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Protein

Cytochrome P450 98A3

Gene

CYP98A3

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

Functioni

Cytochrome P450 which catalyzes 3'-hydroxylation of p-coumaric esters of shikimic/quinic acids to form lignin monomers. Can use p-coumarate, p-coumaraldehyde, p-coumaroyl methyl ester, 5-O-(4-coumaroyl) D-quinate and 5-O-(4-coumaroyl) shikimate as substrates, but not p-coumaryl alcohol, p-coumaroyl CoA, 1-O-p-coumaroyl-beta-D-glucose, p-hydroxy-cinnamyl alcohol, cinnamate, caffeate or ferulate. Has a weak activity on tri(p-coumaroyl)spermidine, but none on triferuloylspermidine. Hydroxylates preferentially the 5-O-isomer, but can also convert the 4-O- and 3-O-isomers with a lower efficiency. Involved in the biosynthesis of the coumarins scopoletin and scopolin. Essential for the biosynthesis of lignin.5 Publications

Cofactori

hemeBy similarity

Kineticsi

Kcat is 612 min(-1) with 5-O-(4-coumaroyl) shikimate as substrate. Kcat is 399 min(-1) with 5-O-(4-coumaroyl) quinate as substrate.1 Publication

  1. KM=7 µM for 5-O-(4-coumaroyl) shikimate1 Publication
  2. KM=18 µM for 5-O-(4-coumaroyl) quinate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi438 – 4381Iron (heme axial ligand)By similarity

    GO - Molecular functioni

    GO - Biological processi

    • coumarin biosynthetic process Source: TAIR
    • flavonoid biosynthetic process Source: TAIR
    • lignin biosynthetic process Source: TAIR
    • phenylpropanoid biosynthetic process Source: TAIR
    Complete GO annotation...

    Keywords - Molecular functioni

    Monooxygenase, Oxidoreductase

    Keywords - Ligandi

    Heme, Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:AT2G40890-MONOMER.
    SABIO-RKO22203.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytochrome P450 98A3 (EC:1.14.-.-)
    Alternative name(s):
    Protein REDUCED EPIDERMAL FLUORESCENCE 8
    p-coumaroylshikimate/quinate 3'-hydrolxylase
    Short name:
    C3'H
    Gene namesi
    Name:CYP98A3
    Synonyms:C3'H, REF8
    Ordered Locus Names:At2g40890
    ORF Names:T20B5.9
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548 Componenti: Chromosome 2

    Organism-specific databases

    TAIRiAT2G40890.

    Subcellular locationi

    Topology

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei1 – 2121HelicalSequence AnalysisAdd
    BLAST

    GO - Cellular componenti

    • endoplasmic reticulum Source: TAIR
    • integral component of membrane Source: UniProtKB-KW
    • intracellular membrane-bounded organelle Source: TAIR
    • mitochondrion Source: TAIR
    • plasma membrane Source: TAIR
    Complete GO annotation...

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Disruption phenotypei

    Dwarf. 91% and 97% reduction of the levels of scopoletin and scopolin respectively, but increased levels of skimmin, the beta-glucoside of umbelliferone. Altered lignin composition and increased susceptiblity to fungal colonization.3 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi444 – 4441G → D in ref8; loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 508508Cytochrome P450 98A3PRO_0000052199Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki172 – 172Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki189 – 189Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

    Keywords - PTMi

    Isopeptide bond, Ubl conjugation

    Proteomic databases

    PaxDbiO22203.
    PRIDEiO22203.

    Expressioni

    Tissue specificityi

    Highly expressed in stems, roots and siliques. Detected in leaves flowers and seedlings. Highest expression detected in differentiating xylem.3 Publications

    Inductioni

    Up-regulated by wounding.1 Publication

    Interactioni

    Protein-protein interaction databases

    BioGridi4023. 1 interaction.
    STRINGi3702.AT2G40890.1.

    Structurei

    3D structure databases

    ProteinModelPortaliO22203.
    SMRiO22203. Positions 26-487.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the cytochrome P450 family.Curated

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG2124.
    HOGENOMiHOG000218628.
    InParanoidiO22203.
    KOiK09754.
    OMAiCTNPENN.
    PhylomeDBiO22203.

    Family and domain databases

    Gene3Di1.10.630.10. 1 hit.
    InterProiIPR001128. Cyt_P450.
    IPR017972. Cyt_P450_CS.
    IPR002401. Cyt_P450_E_grp-I.
    [Graphical view]
    PfamiPF00067. p450. 1 hit.
    [Graphical view]
    PRINTSiPR00463. EP450I.
    PR00385. P450.
    SUPFAMiSSF48264. SSF48264. 1 hit.
    PROSITEiPS00086. CYTOCHROME_P450. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O22203-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSWFLIAVAT IAAVVSYKLI QRLRYKFPPG PSPKPIVGNL YDIKPVRFRC
    60 70 80 90 100
    YYEWAQSYGP IISVWIGSIL NVVVSSAELA KEVLKEHDQK LADRHRNRST
    110 120 130 140 150
    EAFSRNGQDL IWADYGPHYV KVRKVCTLEL FTPKRLESLR PIREDEVTAM
    160 170 180 190 200
    VESVFRDCNL PENRAKGLQL RKYLGAVAFN NITRLAFGKR FMNAEGVVDE
    210 220 230 240 250
    QGLEFKAIVS NGLKLGASLS IAEHIPWLRW MFPADEKAFA EHGARRDRLT
    260 270 280 290 300
    RAIMEEHTLA RQKSSGAKQH FVDALLTLKD QYDLSEDTII GLLWDMITAG
    310 320 330 340 350
    MDTTAITAEW AMAEMIKNPR VQQKVQEEFD RVVGLDRILT EADFSRLPYL
    360 370 380 390 400
    QCVVKESFRL HPPTPLMLPH RSNADVKIGG YDIPKGSNVH VNVWAVARDP
    410 420 430 440 450
    AVWKNPFEFR PERFLEEDVD MKGHDFRLLP FGAGRRVCPG AQLGINLVTS
    460 470 480 490 500
    MMSHLLHHFV WTPPQGTKPE EIDMSENPGL VTYMRTPVQA VATPRLPSDL

    YKRVPYDM
    Length:508
    Mass (Da):57,927
    Last modified:January 1, 1998 - v1
    Checksum:iBD22A574F6B16C35
    GO

    Sequence cautioni

    The sequence AAB86449.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti202 – 2021G → E in AAL06992 (PubMed:14593172).Curated
    Sequence conflicti466 – 4661G → V in BAE98524 (Ref. 4) Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AC002409 Genomic DNA. Translation: AAB86449.2. Different initiation.
    CP002685 Genomic DNA. Translation: AEC09893.1.
    AY056105 mRNA. Translation: AAL06992.1.
    AK226377 mRNA. Translation: BAE98524.1.
    PIRiT00753.
    RefSeqiNP_850337.1. NM_180006.2.
    UniGeneiAt.19895.
    At.24415.

    Genome annotation databases

    EnsemblPlantsiAT2G40890.1; AT2G40890.1; AT2G40890.
    GeneIDi818686.
    KEGGiath:AT2G40890.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AC002409 Genomic DNA. Translation: AAB86449.2. Different initiation.
    CP002685 Genomic DNA. Translation: AEC09893.1.
    AY056105 mRNA. Translation: AAL06992.1.
    AK226377 mRNA. Translation: BAE98524.1.
    PIRiT00753.
    RefSeqiNP_850337.1. NM_180006.2.
    UniGeneiAt.19895.
    At.24415.

    3D structure databases

    ProteinModelPortaliO22203.
    SMRiO22203. Positions 26-487.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4023. 1 interaction.
    STRINGi3702.AT2G40890.1.

    Proteomic databases

    PaxDbiO22203.
    PRIDEiO22203.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT2G40890.1; AT2G40890.1; AT2G40890.
    GeneIDi818686.
    KEGGiath:AT2G40890.

    Organism-specific databases

    GeneFarmi1309. 94.
    TAIRiAT2G40890.

    Phylogenomic databases

    eggNOGiCOG2124.
    HOGENOMiHOG000218628.
    InParanoidiO22203.
    KOiK09754.
    OMAiCTNPENN.
    PhylomeDBiO22203.

    Enzyme and pathway databases

    BioCyciMetaCyc:AT2G40890-MONOMER.
    SABIO-RKO22203.

    Miscellaneous databases

    PROiO22203.

    Family and domain databases

    Gene3Di1.10.630.10. 1 hit.
    InterProiIPR001128. Cyt_P450.
    IPR017972. Cyt_P450_CS.
    IPR002401. Cyt_P450_E_grp-I.
    [Graphical view]
    PfamiPF00067. p450. 1 hit.
    [Graphical view]
    PRINTSiPR00463. EP450I.
    PR00385. P450.
    SUPFAMiSSF48264. SSF48264. 1 hit.
    PROSITEiPS00086. CYTOCHROME_P450. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    3. "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] OF 79-508.
      Strain: cv. Columbia.
    4. "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 (JUL-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "CYP98A3 from Arabidopsis thaliana is a 3'-hydroxylase of phenolic esters, a missing link in the phenylpropanoid pathway."
      Schoch G., Goepfert S., Morant M., Hehn A., Meyer D., Ullmann P., Werck-Reichhart D.
      J. Biol. Chem. 276:36566-36574(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, TISSUE SPECIFICITY, INDUCTION BY WOUNDING.
      Strain: cv. Columbia.
    6. "The Arabidopsis REF8 gene encodes the 3-hydroxylase of phenylpropanoid metabolism."
      Franke R., Humphreys J.M., Hemm M.R., Denault J.W., Ruegger M.O., Cusumano J.C., Chapple C.
      Plant J. 30:33-45(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF GLY-444, TISSUE SPECIFICITY, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
    7. "Changes in secondary metabolism and deposition of an unusual lignin in the ref8 mutant of Arabidopsis."
      Franke R., Hemm M.R., Denault J.W., Ruegger M.O., Humphreys J.M., Chapple C.
      Plant J. 30:47-59(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
      Strain: cv. Columbia.
    8. "Accumulation of coumarins in Arabidopsis thaliana."
      Kai K., Shimizu B., Mizutani M., Watanabe K., Sakata K.
      Phytochemistry 67:379-386(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
      Strain: cv. Columbia.
    9. "A coumaroyl-ester-3-hydroxylase insertion mutant reveals the existence of nonredundant meta-hydroxylation pathways and essential roles for phenolic precursors in cell expansion and plant growth."
      Abdulrazzak N., Pollet B., Ehlting J., Larsen K., Asnaghi C., Ronseau S., Proux C., Erhardt M., Seltzer V., Renou J.P., Ullmann P., Pauly M., Lapierre C., Werck-Reichhart D.
      Plant Physiol. 140:30-48(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    10. "Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants."
      Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.
      Mol. Cell. Proteomics 6:601-610(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-172 AND LYS-189.
      Strain: cv. Landsberg erecta.
    11. Cited for: CATALYTIC ACTIVITY, TISSUE SPECIFICITY, 3D-STRUCTURE MODELING.
    12. "Gene engineering, purification, crystallization and preliminary X-ray diffraction of cytochrome P450 p-coumarate-3-hydroxylase (C3H), the Arabidopsis membrane protein."
      Kim Y.H., Kwon T., Yang H.J., Kim W., Youn H., Lee J.Y., Youn B.
      Protein Expr. Purif. 79:149-155(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION.

    Entry informationi

    Entry nameiC98A3_ARATH
    AccessioniPrimary (citable) accession number: O22203
    Secondary accession number(s): Q0WWH4, Q940C7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: January 1, 1998
    Last modified: July 22, 2015
    This is version 129 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

    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 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.