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Protein

Zinc-finger homeodomain protein 2

Gene

ZHD1

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

Functioni

Essential protein. Putative transcription factor.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei209 – 2091Required for DNA-bindingBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri49 – 9850ZF-HD dimerization-typePROSITE-ProRule annotationAdd
BLAST
DNA bindingi157 – 22064Homeobox; atypicalAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: TAIR
  • metal ion binding Source: UniProtKB-KW
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

  • embryo development ending in seed dormancy Source: TAIR
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Zinc-finger homeodomain protein 2
Short name:
AtZHD2
Alternative name(s):
Homeobox protein 22
Short name:
AtHB-22
Protein MATERNAL EFFECT EMBRYO ARREST 68
Gene namesi
Name:ZHD1
Synonyms:HB22, MEE68
Ordered Locus Names:At4g24660
ORF Names:F22K18.140
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G24660.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Arrested at early embryo stages.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 220220Zinc-finger homeodomain protein 2PRO_0000056846Add
BLAST

Proteomic databases

PaxDbiQ9SB61.

Expressioni

Tissue specificityi

Mostly expressed in flowers and, to a lower extent, in inflorescence, stems and leaves.1 Publication

Gene expression databases

GenevisibleiQ9SB61. AT.

Interactioni

Subunit structurei

Homo or heterodimer. Interacts with ZHD1, ZHD3, ZHD4, ZHD5, ZHD6, ZHD7, ZHD8, ZHD9, ZHD10 and ZHD11.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
ZHD8Q9LXG03EBI-1806256,EBI-1806405

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi13857. 2 interactions.
IntActiQ9SB61. 10 interactions.
STRINGi3702.AT4G24660.1.

Structurei

Secondary structure

1
220
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi166 – 17914Combined sources
Helixi189 – 1979Combined sources
Helixi202 – 2109Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WH7NMR-A148-214[»]
ProteinModelPortaliQ9SB61.
SMRiQ9SB61. Positions 156-215.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9SB61.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi33 – 386Poly-Gly

Domaini

The homeodomain differs form the typical one by having namely 4 instead of 3 extra amino acids inserted in the loop between helix 1 and helix 2.

Sequence similaritiesi

Contains 1 homeobox DNA-binding domain.Curated
Contains 1 ZF-HD dimerization-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri49 – 9850ZF-HD dimerization-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Homeobox, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IX1N. Eukaryota.
ENOG410YEN7. LUCA.
HOGENOMiHOG000238105.
InParanoidiQ9SB61.
OMAiNHAVNIG.
PhylomeDBiQ9SB61.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR009057. Homeodomain-like.
IPR006455. Homeodomain_ZF_HD.
IPR006456. ZF_HD_homeobox_Cys/His_dimer.
[Graphical view]
PfamiPF04770. ZF-HD_dimer. 1 hit.
[Graphical view]
ProDomiPD125774. ZF_HD_N. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF46689. SSF46689. 1 hit.
TIGRFAMsiTIGR01565. homeo_ZF_HD. 1 hit.
TIGR01566. ZF_HD_prot_N. 1 hit.
PROSITEiPS51523. ZF_HD_DIMER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9SB61-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNFEDQEEDM EMSGVNPPCG YDSLSGEGAT SSGGGGVGRS KGVGAKIRYR
60 70 80 90 100
ECLKNHAVNI GGHAVDGCCE FMPSGEDGTL DALKCAACGC HRNFHRKETE
110 120 130 140 150
SIGGRAHRVP TYYNRPPQPH QPPGYLHLTS PAAPYRPPAA SGDEEDTSNP
160 170 180 190 200
SSSGGTTKRF RTKFTAEQKE KMLAFAERLG WRIQKHDDVA VEQFCAETGV
210 220
RRQVLKIWMH NNKNSLGKKP
Length:220
Mass (Da):24,023
Last modified:May 1, 2000 - v1
Checksum:i9E8F5BF68AA06897
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL035356 Genomic DNA. Translation: CAA22997.1.
AL161561 Genomic DNA. Translation: CAB79376.1.
CP002687 Genomic DNA. Translation: AEE84939.1.
AF439841 mRNA. Translation: AAL27510.1.
AY125563 mRNA. Translation: AAM78073.1.
PIRiT05568.
RefSeqiNP_194197.1. NM_118599.1.
UniGeneiAt.2543.

Genome annotation databases

EnsemblPlantsiAT4G24660.1; AT4G24660.1; AT4G24660.
GeneIDi828568.
GrameneiAT4G24660.1; AT4G24660.1; AT4G24660.
KEGGiath:AT4G24660.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL035356 Genomic DNA. Translation: CAA22997.1.
AL161561 Genomic DNA. Translation: CAB79376.1.
CP002687 Genomic DNA. Translation: AEE84939.1.
AF439841 mRNA. Translation: AAL27510.1.
AY125563 mRNA. Translation: AAM78073.1.
PIRiT05568.
RefSeqiNP_194197.1. NM_118599.1.
UniGeneiAt.2543.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WH7NMR-A148-214[»]
ProteinModelPortaliQ9SB61.
SMRiQ9SB61. Positions 156-215.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi13857. 2 interactions.
IntActiQ9SB61. 10 interactions.
STRINGi3702.AT4G24660.1.

Proteomic databases

PaxDbiQ9SB61.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G24660.1; AT4G24660.1; AT4G24660.
GeneIDi828568.
GrameneiAT4G24660.1; AT4G24660.1; AT4G24660.
KEGGiath:AT4G24660.

Organism-specific databases

TAIRiAT4G24660.

Phylogenomic databases

eggNOGiENOG410IX1N. Eukaryota.
ENOG410YEN7. LUCA.
HOGENOMiHOG000238105.
InParanoidiQ9SB61.
OMAiNHAVNIG.
PhylomeDBiQ9SB61.

Miscellaneous databases

EvolutionaryTraceiQ9SB61.
PROiQ9SB61.

Gene expression databases

GenevisibleiQ9SB61. AT.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR009057. Homeodomain-like.
IPR006455. Homeodomain_ZF_HD.
IPR006456. ZF_HD_homeobox_Cys/His_dimer.
[Graphical view]
PfamiPF04770. ZF-HD_dimer. 1 hit.
[Graphical view]
ProDomiPD125774. ZF_HD_N. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF46689. SSF46689. 1 hit.
TIGRFAMsiTIGR01565. homeo_ZF_HD. 1 hit.
TIGR01566. ZF_HD_prot_N. 1 hit.
PROSITEiPS51523. ZF_HD_DIMER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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.
  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].
    Strain: cv. Columbia.
  4. "Characterization of a novel class of plant homeodomain proteins that bind to the C4 phosphoenolpyruvate carboxylase gene of Flaveria trinervia."
    Windhoevel A., Hein I., Dabrowa R., Stockhaus J.
    Plant Mol. Biol. 45:201-214(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  5. "Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis."
    Pagnussat G.C., Yu H.-J., Ngo Q.A., Rajani S., Mayalagu S., Johnson C.S., Capron A., Xie L.-F., Ye D., Sundaresan V.
    Development 132:603-614(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  6. "The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development."
    Tan Q.K., Irish V.F.
    Plant Physiol. 140:1095-1108(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: HOMODIMERIZATION, INTERACTION WITH ZHD1; ZHD3; ZHD4; ZHD5; ZHD6; ZHD7; ZHD8; ZHD9; ZHD10 AND ZHD11, TISSUE SPECIFICITY, GENE FAMILY.
  7. "Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families."
    Hu W., dePamphilis C.W., Ma H.
    J. Integr. Plant Biol. 50:1031-1045(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
  8. "Nuclear import and DNA binding of the ZHD5 transcription factor is modulated by a competitive peptide inhibitor in Arabidopsis."
    Hong S.-Y., Kim O.-K., Kim S.-G., Yang M.-S., Park C.-M.
    J. Biol. Chem. 286:1659-1668(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
    Strain: cv. Columbia.
  9. "Solution structure of homeobox domain of Arabidopsis thaliana hypothetical protein F22K18.140."
    RIKEN structural genomics initiative (RSGI)
    Submitted (NOV-2004) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 148-215.

Entry informationi

Entry nameiZHD2_ARATH
AccessioniPrimary (citable) accession number: Q9SB61
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: May 1, 2000
Last modified: February 17, 2016
This is version 108 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.