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Protein

3-ketoacyl-CoA thiolase 2, peroxisomal

Gene

PED1

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

Functioni

Involved in long chain fatty-acid beta-oxidation prior to gluconeogenesis during germination and subsequent seedling growth. Confers sensitivity to 2,4-dichlorophenoxybutiric acid (2,4-DB). Required for local and systemic induction of jasmonic acid (JA) biosynthesis after wounding. Seems to be involved in JA biosynthesis during senescence.5 Publications

Catalytic activityi

Acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA.

Kineticsi

  1. KM=77.5 µM for acetoacetyl-CoA (at 25 degrees Celsius)1 Publication
  1. Vmax=5000 nmol/min/mg enzyme (at 25 degrees Celsius)1 Publication

Pathwayi: fatty acid metabolism

This protein is involved in the pathway fatty acid metabolism, which is part of Lipid metabolism.
View all proteins of this organism that are known to be involved in the pathway fatty acid metabolism and in Lipid metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei138 – 1381Acyl-thioester intermediateBy similarity
Active sitei393 – 3931Proton acceptorPROSITE-ProRule annotation
Active sitei425 – 4251Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  • acetyl-CoA C-acyltransferase activity Source: TAIR

GO - Biological processi

  • fatty acid beta-oxidation Source: TAIR
  • glyoxysome organization Source: TAIR
  • jasmonic acid biosynthetic process Source: TAIR
  • oxylipin biosynthetic process Source: UniProtKB-KW
  • positive regulation of abscisic acid-activated signaling pathway Source: TAIR
  • response to wounding Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Fatty acid biosynthesis, Fatty acid metabolism, Lipid biosynthesis, Lipid metabolism, Oxylipin biosynthesis

Enzyme and pathway databases

BioCyciMetaCyc:AT2G33150-MONOMER.
BRENDAi2.3.1.16. 399.
ReactomeiR-ATH-2046106. alpha-linolenic acid (ALA) metabolism.
R-ATH-390247. Beta-oxidation of very long chain fatty acids.
UniPathwayiUPA00199.

Names & Taxonomyi

Protein namesi
Recommended name:
3-ketoacyl-CoA thiolase 2, peroxisomal (EC:2.3.1.16)
Alternative name(s):
Acetyl-CoA acyltransferase 2
Beta-ketothiolase 2
Peroxisomal 3-oxoacyl-CoA thiolase 2
Peroxisome defective protein 1
Gene namesi
Name:PED1
Synonyms:KAT2
Ordered Locus Names:At2g33150
ORF Names:F25I18.11
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G33150.

Subcellular locationi

  • Peroxisome
  • Glyoxysome

  • Note: Peroxisomal targeting signal type 2 (PTS2-type) import is temperature and ATP-dependent, induced by zinc ions and PTS1-type import, but repressed by mature forms of PED1.

GO - Cellular componenti

  • chloroplast Source: TAIR
  • glyoxysome Source: UniProtKB-SubCell
  • membrane Source: TAIR
  • mitochondrion Source: TAIR
  • nucleolus Source: TAIR
  • peroxisome Source: TAIR
  • vacuolar membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Glyoxysome, Peroxisome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3434PeroxisomeSequence analysisAdd
BLAST
Chaini35 – 4624283-ketoacyl-CoA thiolase 2, peroxisomalPRO_0000034073Add
BLAST

Proteomic databases

PaxDbiQ56WD9.
PRIDEiQ56WD9.

Expressioni

Tissue specificityi

Accumulates in etiolated cotyledons and in seedlings, also present in roots, flowers and siliques (at protein level). High levels in wounded leaves.4 Publications

Developmental stagei

Levels increase strongly upon imbibition and decrease 3 days later. Strongly induced in leaves during senescence.3 Publications

Inductioni

Expressed in the dark, repressed by light (at protein level). Induced by dehydration, by abscisic acid (ABA) and by wounding, both locally and systemically.3 Publications

Gene expression databases

GenevisibleiQ56WD9. AT.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi3223. 5 interactions.
IntActiQ56WD9. 3 interactions.
MINTiMINT-8059930.
STRINGi3702.AT2G33150.1.

Structurei

Secondary structure

1
462
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi41 – 477Combined sources
Helixi48 – 503Combined sources
Beta strandi52 – 598Combined sources
Turni65 – 673Combined sources
Turni69 – 724Combined sources
Helixi75 – 9016Combined sources
Helixi94 – 963Combined sources
Beta strandi100 – 1034Combined sources
Beta strandi106 – 1083Combined sources
Helixi109 – 12214Combined sources
Beta strandi131 – 1355Combined sources
Helixi137 – 1393Combined sources
Helixi140 – 15314Combined sources
Beta strandi158 – 16710Combined sources
Turni168 – 1703Combined sources
Helixi181 – 1855Combined sources
Helixi187 – 1915Combined sources
Helixi196 – 20712Combined sources
Helixi211 – 23020Combined sources
Turni231 – 2377Combined sources
Beta strandi241 – 2466Combined sources
Turni248 – 2503Combined sources
Beta strandi253 – 2586Combined sources
Helixi270 – 2745Combined sources
Beta strandi279 – 2813Combined sources
Helixi288 – 2903Combined sources
Beta strandi295 – 30511Combined sources
Helixi306 – 3127Combined sources
Beta strandi318 – 32710Combined sources
Helixi330 – 3356Combined sources
Helixi336 – 34712Combined sources
Helixi352 – 3543Combined sources
Beta strandi357 – 3604Combined sources
Helixi365 – 37511Combined sources
Helixi379 – 3813Combined sources
Helixi388 – 3914Combined sources
Helixi397 – 41317Combined sources
Beta strandi419 – 4268Combined sources
Turni427 – 4293Combined sources
Beta strandi430 – 4389Combined sources
Helixi441 – 4466Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2C7YX-ray2.10A/B38-441[»]
2C7ZX-ray2.37A38-441[»]
2WU9X-ray1.50A/B36-462[»]
ProteinModelPortaliQ56WD9.
SMRiQ56WD9. Positions 46-448.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ56WD9.

Family & Domainsi

Sequence similaritiesi

Belongs to the thiolase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG1389. Eukaryota.
COG0183. LUCA.
HOGENOMiHOG000012239.
InParanoidiQ56WD9.
KOiK07513.
OMAiPQGKEDG.
PhylomeDBiQ56WD9.

Family and domain databases

Gene3Di3.40.47.10. 4 hits.
InterProiIPR002155. Thiolase.
IPR016039. Thiolase-like.
IPR020615. Thiolase_acyl_enz_int_AS.
IPR020610. Thiolase_AS.
IPR020617. Thiolase_C.
IPR020613. Thiolase_CS.
IPR020616. Thiolase_N.
[Graphical view]
PfamiPF02803. Thiolase_C. 1 hit.
PF00108. Thiolase_N. 1 hit.
[Graphical view]
SUPFAMiSSF53901. SSF53901. 2 hits.
TIGRFAMsiTIGR01930. AcCoA-C-Actrans. 1 hit.
PROSITEiPS00098. THIOLASE_1. 1 hit.
PS00737. THIOLASE_2. 1 hit.
PS00099. THIOLASE_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q56WD9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKAIERQRV LLEHLRPSSS SSHNYEASLS ASACLAGDSA AYQRTSLYGD
60 70 80 90 100
DVVIVAAHRT PLCKSKRGNF KDTYPDDLLA PVLRALIEKT NLNPSEVGDI
110 120 130 140 150
VVGTVLAPGS QRASECRMAA FYAGFPETVA VRTVNRQCSS GLQAVADVAA
160 170 180 190 200
AIKAGFYDIG IGAGLESMTT NPMAWEGSVN PAVKKFAQAQ NCLLPMGVTS
210 220 230 240 250
ENVAQRFGVS RQEQDQAAVD SHRKAAAATA AGKFKDEIIP VKTKLVDPKT
260 270 280 290 300
GDEKPITVSV DDGIRPTTTL ASLGKLKPVF KKDGTTTAGN SSQVSDGAGA
310 320 330 340 350
VLLMKRSVAM QKGLPVLGVF RTFAAVGVDP AIMGIGPAVA IPAAVKAAGL
360 370 380 390 400
ELDDIDLFEI NEAFASQFVY CRNKLGLDPE KINVNGGAMA IGHPLGATGA
410 420 430 440 450
RCVATLLHEM KRRGKDCRFG VVSMCIGTGM GAAAVFERGD GVDELRNARK
460
VEAQGLLSKD AR
Length:462
Mass (Da):48,579
Last modified:August 30, 2005 - v2
Checksum:i7405F81968489ADB
GO

Sequence cautioni

The sequence AAL25590.1 differs from that shown. Reason: Frameshift at position 375. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti17 – 171P → F (PubMed:14630959).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB008854 mRNA. Translation: BAA25248.1.
AB008855 Genomic DNA. Translation: BAA25249.1.
AC002334 Genomic DNA. Translation: AAC04908.1.
CP002685 Genomic DNA. Translation: AEC08791.1.
AY058176 mRNA. Translation: AAL25590.1. Frameshift.
AF327529 mRNA. Translation: AAG42910.1.
AF349530 mRNA. Translation: AAK15577.1.
AY052702 mRNA. Translation: AAK96606.1.
AY063720 mRNA. Translation: AAL36070.1.
AY087543 mRNA. Translation: AAM65085.1.
AK222103 mRNA. Translation: BAD95031.1.
PIRiT52110.
RefSeqiNP_180873.1. NM_128874.3.
UniGeneiAt.23661.
At.72951.

Genome annotation databases

EnsemblPlantsiAT2G33150.1; AT2G33150.1; AT2G33150.
GeneIDi817876.
GrameneiAT2G33150.1; AT2G33150.1; AT2G33150.
KEGGiath:AT2G33150.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB008854 mRNA. Translation: BAA25248.1.
AB008855 Genomic DNA. Translation: BAA25249.1.
AC002334 Genomic DNA. Translation: AAC04908.1.
CP002685 Genomic DNA. Translation: AEC08791.1.
AY058176 mRNA. Translation: AAL25590.1. Frameshift.
AF327529 mRNA. Translation: AAG42910.1.
AF349530 mRNA. Translation: AAK15577.1.
AY052702 mRNA. Translation: AAK96606.1.
AY063720 mRNA. Translation: AAL36070.1.
AY087543 mRNA. Translation: AAM65085.1.
AK222103 mRNA. Translation: BAD95031.1.
PIRiT52110.
RefSeqiNP_180873.1. NM_128874.3.
UniGeneiAt.23661.
At.72951.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2C7YX-ray2.10A/B38-441[»]
2C7ZX-ray2.37A38-441[»]
2WU9X-ray1.50A/B36-462[»]
ProteinModelPortaliQ56WD9.
SMRiQ56WD9. Positions 46-448.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi3223. 5 interactions.
IntActiQ56WD9. 3 interactions.
MINTiMINT-8059930.
STRINGi3702.AT2G33150.1.

Proteomic databases

PaxDbiQ56WD9.
PRIDEiQ56WD9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G33150.1; AT2G33150.1; AT2G33150.
GeneIDi817876.
GrameneiAT2G33150.1; AT2G33150.1; AT2G33150.
KEGGiath:AT2G33150.

Organism-specific databases

TAIRiAT2G33150.

Phylogenomic databases

eggNOGiKOG1389. Eukaryota.
COG0183. LUCA.
HOGENOMiHOG000012239.
InParanoidiQ56WD9.
KOiK07513.
OMAiPQGKEDG.
PhylomeDBiQ56WD9.

Enzyme and pathway databases

UniPathwayiUPA00199.
BioCyciMetaCyc:AT2G33150-MONOMER.
BRENDAi2.3.1.16. 399.
ReactomeiR-ATH-2046106. alpha-linolenic acid (ALA) metabolism.
R-ATH-390247. Beta-oxidation of very long chain fatty acids.

Miscellaneous databases

EvolutionaryTraceiQ56WD9.
PROiQ56WD9.

Gene expression databases

GenevisibleiQ56WD9. AT.

Family and domain databases

Gene3Di3.40.47.10. 4 hits.
InterProiIPR002155. Thiolase.
IPR016039. Thiolase-like.
IPR020615. Thiolase_acyl_enz_int_AS.
IPR020610. Thiolase_AS.
IPR020617. Thiolase_C.
IPR020613. Thiolase_CS.
IPR020616. Thiolase_N.
[Graphical view]
PfamiPF02803. Thiolase_C. 1 hit.
PF00108. Thiolase_N. 1 hit.
[Graphical view]
SUPFAMiSSF53901. SSF53901. 2 hits.
TIGRFAMsiTIGR01930. AcCoA-C-Actrans. 1 hit.
PROSITEiPS00098. THIOLASE_1. 1 hit.
PS00737. THIOLASE_2. 1 hit.
PS00099. THIOLASE_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "2,4-Dichlorophenoxybutyric acid-resistant mutants of Arabidopsis have defects in glyoxysomal fatty acid beta-oxidation."
    Hayashi M., Toriyama K., Kondo M., Nishimura M.
    Plant Cell 10:183-195(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, INDUCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    Strain: cv. Columbia and cv. Landsberg erecta.
  2. "Import of the peroxisomal targeting signal type 2 protein 3-ketoacyl-coenzyme A thiolase into glyoxysomes."
    Johnson T.L., Olsen L.J.
    Plant Physiol. 133:1991-1999(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, PTS2-TYPE IMPORT.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "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.
  6. "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].
  7. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 120-462.
    Strain: cv. Columbia.
  8. "A novel acyl-CoA oxidase that can oxidize short-chain acyl-CoA in plant peroxisomes."
    Hayashi H., De Bellis L., Ciurli A., Kondo M., Hayashi M., Nishimura M.
    J. Biol. Chem. 274:12715-12721(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, INDUCTION.
  9. "Co-ordinate regulation of genes involved in storage lipid mobilization in Arabidopsis thaliana."
    Rylott E.L., Hooks M.A., Graham I.A.
    Biochem. Soc. Trans. 29:283-287(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.
  10. "Requirement for 3-ketoacyl-CoA thiolase-2 in peroxisome development, fatty acid beta-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings."
    Germain V., Rylott E.L., Larson T.R., Sherson S.M., Bechtold N., Carde J.-P., Bryce J.H., Graham I.A., Smith S.M.
    Plant J. 28:1-12(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
  11. "Evidence supporting a role of jasmonic acid in Arabidopsis leaf senescence."
    He Y., Fukushige H., Hildebrand D.F., Gan S.
    Plant Physiol. 128:876-884(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DEVELOPMENTAL STAGE.
  12. "Gene-specific involvement of beta-oxidation in wound-activated responses in Arabidopsis."
    Cruz-Castillo M., Martinez C., Buchala A., Metraux J.-P., Leon J.
    Plant Physiol. 135:85-94(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, INDUCTION.
  13. "A defect in glyoxysomal fatty acid beta-oxidation reduces jasmonic acid accumulation in Arabidopsis."
    Afitlhile M.M., Fukushige H., Nishimura M., Hildebrand D.F.
    Plant Physiol. Biochem. 43:603-609(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  14. "The crystal structure of a plant 3-ketoacyl-CoA thiolase reveals the potential for redox control of peroxisomal fatty acid beta-oxidation."
    Sundaramoorthy R., Micossi E., Alphey M.S., Germain V., Bryce J.H., Smith S.M., Leonard G.A., Hunter W.N.
    J. Mol. Biol. 359:347-357(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 38-441, SUBUNIT.

Entry informationi

Entry nameiTHIK2_ARATH
AccessioniPrimary (citable) accession number: Q56WD9
Secondary accession number(s): Q93Z35, Q9S7M3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: August 30, 2005
Last modified: February 17, 2016
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.