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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

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 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

GO - Biological processi

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

Topology

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

GO - Cellular componenti

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

ExpressionAtlasiQ93ZA0. baseline and differential.
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.
IntActiQ93ZA0. 2 interactions.
STRINGi3702.AT4G13250.1-P.

Structurei

3D structure databases

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

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

        10         20         30         40         50
MTTLTKIQVY PQVLEHRLFF RDPIRVGSRL TCRERSNRVY VHRCEKKVER
60 70 80 90 100
KRKVEKFKGN GSWDSLKSGF LGFSKLGFLS KDEYNQKVEN LEMVFSSVAV
110 120 130 140 150
QIARYIVTMT STGAILLIGF QLSGGDSSMN SLVWYSWLGG IIIGTMTGAN
160 170 180 190 200
MVLEDHYRAG PRNVVITGST RGLGKALARE FLLSGDRVIV TSRSSESVDM
210 220 230 240 250
TVKELEQNLK EIMSNASESA RKKLSDAKVV GIACDVCKPE DVEKLSNFAV
260 270 280 290 300
KELGSINIWI NNAGTNKGFR PLLEFTEEDI TQIVSTNLIG SILCTRGAMD
310 320 330 340 350
VMSRQHSGGH IFNMDGAGSG GSSTPLTAVY GSTKCGLRQF HGSIVKESQK
360 370 380 390 400
TNVGLHTASP GMVLTELLLS GSSIKNKQMF NIICELPETV ARTLVPRMRV
410 420 430 440 450
VKGSGKAVNY LTPPRILLAI VTSWLRRGRW FDDQGRALYA AEADRLRNWA
460 470 480 490
ENRTRLSLTD AMEMYTENTW VSVFSLSVVC AFIILQSTTP SSFPGT
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. Curated
The sequence CAB78367.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.
IntActi Q93ZA0. 2 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

ExpressionAtlasi Q93ZA0. baseline and differential.
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: November 26, 2014
This is version 88 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