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Q93ZA0 (NYC1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 82. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:NYC1
Ordered Locus Names:At4g13250
ORF Names:F17N18.140
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length496 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in chlorophyll b degradation. Belongs to the chlorophyll catabolic enzymes (CCEs). Ref.5

Catalytic activity

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

Subunit structure

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. Ref.6 Ref.7

Subcellular location

Plastidchloroplast thylakoid membrane; Multi-pass membrane protein Potential Ref.6.

Developmental stage

Up-regulated during senescence. Ref.7

Disruption phenotype

Decrease in chlorophyll b during dark incubation substantially suppressed. Ref.5

Sequence similarities

Belongs to the short-chain dehydrogenases/reductases (SDR) family.

Sequence caution

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.

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: Q93ZA0-1)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 4343Chloroplast Potential
Chain44 – 496453Probable chlorophyll(ide) b reductase NYC1, chloroplastic
PRO_0000391415

Regions

Transmembrane105 – 12521Helical; Potential
Transmembrane132 – 15221Helical; Potential
Transmembrane470 – 49021Helical; Potential
Nucleotide binding166 – 19025NAD By similarity
Coiled coil195 – 22430 Potential

Sites

Active site3301Proton acceptor By similarity

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: 9174A2DF927565BF

FASTA49654,845
        10         20         30         40         50         60 
MTTLTKIQVY PQVLEHRLFF RDPIRVGSRL TCRERSNRVY VHRCEKKVER KRKVEKFKGN 

        70         80         90        100        110        120 
GSWDSLKSGF LGFSKLGFLS KDEYNQKVEN LEMVFSSVAV QIARYIVTMT STGAILLIGF 

       130        140        150        160        170        180 
QLSGGDSSMN SLVWYSWLGG IIIGTMTGAN MVLEDHYRAG PRNVVITGST RGLGKALARE 

       190        200        210        220        230        240 
FLLSGDRVIV TSRSSESVDM TVKELEQNLK EIMSNASESA RKKLSDAKVV GIACDVCKPE 

       250        260        270        280        290        300 
DVEKLSNFAV KELGSINIWI NNAGTNKGFR PLLEFTEEDI TQIVSTNLIG SILCTRGAMD 

       310        320        330        340        350        360 
VMSRQHSGGH IFNMDGAGSG GSSTPLTAVY GSTKCGLRQF HGSIVKESQK TNVGLHTASP 

       370        380        390        400        410        420 
GMVLTELLLS GSSIKNKQMF NIICELPETV ARTLVPRMRV VKGSGKAVNY LTPPRILLAI 

       430        440        450        460        470        480 
VTSWLRRGRW FDDQGRALYA AEADRLRNWA ENRTRLSLTD AMEMYTENTW VSVFSLSVVC 

       490 
AFIILQSTTP SSFPGT 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRT07705.
RefSeqNP_567400.1. NM_117396.3.
UniGeneAt.3267.

3D structure databases

ProteinModelPortalQ93ZA0.
SMRQ93ZA0. Positions 165-463.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid12239. 6 interactions.
STRING3702.AT4G13250.1-P.

Proteomic databases

PRIDEQ93ZA0.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT4G13250.1; AT4G13250.1; AT4G13250.
GeneID826942.
KEGGath:AT4G13250.

Organism-specific databases

TAIRAT4G13250.

Phylogenomic databases

eggNOGCOG1028.
HOGENOMHOG000005933.
InParanoidQ93ZA0.
KOK13606.
OMAEMYTENT.
PhylomeDBQ93ZA0.
ProtClustDBCLSN2689409.

Enzyme and pathway databases

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

Gene expression databases

ArrayExpressQ93ZA0.
GenevestigatorQ93ZA0.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
InterProIPR002198. DH_sc/Rdtase_SDR.
IPR002347. Glc/ribitol_DH.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamPF00106. adh_short. 1 hit.
[Graphical view]
PRINTSPR00081. GDHRDH.
ProtoNetSearch...

Entry information

Entry nameNYC1_ARATH
AccessionPrimary (citable) accession number: Q93ZA0
Secondary accession number(s): Q9SVQ2
Entry history
Integrated into UniProtKB/Swiss-Prot: February 9, 2010
Last sequence update: December 1, 2001
Last modified: March 19, 2014
This is version 82 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names