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Protein

Protein SAWADEE HOMEODOMAIN HOMOLOG 1

Gene

SHH1

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

Functioni

Involved in RNA-directed DNA methylation (RdDM). Required for the silencing of some endogenous RdDM targets and accumulation of 24-nt siRNAs, but not for the production of Pol V-dependent transcripts. Functions in transcriptional silencing through both DNA methylation-dependent and -independent pathways. Required for both maintenance and de-novo DNA methylation. Plays a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM.4 Publications

Miscellaneous

Associates in vivo with Pol IV but not with Pol V (PubMed:23637343) and this interaction is not dependent on its H3K9me binding activity (PubMed:23636332). Glu-130 and Asp-141 interact with the H3K4 side chain while the H3K9me1/2/3 side chains insert into a hydrophobic aromatic cage formed by Tyr-140, Phe-162 and Phe-165 (PubMed:23636332).2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi191Zinc1
Metal bindingi225Zinc1
Metal bindingi230Zinc1
Metal bindingi232Zinc1

GO - Molecular functioni

GO - Biological processi

  • DNA methylation Source: TAIR
  • gene silencing by RNA Source: TAIR
  • methylation-dependent chromatin silencing Source: TAIR

Keywordsi

LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Protein SAWADEE HOMEODOMAIN HOMOLOG 1
Alternative name(s):
DNA-binding transcription factor 1
Gene namesi
Name:SHH1
Synonyms:DTF1
Ordered Locus Names:At1g15215
ORF Names:F9L1.16
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

AraportiAT1G15215.
TAIRilocus:1005716727. AT1G15215.

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Loss of DRM2 controlled DNA methylation, but no effect on CMT3 or MET1 controlled methylation.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi130E → A: DNA methylation defects. 1 Publication1
Mutagenesisi140Y → A: Loss of interaction with H3K9 and DNA methylation defects. 2 Publications1
Mutagenesisi141D → A: Strong DNA methylation defects. 1 Publication1
Mutagenesisi162F → A: Loss of interaction with H3K9 and strong DNA methylation defects, when associated with A-165. 2 Publications1
Mutagenesisi165F → A: Loss of interaction with H3K9 and strong DNA methylation defects, when associated with A-162. 2 Publications1
Mutagenesisi191C → A: Decreased stability of the protein. 1 Publication1
Mutagenesisi212Y → A: DNA methylation defects. 1 Publication1
Mutagenesisi225H → A: Decreased stability of the protein. Decreased stability of the protein; when associated with A-232. 1 Publication1
Mutagenesisi232C → A: Decreased stability of the protein; when associated with A-225. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004233171 – 258Protein SAWADEE HOMEODOMAIN HOMOLOG 1Add BLAST258

Proteomic databases

PaxDbiQ9XI47.

Expressioni

Gene expression databases

ExpressionAtlasiQ9XI47. baseline and differential.

Interactioni

Subunit structurei

Associates with the RNA polymerase IV (Pol IV) complex. Interacts with NRPD1, NRPD2, NRPD3, NRPD3B, CLSY1 and CLSY2.3 Publications

Protein-protein interaction databases

BioGridi23328. 8 interactors.
STRINGi3702.AT1G15215.2.

Structurei

Secondary structure

1258
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi129 – 132Combined sources4
Turni134 – 136Combined sources3
Beta strandi139 – 150Combined sources12
Beta strandi156 – 162Combined sources7
Helixi167 – 169Combined sources3
Beta strandi171 – 174Combined sources4
Helixi175 – 178Combined sources4
Beta strandi179 – 181Combined sources3
Helixi188 – 193Combined sources6
Beta strandi199 – 206Combined sources8
Beta strandi209 – 221Combined sources13
Beta strandi233 – 238Combined sources6
Turni239 – 241Combined sources3
Beta strandi244 – 247Combined sources4
Helixi249 – 251Combined sources3
Beta strandi252 – 254Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IUPX-ray1.90A/B125-258[»]
4IUQX-ray2.81A/B125-258[»]
4IURX-ray2.50A/B125-258[»]
4IUTX-ray2.70A/B125-258[»]
4IUUX-ray2.70A/B125-258[»]
4IUVX-ray2.80A/B125-258[»]
ProteinModelPortaliQ9XI47.
SMRiQ9XI47.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni138 – 244SAWADEE domainAdd BLAST107

Domaini

The SAWADEE domain (138-244) binds to mono-, di-, or trimethylated H3K9 histone peptides, but this interaction is impaired if H3K4me2/3 methylation is present (PubMed:23637343 PubMed:23636332).2 Publications

Phylogenomic databases

eggNOGiENOG410IWZD. Eukaryota.
ENOG411141H. LUCA.
HOGENOMiHOG000241854.
InParanoidiQ9XI47.
OMAiSARDYAW.
OrthoDBiEOG09360JX0.
PhylomeDBiQ9XI47.

Family and domain databases

InterProiView protein in InterPro
IPR032001. SAWADEE_dom.
PfamiView protein in Pfam
PF16719. SAWADEE. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9XI47-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAASDDSSHY FTEFTLSEIV DMENLYKELG DQSLHKDFCQ TVASTFSCSV
60 70 80 90 100
NRNGKSSITW KQVQIWFQEK LKHQSQPKSK TLPSPPLQIH DLSNPSSYAS
110 120 130 140 150
NASNATFVGN STFVQTRKGK ASDLADLAFE AKSARDYAWY DVSSFLTYRV
160 170 180 190 200
LRTGELEVRV RFSGFDNRHD EWVNVKTSVR ERSIPVEPSE CGRVNVGDLL
210 220 230 240 250
LCFQEREDQA LYCDGHVLNI KRGIHDHARC NCVFLVRYEL DNTEESLGLE

RICRRPEE
Length:258
Mass (Da):29,506
Last modified:November 1, 1999 - v1
Checksum:iA4A4F409CEC26DAD
GO
Isoform 2 (identifier: Q9XI47-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     244-258: EESLGLERICRRPEE → ECMFRNRWD

Show »
Length:252
Mass (Da):28,946
Checksum:i695AF6FB2B3FB72C
GO
Isoform 3 (identifier: Q9XI47-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-21: Missing.
     244-258: EESLGLERICRRPEE → ECMFRNRWD

Show »
Length:231
Mass (Da):26,599
Checksum:i709969DF3EFE92A7
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0476741 – 21Missing in isoform 3. 2 PublicationsAdd BLAST21
Alternative sequenceiVSP_047675244 – 258EESLG…RRPEE → ECMFRNRWD in isoform 2 and isoform 3. 2 PublicationsAdd BLAST15

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC007591 Genomic DNA. Translation: AAD39678.1.
CP002684 Genomic DNA. Translation: AEE29286.1.
CP002684 Genomic DNA. Translation: AEE29287.1.
CP002684 Genomic DNA. Translation: AEE29288.1.
AK117440 mRNA. Translation: BAC42105.1.
BT005197 mRNA. Translation: AAO50730.1.
PIRiC86286.
RefSeqiNP_001031048.1. NM_001035971.2. [Q9XI47-2]
NP_001319007.1. NM_001332154.1.
NP_849666.2. NM_179335.3. [Q9XI47-1]
UniGeneiAt.26582.
At.44195.

Genome annotation databases

EnsemblPlantsiAT1G15215.2; AT1G15215.2; AT1G15215. [Q9XI47-1]
AT1G15215.3; AT1G15215.3; AT1G15215. [Q9XI47-2]
GeneIDi838088.
GrameneiAT1G15215.2; AT1G15215.2; AT1G15215.
AT1G15215.3; AT1G15215.3; AT1G15215.
KEGGiath:AT1G15215.

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiSHH1_ARATH
AccessioniPrimary (citable) accession number: Q9XI47
Secondary accession number(s): A8MRU8, Q2V4N1, Q8GYR2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 18, 2013
Last sequence update: November 1, 1999
Last modified: August 30, 2017
This is version 97 of the entry and version 1 of the sequence. See 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