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Q93ZA0

- NYC1_ARATH

UniProt

Q93ZA0 - NYC1_ARATH

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Protein
Probable chlorophyll(ide) b reductase NYC1, chloroplastic
Gene
NYC1, At4g13250, F17N18.140
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 acceptor By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi166 – 19025NAD By similarity
Add
BLAST

GO - Molecular functioni

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

GO - Biological processi

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

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

Plastidchloroplast thylakoid membrane; Multi-pass membrane protein Reviewed prediction 1 Publication

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei105 – 12521Helical; Reviewed prediction
Add
BLAST
Transmembranei132 – 15221Helical; Reviewed prediction
Add
BLAST
Transmembranei470 – 49021Helical; Reviewed prediction
Add
BLAST

GO - Cellular componenti

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

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 – 4343Chloroplast Reviewed prediction
Add
BLAST
Chaini44 – 496453Probable chlorophyll(ide) b reductase NYC1, chloroplastic
PRO_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.

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili195 – 22430 Reviewed prediction
Add
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

« Hide 'large scale' publications
  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: June 11, 2014
This is version 85 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

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