Q9FK25 (OMT1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Flavone 3'-O-methyltransferase 1
Short name=AtOMT1
EC=2.1.1.42

Alternative name(s):
Caffeate O-methyltransferase 1
EC=2.1.1.68
Quercetin 3'-O-methyltransferase 1

Gene names

Name:	OMT1
Synonyms:	COMT1
Ordered Locus Names:	At5g54160
ORF Names:	K18G13.3

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	363 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.7 Ref.8 Ref.10 Ref.11
Catalytic activity	S-adenosyl-L-methionine + 3'-hydroxyflavone = S-adenosyl-L-homocysteine + 3'-methoxyflavone. Ref.8 S-adenosyl-L-methionine + 3,4-dihydroxy-trans-cinnamate = S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-trans-cinnamate. Ref.8
Enzyme regulation	Does not require magnesium. Completely inhibited by 5 mM of either NiSO4 or p-chloromercuribenzoate (pCMB). Ref.7
Pathway	Flavonoid metabolism; quercetin degradation.
Subunit structure	Monomer.
Tissue specificity	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. Ref.8 Ref.11
Developmental stage	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. Ref.8 Ref.11
Disruption phenotype	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. Ref.8 Ref.10 Ref.11
Sequence similarities	Belongs to the methyltransferase superfamily. Type 2 family. COMT subfamily.
Biophysicochemical properties	Kinetic parameters: KM=1.76 µM for quercetin (at 30 degrees Celsius, Ref.7) Ref.7 Ref.10 KM=3.38 µM for myricetin (at 30 degrees Celsius, Ref.7) KM=24.2 µM for caffeic acid (at pH 7.5, Ref.10) KM=32 µM for 5-OH ferulic acid (at pH 7.5, Ref.10) KM=19.7 µM for caffeyl aldehyde (at pH 7.5, Ref.10) KM=17.9 µM for 5-OH coniferyl aldehyde (at pH 7.5, Ref.10) KM=51.5 µM for caffeyl alcohol (at pH 7.5, Ref.10) KM=31.6 µM for 5-OH coniferyl alcohol (at pH 7.5, Ref.10) KM=23.7 µM for quercetin (at pH 7.5, Ref.10) Vmax=384.6 pmol/sec/mg enzyme with quercetin as substrate Vmax=227.3 pmol/sec/mg enzyme with myricetin as substrate Vmax=3.8 pmol/sec/µg enzyme with quercetin as substrate (at pH 7.5, Ref.10) Vmax=51.9 pmol/sec/µg enzyme with 5-OH coniferyl alcohol as substrate (at pH 7.5, Ref.10) Vmax=35.3 pmol/sec/µg enzyme with caffeyl alcohol as substrate (at pH 7.5, Ref.10) Vmax=66.2 pmol/sec/µg enzyme with 5-OH coniferyl aldehyde as substrate (at pH 7.5, Ref.10) Vmax=35.9 pmol/sec/µg enzyme with caffeyl aldehyde as substrate (at pH 7.5, Ref.10) Vmax=30.1 pmol/sec/µg enzyme with 5-OH ferulic acid as substrate (at pH 7.5, Ref.10) Vmax=14.6 pmol/sec/µg enzyme with caffeic acid as substrate (at pH 7.5, Ref.10) pH dependence: Optimum pH is 7.5.

Ontologies

Keywords
Ligand	S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	flavonol biosynthetic process Inferred from direct assay Ref.7. Source: TAIR lignin biosynthetic process Inferred from mutant phenotype Ref.8. Source: TAIR
Cellular_component	cytoplasm Inferred from direct assay PubMed 15610358. Source: TAIR nucleus Inferred from direct assay PubMed 15610358. Source: TAIR plasma membrane Inferred from direct assay PubMed 17317660. Source: TAIR plasmodesma Inferred from direct assay PubMed 21533090. Source: TAIR
Molecular_function	caffeate O-methyltransferase activity Inferred from mutant phenotype Ref.8. Source: TAIR luteolin O-methyltransferase activity Inferred from direct assay Ref.7. Source: UniProtKB myricetin 3'-O-methyltransferase activity Inferred from direct assay Ref.7. Source: TAIR quercetin 3-O-methyltransferase activity Inferred from direct assay Ref.7. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
BRL1	Q9ZPS9	1	EBI-1633761,EBI-2292728
GRF6	P48349	1	EBI-1633761,EBI-1633785

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 363

363

Flavone 3'-O-methyltransferase 1

PRO_0000063217

Sites

Active site

267

1

Proton acceptor By similarity

Binding site

206

1

S-adenosyl-L-methionine; via carbonyl oxygen By similarity

Binding site

229

1

S-adenosyl-L-methionine By similarity

Binding site

249

1

S-adenosyl-L-methionine By similarity

Binding site

250

1

S-adenosyl-L-methionine; via amide nitrogen By similarity

Binding site

263

1

S-adenosyl-L-methionine By similarity

Amino acid modifications

Modified residue

96

1

Phosphoserine Ref.9

Experimental info

Sequence conflict

229

1

D → N in AAB96879. Ref.1

Sequence conflict

295

1

E → V in CAA81580. Ref.6

Sequence conflict

301

1

T → S in CAA81580. Ref.6

Sequence conflict

348

1

V → C in CAA81580. Ref.6

Secondary structure

1

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363

Helix Strand Turn

Details...

Beta strand

12 – 14

3

Helix

20 – 23

4

Turn

29 – 31

3

Helix

32 – 36

5

Turn

40 – 42

3

Helix

45 – 50

6

Helix

57 – 60

4

Beta strand

63 – 68

6

Helix

74 – 78

5

Helix

81 – 84

4

Beta strand

85 – 87

3

Beta strand

90 – 92

3

Beta strand

96 – 98

3

Beta strand

102 – 104

3

Turn

111 – 113

3

Beta strand

117 – 119

3

Helix

125 – 128

4

Beta strand

135 – 137

3

Helix

142 – 145

4

Helix

151 – 155

5

Helix

160 – 166

7

Helix

168 – 192

25

Beta strand

200 – 204

5

Beta strand

208 – 210

3

Turn

213 – 216

4

Beta strand

221 – 229

9

Turn

231 – 233

3

Beta strand

243 – 248

6

Beta strand

250 – 252

3

Beta strand

258 – 265

8

Turn

266 – 268

3

Helix

273 – 283

11

Beta strand

290 – 295

6

Helix

306 – 309

4

Helix

314 – 320

7

Beta strand

322 – 324

3

Helix

330 – 340

11

Beta strand

343 – 350

8

Beta strand

355 – 360

6

Sequences

	Sequence		Length	Mass (Da)
	Q9FK25 [UniParc]. Last modified March 1, 2001. Version 1. Checksum: B4380028D89C43DC	FASTA	363	39,618
	10 20 30 40 50 60 MGSTAETQLT PVQVTDDEAA LFAMQLASAS VLPMALKSAL ELDLLEIMAK NGSPMSPTEI 70 80 90 100 110 120 ASKLPTKNPE APVMLDRILR LLTSYSVLTC SNRKLSGDGV ERIYGLGPVC KYLTKNEDGV 130 140 150 160 170 180 SIAALCLMNQ DKVLMESWYH LKDAILDGGI PFNKAYGMSA FEYHGTDPRF NKVFNNGMSN 190 200 210 220 230 240 HSTITMKKIL ETYKGFEGLT SLVDVGGGIG ATLKMIVSKY PNLKGINFDL PHVIEDAPSH 250 260 270 280 290 300 PGIEHVGGDM FVSVPKGDAI FMKWICHDWS DEHCVKFLKN CYESLPEDGK VILAECILPE 310 320 330 340 350 360 TPDSSLSTKQ VVHVDCIMLA HNPGGKERTE KEFEALAKAS GFKGIKVVCD AFGVNLIELL KKL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs." Cooke R., Raynal M., Laudie M., Grellet F., Delseny M., Morris P.-C., Guerrier D., Giraudat J., Quigley F., Clabault G., Li Y.-F., Mache R., Krivitzky M., Gy I.J.-J., Kreis M., Lecharny A., Parmentier Y., Marbach J. , Fleck J., Clement B., Philipps G., Herve C., Bardet C., Tremousaygue D., Lescure B., Lacomme C., Roby D., Jourjon M.-F., Chabrier P., Charpenteau J.-L., Desprez T., Amselem J., Chiapello H., Hoefte H. Plant J. 9:101-124(1996) [PubMed] [Europe PMC] [Abstract] 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]	"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S. Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-96, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
[10]	"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.
[11]	"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.
[12]	"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.
[13]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00542876.

RefSeq

NP_200227.1. NM_124796.3.

UniGene

At.47593.
At.72792.
At.74847.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NII	model	-	A	1-363	[»]

ProteinModelPortal

Q9FK25.

SMR

Q9FK25. Positions 10-363.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9FK25. 2 interactions.

MINT

MINT-8066865.

Proteomic databases

PaxDb

Q9FK25.

PRIDE

Q9FK25.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT5G54160.1; AT5G54160.1; AT5G54160.

GeneID

835504.

KEGG

ath:AT5G54160.

Organism-specific databases

TAIR

At5g54160.

Phylogenomic databases

eggNOG

COG0500.

HOGENOM

HOG000238276.

InParanoid

Q9FK25.

KO

K05279.

OMA

ANAWAIE.

PhylomeDB

Q9FK25.

ProtClustDB

CLSN2916438.

Enzyme and pathway databases

BRENDA

2.1.1.76. 399.

UniPathway

UPA00724.

Gene expression databases

Genevestigator

Q9FK25.

GermOnline

AT5G54160. Arabidopsis thaliana.

Family and domain databases

Gene3D

1.10.10.10. 1 hit.

InterPro

IPR016461. COMT.
IPR001077. O_MeTrfase_2.
IPR012967. Plant_MeTrfase_dimerisation.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]

Pfam

PF08100. Dimerisation. 1 hit.
PF00891. Methyltransf_2. 1 hit.
[Graphical view]

PIRSF

PIRSF005739. O-mtase. 1 hit.

ProtoNet

Search...

Entry information

Entry name

OMT1_ARATH

Accession

Primary (citable) accession number: Q9FK25
Secondary accession number(s): O49964, Q42170

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 19, 2002
Last sequence update:	March 1, 2001
Last modified:	May 29, 2013
This is version 98 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program