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NYC1_ARATH
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   03-AUG-2022, entry version 127.
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.AT4G13250.1; -.
DR   PaxDb; Q93ZA0; -.
DR   PRIDE; Q93ZA0; -.
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; locus:2119330; AT4G13250.
DR   eggNOG; KOG0725; Eukaryota.
DR   HOGENOM; CLU_010194_46_1_1; -.
DR   InParanoid; Q93ZA0; -.
DR   OMA; ANKGFRP; -.
DR   PhylomeDB; Q93ZA0; -.
DR   BioCyc; ARA:AT4G13250-MON; -.
DR   BioCyc; MetaCyc:AT4G13250-MON; -.
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:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
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   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   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
 
 
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