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Q93ZA0

- NYC1_ARATH

UniProt

Q93ZA0 - NYC1_ARATH

Protein

Probable chlorophyll(ide) b reductase NYC1, chloroplastic

Gene

NYC1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 86 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
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    Functioni

    Involved in chlorophyll b degradation. Belongs to the chlorophyll catabolic enzymes (CCEs).1 Publication

    Catalytic activityi

    71-hydroxychlorophyllide a + NAD(P)+ = chlorophyllide b + NAD(P)H.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei330 – 3301Proton acceptorBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi166 – 19025NADBy similarityAdd
    BLAST

    GO - Molecular functioni

    1. chlorophyll(ide) b reductase activity Source: TAIR
    2. protein binding Source: TAIR

    GO - Biological processi

    1. chlorophyll catabolic process Source: TAIR
    2. PSII associated light-harvesting complex II catabolic process Source: TAIR

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Chlorophyll catabolism

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciARA:AT4G13250-MONOMER.
    ARA:GQT-1209-MONOMER.
    MetaCyc:AT4G13250-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Probable chlorophyll(ide) b reductase NYC1, chloroplastic (EC:1.1.1.294)
    Alternative name(s):
    Protein NON-YELLOW COLORING 1
    Short name:
    AtNYC1
    Gene namesi
    Name:NYC1
    Ordered Locus Names:At4g13250
    ORF Names:F17N18.140
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 4

    Organism-specific databases

    TAIRiAT4G13250.

    Subcellular locationi

    GO - Cellular componenti

    1. chloroplast Source: TAIR
    2. chloroplast thylakoid membrane Source: UniProtKB-SubCell
    3. integral component of membrane Source: UniProtKB-KW

    Keywords - Cellular componenti

    Chloroplast, Membrane, Plastid, Thylakoid

    Pathology & Biotechi

    Disruption phenotypei

    Decrease in chlorophyll b during dark incubation substantially suppressed.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 4343ChloroplastSequence AnalysisAdd
    BLAST
    Chaini44 – 496453Probable chlorophyll(ide) b reductase NYC1, chloroplasticPRO_0000391415Add
    BLAST

    Proteomic databases

    PRIDEiQ93ZA0.

    Expressioni

    Developmental stagei

    Up-regulated during senescence.1 Publication

    Gene expression databases

    ArrayExpressiQ93ZA0.
    GenevestigatoriQ93ZA0.

    Interactioni

    Subunit structurei

    Interacts with NOL to form a complex that acts as a chlorophyll b reductase. Interacts with HCAR, RCCR, SGR1 and the LHCII complex. Part of a SGR1-CCE-LHCII complex, which acts in chlorophyll breakdown.2 Publications

    Protein-protein interaction databases

    BioGridi12239. 6 interactions.
    STRINGi3702.AT4G13250.1-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ93ZA0.
    SMRiQ93ZA0. Positions 165-463.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei105 – 12521HelicalSequence AnalysisAdd
    BLAST
    Transmembranei132 – 15221HelicalSequence AnalysisAdd
    BLAST
    Transmembranei470 – 49021HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili195 – 22430Sequence AnalysisAdd
    BLAST

    Sequence similaritiesi

    Keywords - Domaini

    Coiled coil, Transit peptide, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG1028.
    HOGENOMiHOG000005933.
    InParanoidiQ93ZA0.
    KOiK13606.
    OMAiYTENTWV.
    PhylomeDBiQ93ZA0.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR002198. DH_sc/Rdtase_SDR.
    IPR002347. Glc/ribitol_DH.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00106. adh_short. 1 hit.
    [Graphical view]
    PRINTSiPR00081. GDHRDH.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 1 isoform i produced by alternative splicing. Align

    Note: A number of isoforms are produced. According to EST sequences.

    Isoform 1 (identifier: Q93ZA0-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MTTLTKIQVY PQVLEHRLFF RDPIRVGSRL TCRERSNRVY VHRCEKKVER    50
    KRKVEKFKGN GSWDSLKSGF LGFSKLGFLS KDEYNQKVEN LEMVFSSVAV 100
    QIARYIVTMT STGAILLIGF QLSGGDSSMN SLVWYSWLGG IIIGTMTGAN 150
    MVLEDHYRAG PRNVVITGST RGLGKALARE FLLSGDRVIV TSRSSESVDM 200
    TVKELEQNLK EIMSNASESA RKKLSDAKVV GIACDVCKPE DVEKLSNFAV 250
    KELGSINIWI NNAGTNKGFR PLLEFTEEDI TQIVSTNLIG SILCTRGAMD 300
    VMSRQHSGGH IFNMDGAGSG GSSTPLTAVY GSTKCGLRQF HGSIVKESQK 350
    TNVGLHTASP GMVLTELLLS GSSIKNKQMF NIICELPETV ARTLVPRMRV 400
    VKGSGKAVNY LTPPRILLAI VTSWLRRGRW FDDQGRALYA AEADRLRNWA 450
    ENRTRLSLTD AMEMYTENTW VSVFSLSVVC AFIILQSTTP SSFPGT 496
    Length:496
    Mass (Da):54,845
    Last modified:December 1, 2001 - v1
    Checksum:i9174A2DF927565BF
    GO

    Sequence cautioni

    The sequence CAB41935.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence CAB78367.1 differs from that shown. Reason: Erroneous gene model prediction.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB255028 mRNA. Translation: BAF49743.1.
    AL049751 Genomic DNA. Translation: CAB41935.1. Sequence problems.
    AL161535 Genomic DNA. Translation: CAB78367.1. Sequence problems.
    CP002687 Genomic DNA. Translation: AEE83251.1.
    AY057697 mRNA. Translation: AAL15327.1.
    PIRiT07705.
    RefSeqiNP_567400.1. NM_117396.3. [Q93ZA0-1]
    UniGeneiAt.3267.

    Genome annotation databases

    EnsemblPlantsiAT4G13250.1; AT4G13250.1; AT4G13250. [Q93ZA0-1]
    GeneIDi826942.
    KEGGiath:AT4G13250.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB255028 mRNA. Translation: BAF49743.1 .
    AL049751 Genomic DNA. Translation: CAB41935.1 . Sequence problems.
    AL161535 Genomic DNA. Translation: CAB78367.1 . Sequence problems.
    CP002687 Genomic DNA. Translation: AEE83251.1 .
    AY057697 mRNA. Translation: AAL15327.1 .
    PIRi T07705.
    RefSeqi NP_567400.1. NM_117396.3. [Q93ZA0-1 ]
    UniGenei At.3267.

    3D structure databases

    ProteinModelPortali Q93ZA0.
    SMRi Q93ZA0. Positions 165-463.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 12239. 6 interactions.
    STRINGi 3702.AT4G13250.1-P.

    Proteomic databases

    PRIDEi Q93ZA0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G13250.1 ; AT4G13250.1 ; AT4G13250 . [Q93ZA0-1 ]
    GeneIDi 826942.
    KEGGi ath:AT4G13250.

    Organism-specific databases

    TAIRi AT4G13250.

    Phylogenomic databases

    eggNOGi COG1028.
    HOGENOMi HOG000005933.
    InParanoidi Q93ZA0.
    KOi K13606.
    OMAi YTENTWV.
    PhylomeDBi Q93ZA0.

    Enzyme and pathway databases

    BioCyci ARA:AT4G13250-MONOMER.
    ARA:GQT-1209-MONOMER.
    MetaCyc:AT4G13250-MONOMER.

    Gene expression databases

    ArrayExpressi Q93ZA0.
    Genevestigatori Q93ZA0.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    InterProi IPR002198. DH_sc/Rdtase_SDR.
    IPR002347. Glc/ribitol_DH.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    Pfami PF00106. adh_short. 1 hit.
    [Graphical view ]
    PRINTSi PR00081. GDHRDH.
    ProtoNeti Search...

    Publicationsi

    1. "Rice NON-YELLOW COLORING1 is involved in light-harvesting complex II and grana degradation during leaf senescence."
      Kusaba M., Ito H., Morita R., Iida S., Sato Y., Fujimoto M., Kawasaki S., Tanaka R., Hirochika H., Nishimura M., Tanaka A.
      Plant Cell 19:1362-1375(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
      Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
      , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
      Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Participation of chlorophyll b reductase in the initial step of the degradation of light-harvesting chlorophyll a/b-protein complexes in Arabidopsis."
      Horie Y., Ito H., Kusaba M., Tanaka R., Tanaka A.
      J. Biol. Chem. 284:17449-17456(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
      Strain: cv. Columbia.
    6. "STAY-GREEN and chlorophyll catabolic enzymes interact at light-harvesting complex II for chlorophyll detoxification during leaf senescence in Arabidopsis."
      Sakuraba Y., Schelbert S., Park S.Y., Han S.H., Lee B.D., Andres C.B., Kessler F., Hortensteiner S., Paek N.C.
      Plant Cell 24:507-518(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, INTERACTION WITH SGR1; RCCR; NOL AND LHCII COMPLEX.
    7. "7-Hydroxymethyl chlorophyll a reductase functions in metabolic channeling of chlorophyll breakdown intermediates during leaf senescence."
      Sakuraba Y., Kim Y.S., Yoo S.C., Hortensteiner S., Paek N.C.
      Biochem. Biophys. Res. Commun. 430:32-37(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH HCAR, DEVELOPMENTAL STAGE.

    Entry informationi

    Entry nameiNYC1_ARATH
    AccessioniPrimary (citable) accession number: Q93ZA0
    Secondary accession number(s): Q9SVQ2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 9, 2010
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 86 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3