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Protein

Homeobox-leucine zipper protein PROTODERMAL FACTOR 2

Gene

PDF2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Probable transcription factor that binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters. Functionally redundant to ATML1.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi62 – 12160HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: TAIR
  • lipid binding Source: InterPro
  • sequence-specific DNA binding Source: InterPro
  • transcription factor activity, sequence-specific DNA binding Source: TAIR

GO - Biological processi

  • cotyledon development Source: TAIR
  • epidermal cell differentiation Source: TAIR
  • seed germination Source: TAIR
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Differentiation, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
Alternative name(s):
HD-ZIP protein PDF2
Homeodomain transcription factor PDF2
Gene namesi
Name:PDF2
Ordered Locus Names:At4g04890
ORF Names:T1J1.3
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G04890.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 743743Homeobox-leucine zipper protein PROTODERMAL FACTOR 2PRO_0000331735Add
BLAST

Proteomic databases

PaxDbiQ93V99.
PRIDEiQ93V99.

PTM databases

iPTMnetiQ93V99.

Expressioni

Tissue specificityi

Specifically expressed in the layer 1 (L1) of shoot meristems.1 Publication

Gene expression databases

GenevisibleiQ93V99. AT.

Interactioni

Protein-protein interaction databases

BioGridi11139. 8 interactions.
IntActiQ93V99. 3 interactions.
STRINGi3702.AT4G04890.1.

Structurei

3D structure databases

ProteinModelPortaliQ93V99.
SMRiQ93V99. Positions 62-127.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini244 – 476233STARTPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili110 – 19283Sequence analysisAdd
BLAST

Sequence similaritiesi

Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation
Contains 1 START domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil, Homeobox

Phylogenomic databases

eggNOGiENOG410IIN5. Eukaryota.
ENOG411107H. LUCA.
HOGENOMiHOG000243256.
InParanoidiQ93V99.
KOiK09338.
OMAiWIEHMEV.
PhylomeDBiQ93V99.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
3.30.530.20. 1 hit.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR023393. START-like_dom.
IPR002913. START_lipid-bd_dom.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF01852. START. 1 hit.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
SM00234. START. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS50848. START. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q93V99-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYHPNMFESH HMFDMTPKST SDNDLGITGS REDDFETKSG TEVTTENPSG
60 70 80 90 100
EELQDPSQRP NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLN
110 120 130 140 150
LEPLQVKFWF QNKRTQMKAQ SERHENQILK SDNDKLRAEN NRYKEALSNA
160 170 180 190 200
TCPNCGGPAA IGEMSFDEQH LRIENARLRE EIDRISAIAA KYVGKPLGSS
210 220 230 240 250
FAPLAIHAPS RSLDLEVGNF GNQTGFVGEM YGTGDILRSV SIPSETDKPI
260 270 280 290 300
IVELAVAAME ELVRMAQTGD PLWLSTDNSV EILNEEEYFR TFPRGIGPKP
310 320 330 340 350
LGLRSEASRQ SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST
360 370 380 390 400
GVAGNYNGAL QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL
410 420 430 440 450
DSLRPSTPIL RTRRRPSGCL IQELPNGYSK VTWIEHMEVD DRSVHNMYKP
460 470 480 490 500
LVQSGLAFGA KRWVATLERQ CERLASSMAS NIPGDLSVIT SPEGRKSMLK
510 520 530 540 550
LAERMVMSFC SGVGASTAHA WTTMSTTGSD DVRVMTRKSM DDPGRPPGIV
560 570 580 590 600
LSAATSFWIP VAPKRVFDFL RDENSRKEWD ILSNGGMVQE MAHIANGHEP
610 620 630 640 650
GNCVSLLRVN SGNSSQSNML ILQESCTDAS GSYVIYAPVD IVAMNVVLSG
660 670 680 690 700
GDPDYVALLP SGFAILPDGS VGGGDGNQHQ EMVSTTSSGS CGGSLLTVAF
710 720 730 740
QILVDSVPTA KLSLGSVATV NSLIKCTVER IKAAVSCDVG GGA
Length:743
Mass (Da):81,530
Last modified:December 1, 2001 - v1
Checksum:iDF305491CC69EF8C
GO

Sequence cautioni

The sequence AAD17342.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB81031.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB056455 Genomic DNA. Translation: BAB58961.1.
AF128393 Genomic DNA. Translation: AAD17342.1. Sequence problems.
AL161502 Genomic DNA. Translation: CAB81031.1. Different initiation.
CP002687 Genomic DNA. Translation: AEE82438.1.
AF424560 mRNA. Translation: AAL11554.1.
AY062575 mRNA. Translation: AAL32653.1.
BT000144 mRNA. Translation: AAN15463.1.
PIRiE85061.
RefSeqiNP_567274.1. NM_116727.3.
UniGeneiAt.4047.

Genome annotation databases

EnsemblPlantsiAT4G04890.1; AT4G04890.1; AT4G04890.
GeneIDi825828.
GrameneiAT4G04890.1; AT4G04890.1; AT4G04890.
KEGGiath:AT4G04890.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB056455 Genomic DNA. Translation: BAB58961.1.
AF128393 Genomic DNA. Translation: AAD17342.1. Sequence problems.
AL161502 Genomic DNA. Translation: CAB81031.1. Different initiation.
CP002687 Genomic DNA. Translation: AEE82438.1.
AF424560 mRNA. Translation: AAL11554.1.
AY062575 mRNA. Translation: AAL32653.1.
BT000144 mRNA. Translation: AAN15463.1.
PIRiE85061.
RefSeqiNP_567274.1. NM_116727.3.
UniGeneiAt.4047.

3D structure databases

ProteinModelPortaliQ93V99.
SMRiQ93V99. Positions 62-127.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi11139. 8 interactions.
IntActiQ93V99. 3 interactions.
STRINGi3702.AT4G04890.1.

PTM databases

iPTMnetiQ93V99.

Proteomic databases

PaxDbiQ93V99.
PRIDEiQ93V99.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G04890.1; AT4G04890.1; AT4G04890.
GeneIDi825828.
GrameneiAT4G04890.1; AT4G04890.1; AT4G04890.
KEGGiath:AT4G04890.

Organism-specific databases

TAIRiAT4G04890.

Phylogenomic databases

eggNOGiENOG410IIN5. Eukaryota.
ENOG411107H. LUCA.
HOGENOMiHOG000243256.
InParanoidiQ93V99.
KOiK09338.
OMAiWIEHMEV.
PhylomeDBiQ93V99.

Miscellaneous databases

PROiQ93V99.

Gene expression databases

GenevisibleiQ93V99. AT.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
3.30.530.20. 1 hit.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR023393. START-like_dom.
IPR002913. START_lipid-bd_dom.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF01852. START. 1 hit.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
SM00234. START. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS50848. START. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis."
    Abe M., Katsumata H., Komeda Y., Takahashi T.
    Development 130:635-643(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, TISSUE SPECIFICITY.
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [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. "Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2."
    Tavares R., Aubourg S., Lecharny A., Kreis M.
    Plant Mol. Biol. 42:703-717(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY.
  6. "Characterization of the class IV homeodomain-leucine zipper gene family in Arabidopsis."
    Nakamura M., Katsumata H., Abe M., Yabe N., Komeda Y., Yamamoto K.T., Takahashi T.
    Plant Physiol. 141:1363-1375(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.

Entry informationi

Entry nameiPDF2_ARATH
AccessioniPrimary (citable) accession number: Q93V99
Secondary accession number(s): Q9M0Z0, Q9ZPH7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 29, 2008
Last sequence update: December 1, 2001
Last modified: February 17, 2016
This is version 106 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

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.