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Protein

Probable pheophorbidase

Gene

PPD

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Involved in the chlorophyll breakdown by its action in fluorescent chlorophyll catabolites (FCCs) demethylation. Demethylates the C132-carboxymethyl group present at the isocyclic ring of chlorophyll. Also able to catalyze pheophorbides in vitro. Methylesterase shown to have carboxylesterase activity, methyl indole-3-acetic acid (MeIAA) esterase activity and methyl jasmonate (MeJA) esterase activity in vitro.2 Publications

Catalytic activityi

Pheophorbide a + H2O = pyropheophorbide a + methanol + CO2.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei87 – 871Acyl-ester intermediateBy similarity
Active sitei211 – 2111Charge relay systemPROSITE-ProRule annotation
Active sitei239 – 2391Charge relay systemPROSITE-ProRule annotation

GO - Molecular functioni

  • carboxylic ester hydrolase activity Source: UniProtKB
  • hydrolase activity, acting on ester bonds Source: TAIR
  • methyl indole-3-acetate esterase activity Source: TAIR
  • methyl jasmonate esterase activity Source: TAIR
  • pheophoridase activity Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

  • chlorophyll a catabolic process Source: UniProtKB
  • demethylation Source: UniProtKB
  • leaf senescence Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Chlorophyll catabolism

Enzyme and pathway databases

BioCyciARA:AT4G16690-MONOMER.

Protein family/group databases

ESTHERiarath-AT4G16690. Hydroxynitrile_lyase.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable pheophorbidase (EC:3.1.1.82)
Short name:
AtPPD
Alternative name(s):
FCC methylesterase
Methylesterase 16
Short name:
AtMES16
Gene namesi
Name:PPD
Synonyms:MES16
Ordered Locus Names:At4g16690
ORF Names:dl4370c, FCAALL.12
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G16690.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Accumulation of fluorescent chlorophyll catabolites (FCC) during senescence. No effect on root length when grown in presence of exogenous MeIAA.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 262262Probable pheophorbidasePRO_0000391349Add
BLAST

Proteomic databases

PaxDbiO23512.
PRIDEiO23512.

PTM databases

iPTMnetiO23512.

Expressioni

Gene expression databases

GenevisibleiO23512. AT.

Interactioni

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi12664. 1 interaction.
STRINGi3702.AT4G16690.1.

Structurei

3D structure databases

ProteinModelPortaliO23512.
SMRiO23512. Positions 12-254.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG410JX5E. Eukaryota.
ENOG41104A6. LUCA.
HOGENOMiHOG000133452.
InParanoidiO23512.
KOiK13544.
OMAiVENWPPS.
PhylomeDBiO23512.

Family and domain databases

Gene3Di3.40.50.1820. 1 hit.
InterProiIPR029058. AB_hydrolase.
IPR000073. AB_hydrolase_1.
[Graphical view]
PfamiPF12697. Abhydrolase_6. 1 hit.
[Graphical view]
SUPFAMiSSF53474. SSF53474. 1 hit.
PROSITEiPS00120. LIPASE_SER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O23512-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGGEGGAEPV IHFVFVHGAS HGAWCWYKLT TLLDAAGFKS TSVDLTGAGI
60 70 80 90 100
SLIDSNIVFD SDQYNRPLFS LLSDLPPHHK VILVGHSIGG GSVTEALCKF
110 120 130 140 150
TDKISMAIYL AASMVQPGSI PSPHLSNIHV GEEDIWEYTY GEGTDKPPTG
160 170 180 190 200
VLMKPEFIRH YYYSQSPLED VTLSSKLLRP APMRAFQDLD KLPPNPEAEK
210 220 230 240 250
VPRVYIKTAK DNLFDSVRQD LLVENWPPSQ LYVLEDSDHS AFFSVPTTLF
260
AYLLRAVSFL QR
Length:262
Mass (Da):29,014
Last modified:January 1, 1998 - v1
Checksum:i5CAA518C1A05212D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z97341 Genomic DNA. Translation: CAB10444.1.
AL161544 Genomic DNA. Translation: CAB78711.1.
CP002687 Genomic DNA. Translation: AEE83784.1.
AY088316 mRNA. Translation: AAM65855.1.
BX828808 mRNA. No translation available.
PIRiB71434.
RefSeqiNP_193402.1. NM_117770.4.
UniGeneiAt.43149.

Genome annotation databases

EnsemblPlantsiAT4G16690.1; AT4G16690.1; AT4G16690.
GeneIDi827371.
GrameneiAT4G16690.1; AT4G16690.1; AT4G16690.
KEGGiath:AT4G16690.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z97341 Genomic DNA. Translation: CAB10444.1.
AL161544 Genomic DNA. Translation: CAB78711.1.
CP002687 Genomic DNA. Translation: AEE83784.1.
AY088316 mRNA. Translation: AAM65855.1.
BX828808 mRNA. No translation available.
PIRiB71434.
RefSeqiNP_193402.1. NM_117770.4.
UniGeneiAt.43149.

3D structure databases

ProteinModelPortaliO23512.
SMRiO23512. Positions 12-254.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi12664. 1 interaction.
STRINGi3702.AT4G16690.1.

Protein family/group databases

ESTHERiarath-AT4G16690. Hydroxynitrile_lyase.

PTM databases

iPTMnetiO23512.

Proteomic databases

PaxDbiO23512.
PRIDEiO23512.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G16690.1; AT4G16690.1; AT4G16690.
GeneIDi827371.
GrameneiAT4G16690.1; AT4G16690.1; AT4G16690.
KEGGiath:AT4G16690.

Organism-specific databases

TAIRiAT4G16690.

Phylogenomic databases

eggNOGiENOG410JX5E. Eukaryota.
ENOG41104A6. LUCA.
HOGENOMiHOG000133452.
InParanoidiO23512.
KOiK13544.
OMAiVENWPPS.
PhylomeDBiO23512.

Enzyme and pathway databases

BioCyciARA:AT4G16690-MONOMER.

Miscellaneous databases

PROiO23512.

Gene expression databases

GenevisibleiO23512. AT.

Family and domain databases

Gene3Di3.40.50.1820. 1 hit.
InterProiIPR029058. AB_hydrolase.
IPR000073. AB_hydrolase_1.
[Graphical view]
PfamiPF12697. Abhydrolase_6. 1 hit.
[Graphical view]
SUPFAMiSSF53474. SSF53474. 1 hit.
PROSITEiPS00120. LIPASE_SER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana."
    Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C., Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P., Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.
    , Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R., De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M., Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M., Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A., Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D., Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A., Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S., Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G., Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.
    Nature 391:485-488(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  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. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  5. "Whole genome sequence comparisons and 'full-length' cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation."
    Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M., Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M., Weissenbach J., Salanoubat M.
    Genome Res. 14:406-413(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 6-262.
    Strain: cv. Columbia.
  6. "Characterization and cloning of the chlorophyll-degrading enzyme pheophorbidase from cotyledons of radish."
    Suzuki Y., Amano T., Shioi Y.
    Plant Physiol. 140:716-725(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  7. "Inactive methyl indole-3-acetic acid ester can be hydrolyzed and activated by several esterases belonging to the AtMES esterase family of Arabidopsis."
    Yang Y., Xu R., Ma C.J., Vlot A.C., Klessig D.F., Pichersky E.
    Plant Physiol. 147:1034-1045(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, FUNCTION, DISRUPTION PHENOTYPE.
  8. "MES16, a member of the methylesterase protein family, specifically demethylates fluorescent chlorophyll catabolites during chlorophyll breakdown in Arabidopsis."
    Christ B., Schelbert S., Aubry S., Suessenbacher I., Mueller T., Kraeutler B., Hoertensteiner S.
    Plant Physiol. 158:628-641(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiPPD_ARATH
AccessioniPrimary (citable) accession number: O23512
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 9, 2010
Last sequence update: January 1, 1998
Last modified: May 11, 2016
This is version 105 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.