Q9ZWM9 (RAV1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
AP2/ERF and B3 domain-containing transcription factor RAV1

Alternative name(s):
Ethylene-responsive transcription factor RAV1
Protein RELATED TO ABI3/VP1 1

Gene names

Name:	RAV1
Ordered Locus Names:	At1g13260
ORF Names:	T6J4.2

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	344 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3'. May function as negative regulator of plant growth and development. Ref.1 Ref.8
Subunit structure	Monomer.
Subcellular location	Nucleus Probable.
Tissue specificity	Expressed in all tissues examined: Roots, rosette leaves, cauline leaves, inflorescence stems, flowers and siliques. Highest expression in roots and rosette leaves. Very low expression in flowers. Ref.1
Induction	Down-regulated by brassinosteroid and zeatin. Ref.8
Domain	Contains two distinct DNA-binding domains. One is located in the N-terminal region and binds to the 5'-CAACA-3' motif. The second is located in the C-terminal region and binds to the 5'-CACCTG-3' motif.
Sequence similarities	Belongs to the AP2/ERF transcription factor family. RAV subfamily. Contains 1 AP2/ERF DNA-binding domain. Contains 1 TF-B3 DNA-binding domain.

Ontologies

Keywords
Biological process	Ethylene signaling pathway Transcription Transcription regulation
Cellular component	Nucleus
Ligand	DNA-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ethylene mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW lateral root development Inferred from mutant phenotype Ref.8. Source: TAIR leaf development Inferred from mutant phenotype Ref.8. Source: TAIR negative regulation of flower development Inferred from mutant phenotype Ref.8. Source: TAIR negative regulation of transcription, DNA-dependent Inferred from direct assay PubMed 19324928. Source: TAIR response to brassinosteroid stimulus Inferred from expression pattern Ref.8. Source: TAIR transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from direct assay PubMed 15610358. Source: TAIR
Molecular_function	DNA binding Inferred from direct assay Ref.6. Source: TAIR sequence-specific DNA binding transcription factor activity Inferred from sequence or structural similarity PubMed 11118137. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 344

344

AP2/ERF and B3 domain-containing transcription factor RAV1

PRO_0000112571

Regions

DNA binding

61 – 116

56

AP2/ERF

DNA binding

188 – 292

105

TF-B3

Secondary structure

1

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344

Helix Strand Turn

Details...

Beta strand

185 – 191

7

Turn

194 – 197

4

Beta strand

198 – 200

3

Beta strand

203 – 205

3

Helix

207 – 210

4

Turn

211 – 213

3

Beta strand

226 – 232

7

Turn

233 – 235

3

Beta strand

236 – 245

10

Turn

246 – 249

4

Beta strand

250 – 256

7

Helix

257 – 263

7

Beta strand

271 – 276

6

Beta strand

279 – 281

3

Beta strand

284 – 289

6

Sequences

	Sequence		Length	Mass (Da)
	Q9ZWM9 [UniParc]. Last modified May 1, 1999. Version 1. Checksum: 7349B640B3505823	FASTA	344	38,597
	10 20 30 40 50 60 MESSSVDEST TSTGSICETP AITPAKKSSV GNLYRMGSGS SVVLDSENGV EAESRKLPSS 70 80 90 100 110 120 KYKGVVPQPN GRWGAQIYEK HQRVWLGTFN EEDEAARAYD VAVHRFRRRD AVTNFKDVKM 130 140 150 160 170 180 DEDEVDFLNS HSKSEIVDML RKHTYNEELE QSKRRRNGNG NMTRTLLTSG LSNDGVSTTG 190 200 210 220 230 240 FRSAEALFEK AVTPSDVGKL NRLVIPKHHA EKHFPLPSSN VSVKGVLLNF EDVNGKVWRF 250 260 270 280 290 300 RYSYWNSSQS YVLTKGWSRF VKEKNLRAGD VVSFSRSNGQ DQQLYIGWKS RSGSDLDAGR 310 320 330 340 VLRLFGVNIS PESSRNDVVG NKRVNDTEML SLVCSKKQRI FHAS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants." Kagaya Y., Ohmiya K., Hattori T. Nucleic Acids Res. 27:470-478(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY. Strain: cv. Columbia. Tissue: Seedling.
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [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]	"The plant B3 superfamily." Swaminathan K., Peterson K., Jack T. Trends Plant Sci. 13:647-655(2008) [PubMed] [Europe PMC] [Abstract] Cited for: GENE FAMILY.
[6]	"Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1." Yamasaki K., Kigawa T., Inoue M., Tateno M., Yamasaki T., Yabuki T., Aoki M., Seki E., Matsuda T., Tomo Y., Hayami N., Terada T., Shirouzu M., Osanai T., Tanaka A., Seki M., Shinozaki K., Yokoyama S. Plant Cell 16:3448-3459(2004) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 182-298.
[7]	"Genome-wide analysis of the ERF gene family in Arabidopsis and rice." Nakano T., Suzuki K., Fujimura T., Shinshi H. Plant Physiol. 140:411-432(2006) [PubMed] [Europe PMC] [Abstract] Cited for: GENE FAMILY, NOMENCLATURE.
[8]	"Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development." Hu Y.X., Wang Y.H., Liu X.F., Li J.Y. Cell Res. 14:8-15(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INDUCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB013886 mRNA. Translation: BAA34250.1.
AC011810 Genomic DNA. Translation: AAG09554.1.
CP002684 Genomic DNA. Translation: AEE28991.1.
AY063855 mRNA. Translation: AAL36211.1.
AY091291 mRNA. Translation: AAM14230.1.

IPI

IPI00544013.

PIR

T51329.

RefSeq

NP_172784.1. NM_101197.3.

UniGene

At.20558.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WID	NMR	-	A	182-298	[»]

ProteinModelPortal

Q9ZWM9.

SMR

Q9ZWM9. Positions 62-115, 182-298.

ModBase

Search...

Protein-protein interaction databases

STRING

3702.AT1G13260.1-P.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT1G13260.1; AT1G13260.1; AT1G13260.

GeneID

837886.

KEGG

ath:AT1G13260.

Organism-specific databases

TAIR

At1g13260.

Phylogenomic databases

eggNOG

NOG266118.

HOGENOM

HOG000237484.

InParanoid

Q9ZWM9.

KO

K09287.

OMA

ICETPAI.

PhylomeDB

Q9ZWM9.

ProtClustDB

CLSN2682511.

Gene expression databases

Genevestigator

Q9ZWM9.

GermOnline

AT1G13260. Arabidopsis thaliana.

Family and domain databases

Gene3D

2.40.330.10. 1 hit.
3.30.730.10. 1 hit.

InterPro

IPR001471. AP2/ERF_dom.
IPR003340. B3_DNA-bd.
IPR016177. DNA-bd_integrase-typ.
IPR015300. DNA-bd_pseudobarrel.
[Graphical view]

Pfam

PF00847. AP2. 1 hit.
PF02362. B3. 1 hit.
[Graphical view]

SMART

SM00380. AP2. 1 hit.
SM01019. B3. 1 hit.
[Graphical view]

SUPFAM

SSF54171. DNA-binding_integrase-type. 1 hit.
SSF101936. Restrict_endonuc_II_EcoRII_N. 1 hit.

PROSITE

PS51032. AP2_ERF. 1 hit.
PS50863. B3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9ZWM9.

Entry information

Entry name

RAV1_ARATH

Accession

Primary (citable) accession number: Q9ZWM9

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 15, 2002
Last sequence update:	May 1, 1999
Last modified:	May 1, 2013
This is version 110 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program