFAV KELGSINIWI NNAGTNKGFR PLLEFTEEDI TQIVSTNLIG SILCTRGAMD
VMSRQHSGGH IFNMDGAGSG GSSTPLTAVY GSTKCGLRQF HGSIVKESQK TNVGLHTASP
GMVLTELLLS GSSIKNKQMF NIICELPETV ARTLVPRMRV VKGSGKAVNY LTPPRILLAI
VTSWLRRGRW FDDQGRALYA AEADRLRNWA ENRTRLSLTD AMEMYTENTW VSVFSLSVVC
AFIILQSTTP SSFPGT
//
