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Q9FK25

- OMT1_ARATH

UniProt

Q9FK25 - OMT1_ARATH

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Protein

Flavone 3'-O-methyltransferase 1

Gene

OMT1

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

Functioni

Methylates OH residues of flavonoid compounds. Converts quercetin into isorhamnetin. Dihydroquercetin is not a substrate. Catalyzes the methylation of monolignols, the lignin precursors. Does not contribute to the phenylpropanoid pattern of the pollen tryphine, but is probably confined to isorhamnetin gylcoside biosynthesis.4 Publications

Catalytic activityi

S-adenosyl-L-methionine + 3'-hydroxyflavone = S-adenosyl-L-homocysteine + 3'-methoxyflavone.1 Publication
S-adenosyl-L-methionine + 3,4-dihydroxy-trans-cinnamate = S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-trans-cinnamate.1 Publication

Enzyme regulationi

Does not require magnesium. Completely inhibited by 5 mM of either NiSO4 or p-chloromercuribenzoate (pCMB).1 Publication

Kineticsi

  1. KM=1.76 µM for quercetin (at 30 degrees Celsius, PubMed:10700397)2 Publications
  2. KM=3.38 µM for myricetin (at 30 degrees Celsius, PubMed:10700397)2 Publications
  3. KM=24.2 µM for caffeic acid (at pH 7.5, PubMed:20652169)2 Publications
  4. KM=32 µM for 5-OH ferulic acid (at pH 7.5, PubMed:20652169)2 Publications
  5. KM=19.7 µM for caffeyl aldehyde (at pH 7.5, PubMed:20652169)2 Publications
  6. KM=17.9 µM for 5-OH coniferyl aldehyde (at pH 7.5, PubMed:20652169)2 Publications
  7. KM=51.5 µM for caffeyl alcohol (at pH 7.5, PubMed:20652169)2 Publications
  8. KM=31.6 µM for 5-OH coniferyl alcohol (at pH 7.5, PubMed:20652169)2 Publications
  9. KM=23.7 µM for quercetin (at pH 7.5, PubMed:20652169)2 Publications

Vmax=384.6 pmol/sec/mg enzyme with quercetin as substrate2 Publications

Vmax=227.3 pmol/sec/mg enzyme with myricetin as substrate2 Publications

Vmax=3.8 pmol/sec/µg enzyme with quercetin as substrate (at pH 7.5, PubMed:20652169)2 Publications

Vmax=51.9 pmol/sec/µg enzyme with 5-OH coniferyl alcohol as substrate (at pH 7.5, PubMed:20652169)2 Publications

Vmax=35.3 pmol/sec/µg enzyme with caffeyl alcohol as substrate (at pH 7.5, PubMed:20652169)2 Publications

Vmax=66.2 pmol/sec/µg enzyme with 5-OH coniferyl aldehyde as substrate (at pH 7.5, PubMed:20652169)2 Publications

Vmax=35.9 pmol/sec/µg enzyme with caffeyl aldehyde as substrate (at pH 7.5, PubMed:20652169)2 Publications

Vmax=30.1 pmol/sec/µg enzyme with 5-OH ferulic acid as substrate (at pH 7.5, PubMed:20652169)2 Publications

Vmax=14.6 pmol/sec/µg enzyme with caffeic acid as substrate (at pH 7.5, PubMed:20652169)2 Publications

pH dependencei

Optimum pH is 7.5.2 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei206 – 2061S-adenosyl-L-methionine; via carbonyl oxygenPROSITE-ProRule annotation
Binding sitei229 – 2291S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei249 – 2491S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei250 – 2501S-adenosyl-L-methionine; via amide nitrogenPROSITE-ProRule annotation
Binding sitei263 – 2631S-adenosyl-L-methioninePROSITE-ProRule annotation
Active sitei267 – 2671Proton acceptorPROSITE-ProRule annotation

GO - Molecular functioni

  1. caffeate O-methyltransferase activity Source: TAIR
  2. luteolin O-methyltransferase activity Source: UniProtKB
  3. myricetin 3'-O-methyltransferase activity Source: TAIR
  4. quercetin 3-O-methyltransferase activity Source: TAIR

GO - Biological processi

  1. flavonol biosynthetic process Source: TAIR
  2. lignin biosynthetic process Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.76. 399.
UniPathwayiUPA00724.

Names & Taxonomyi

Protein namesi
Recommended name:
Flavone 3'-O-methyltransferase 1 (EC:2.1.1.42)
Short name:
AtOMT1
Alternative name(s):
Caffeate O-methyltransferase 1 (EC:2.1.1.68)
Quercetin 3'-O-methyltransferase 1
Gene namesi
Name:OMT1
Synonyms:COMT1
Ordered Locus Names:At5g54160
ORF Names:K18G13.3
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 5

Organism-specific databases

TAIRiAT5G54160.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: TAIR
  2. nucleus Source: TAIR
  3. plasma membrane Source: TAIR
  4. plasmodesma Source: TAIR
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Reduced levels of syringyl (S) units in lignins that contain more 5-hydroxyguaiacyl units (5-OH-G), the precursors of S-units. Substitution of sinapyl (S) alcohol-derived substructures by 5-hydroxyconiferyl alcohol (5OHG)-derived moieties in fiber cell walls. No effect on hydroxycinnamic acid amides in pollen.3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 363363Flavone 3'-O-methyltransferase 1PRO_0000063217Add
BLAST

Proteomic databases

PaxDbiQ9FK25.
PRIDEiQ9FK25.

Expressioni

Tissue specificityi

Expressed in seedlings, leaves, stems, flowers and siliques, mostly in vascular tissues. Mostly expressed in the apical part of the stems and in roots. Expressed in the endothecium and the epidermal anther, but not in the tapetum. Also detected in all epidermal tissues of flower organs, including petals, sepals and the tip of the stigma.2 Publications

Developmental stagei

Observed in young seedling and progressively restricted to vascular tissues. Present in whole blade of young leaves but confined to the vascular tissues of mature leaves. In stems, mostly present in xylem, mature phloem and differentiating fibers. In siliques, only present in the lignified extremities. Expressed during early and late stages of flower development.2 Publications

Gene expression databases

GenevestigatoriQ9FK25.

Interactioni

Subunit structurei

Monomer.

Binary interactionsi

WithEntry#Exp.IntActNotes
BRL1Q9ZPS91EBI-1633761,EBI-2292728
GRF6P483491EBI-1633761,EBI-1633785

Protein-protein interaction databases

BioGridi20748. 2 interactions.
IntActiQ9FK25. 4 interactions.
MINTiMINT-8066865.

Structurei

Secondary structure

1
363
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi12 – 143
Helixi20 – 234
Turni29 – 313
Helixi32 – 365
Turni40 – 423
Helixi45 – 506
Helixi57 – 604
Beta strandi63 – 686
Helixi74 – 785
Helixi81 – 844
Beta strandi85 – 873
Beta strandi90 – 923
Beta strandi96 – 983
Beta strandi102 – 1043
Turni111 – 1133
Beta strandi117 – 1193
Helixi125 – 1284
Beta strandi135 – 1373
Helixi142 – 1454
Helixi151 – 1555
Helixi160 – 1667
Helixi168 – 19225
Beta strandi200 – 2045
Beta strandi208 – 2103
Turni213 – 2164
Beta strandi221 – 2299
Turni231 – 2333
Beta strandi243 – 2486
Beta strandi250 – 2523
Beta strandi258 – 2658
Turni266 – 2683
Helixi273 – 28311
Beta strandi290 – 2956
Helixi306 – 3094
Helixi314 – 3207
Beta strandi322 – 3243
Helixi330 – 34011
Beta strandi343 – 3508
Beta strandi355 – 3606

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NIImodel-A1-363[»]
ProteinModelPortaliQ9FK25.
SMRiQ9FK25. Positions 10-363.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-independent O-methyltransferase family. COMT subfamily.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0500.
HOGENOMiHOG000238276.
KOiK13066.
OMAiCRTEESK.
PhylomeDBiQ9FK25.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.40.50.150. 1 hit.
InterProiIPR016461. COMT.
IPR001077. O_MeTrfase_2.
IPR012967. Plant_MeTrfase_dimerisation.
IPR029063. SAM-dependent_MTases-like.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF08100. Dimerisation. 1 hit.
PF00891. Methyltransf_2. 1 hit.
[Graphical view]
PIRSFiPIRSF005739. O-mtase. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51683. SAM_OMT_II. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9FK25-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGSTAETQLT PVQVTDDEAA LFAMQLASAS VLPMALKSAL ELDLLEIMAK
60 70 80 90 100
NGSPMSPTEI ASKLPTKNPE APVMLDRILR LLTSYSVLTC SNRKLSGDGV
110 120 130 140 150
ERIYGLGPVC KYLTKNEDGV SIAALCLMNQ DKVLMESWYH LKDAILDGGI
160 170 180 190 200
PFNKAYGMSA FEYHGTDPRF NKVFNNGMSN HSTITMKKIL ETYKGFEGLT
210 220 230 240 250
SLVDVGGGIG ATLKMIVSKY PNLKGINFDL PHVIEDAPSH PGIEHVGGDM
260 270 280 290 300
FVSVPKGDAI FMKWICHDWS DEHCVKFLKN CYESLPEDGK VILAECILPE
310 320 330 340 350
TPDSSLSTKQ VVHVDCIMLA HNPGGKERTE KEFEALAKAS GFKGIKVVCD
360
AFGVNLIELL KKL
Length:363
Mass (Da):39,618
Last modified:March 1, 2001 - v1
Checksum:iB4380028D89C43DC
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti229 – 2291D → N in AAB96879. (PubMed:9349713)Curated
Sequence conflicti295 – 2951E → V in CAA81580. (PubMed:8580968)Curated
Sequence conflicti301 – 3011T → S in CAA81580. (PubMed:8580968)Curated
Sequence conflicti348 – 3481V → C in CAA81580. (PubMed:8580968)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U70424 mRNA. Translation: AAB96879.1.
AB013387 Genomic DNA. Translation: BAB11578.1.
CP002688 Genomic DNA. Translation: AED96460.1.
AY062837 mRNA. Translation: AAL32915.1.
AY081565 mRNA. Translation: AAM10127.1.
AY087297 mRNA. Translation: AAM64849.1.
Z27062 mRNA. Translation: CAA81580.1.
RefSeqiNP_200227.1. NM_124796.3.
UniGeneiAt.47593.
At.72792.
At.74847.

Genome annotation databases

EnsemblPlantsiAT5G54160.1; AT5G54160.1; AT5G54160.
GeneIDi835504.
KEGGiath:AT5G54160.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U70424 mRNA. Translation: AAB96879.1 .
AB013387 Genomic DNA. Translation: BAB11578.1 .
CP002688 Genomic DNA. Translation: AED96460.1 .
AY062837 mRNA. Translation: AAL32915.1 .
AY081565 mRNA. Translation: AAM10127.1 .
AY087297 mRNA. Translation: AAM64849.1 .
Z27062 mRNA. Translation: CAA81580.1 .
RefSeqi NP_200227.1. NM_124796.3.
UniGenei At.47593.
At.72792.
At.74847.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1NII model - A 1-363 [» ]
ProteinModelPortali Q9FK25.
SMRi Q9FK25. Positions 10-363.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 20748. 2 interactions.
IntActi Q9FK25. 4 interactions.
MINTi MINT-8066865.

Proteomic databases

PaxDbi Q9FK25.
PRIDEi Q9FK25.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT5G54160.1 ; AT5G54160.1 ; AT5G54160 .
GeneIDi 835504.
KEGGi ath:AT5G54160.

Organism-specific databases

TAIRi AT5G54160.

Phylogenomic databases

eggNOGi COG0500.
HOGENOMi HOG000238276.
KOi K13066.
OMAi CRTEESK.
PhylomeDBi Q9FK25.

Enzyme and pathway databases

UniPathwayi UPA00724 .
BRENDAi 2.1.1.76. 399.

Miscellaneous databases

PROi Q9FK25.

Gene expression databases

Genevestigatori Q9FK25.

Family and domain databases

Gene3Di 1.10.10.10. 1 hit.
3.40.50.150. 1 hit.
InterProi IPR016461. COMT.
IPR001077. O_MeTrfase_2.
IPR012967. Plant_MeTrfase_dimerisation.
IPR029063. SAM-dependent_MTases-like.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view ]
Pfami PF08100. Dimerisation. 1 hit.
PF00891. Methyltransf_2. 1 hit.
[Graphical view ]
PIRSFi PIRSF005739. O-mtase. 1 hit.
SUPFAMi SSF53335. SSF53335. 1 hit.
PROSITEi PS51683. SAM_OMT_II. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "An Arabidopsis gene encoding a putative 14-3-3-interacting protein, caffeic acid/5-hydroxyferulic acid O-methyltransferase."
    Zhang H., Wang J., Goodman H.M.
    Biochim. Biophys. Acta 1353:199-202(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. C24.
    Tissue: Leaf.
  2. "Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence features of the regions of 1,367,185 bp covered by 19 physically assigned P1 and TAC clones."
    Kotani H., Nakamura Y., Sato S., Asamizu E., Kaneko T., Miyajima N., Tabata S.
    DNA Res. 5:203-216(1998) [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. "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].
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 285-363.
    Strain: cv. Columbia.
    Tissue: Green siliques.
  7. "Functional expression of an Arabidopsis cDNA clone encoding a flavonol 3'-O-methyltransferase and characterization of the gene product."
    Muzac I., Wang J., Anzellotti D., Zhang H., Ibrahim R.K.
    Arch. Biochem. Biophys. 375:385-388(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
  8. "A new Arabidopsis thaliana mutant deficient in the expression of O-methyltransferase impacts lignins and sinapoyl esters."
    Goujon T., Sibout R., Pollet B., Maba B., Nussaume L., Bechtold N., Lu F., Ralph J., Mila I., Barriere Y., Lapierre C., Jouanin L.
    Plant Mol. Biol. 51:973-989(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    Strain: cv. Wassilewskija.
  9. "Insights into lignin primary structure and deconstruction from Arabidopsis thaliana COMT (caffeic acid O-methyl transferase) mutant Atomt1."
    Moinuddin S.G.A., Jourdes M., Laskar D.D., Ki C., Cardenas C.L., Kim K.-W., Zhang D., Davin L.B., Lewis N.G.
    Org. Biomol. Chem. 8:3928-3946(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: cv. Wassilewskija.
  10. "The role of CCoAOMT1 and COMT1 in Arabidopsis anthers."
    Fellenberg C., van Ohlen M., Handrick V., Vogt T.
    Planta 236:51-61(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
  11. "The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity."
    Saito K., Yonekura-Sakakibara K., Nakabayashi R., Higashi Y., Yamazaki M., Tohge T., Fernie A.R.
    Plant Physiol. Biochem. 0:0-0(2013)
    Cited for: REVIEW, NOMENCLATURE.
  12. "The three-dimensional structure of Arabidopsis thaliana O-methyltransferase predicted by homology-based modelling."
    Yang H., Ahn J.-H., Ibrahim R.K., Lee S., Lim Y.
    J. Mol. Graph. Model. 23:77-87(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING.

Entry informationi

Entry nameiOMT1_ARATH
AccessioniPrimary (citable) accession number: Q9FK25
Secondary accession number(s): O49964, Q42170
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 19, 2002
Last sequence update: March 1, 2001
Last modified: October 29, 2014
This is version 109 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

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

External Data

Dasty 3