VIM1 Zinc finger (C3HC4-type RING finger) family protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: VIM1
Official Full Name: Zinc finger (C3HC4-type RING finger) family protein
Primary source: TAIR:AT1G57820
Locus tag: AT1G57820
See related: Araport:AT1G57820
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: F12K22.14; F12K22_14; ORTH2; ORTHRUS 2; VARIANT IN METHYLATION 1
Summary: Encodes a 645-amino acid methylcytosine-binding protein with a PHD domain, two RING finger domains, and an SRA domain that is involved in centromere heterochromatinization. This protein functions as an E3 ubiquitin ligase in vitro. The protein has been shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the former. It plays a role in the establishment/maintenance of chromatin structure during cell division and is localized in the nucleus. Plants over-expressing VIM1/ORTH2 show an inhibition in root growth and a delay in flowering. Both over-expression of GFP:ORTH2 and loss of ORTH2/VIM1 lead to decreased levels of DNA methylation. GFP:ORTH2 over-expressers also have increased levels of FWA transcripts.
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Genomic context

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See VIM1 in Genome Data Viewer

Location:: chromosome: 1

Exon count:: 10

Sequence:: Chromosome: 1; NC_003070.9 (21413981..21418115, complement)

Chromosome 1 - NC_003070.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

VIM proteins function in transcriptional regulation via their roles in the MET1 DNA methylation pathway.
Title: VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway.
Observed full-length VIM1 binds preferentially to hemi-methylated DNA with a single modified 5mCpG site. However, when 5hmC replaces one or both cytosine residues at a palindromic CpG site, VIM1 binds with approximately >/=10-fold lower affinity.
Title: Heterologous expression and purification of Arabidopsis thaliana VIM1 protein: in vitro evidence for its inability to recognize hydroxymethylcytosine, a rare base in Arabidopsis DNA.
VIM1, VIM2, and VIM3 have overlapping functions in maintenance of global CpG methylation and epigenetic transcriptional silencing.
Title: Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.
findings suggest that VIM1 (AT1G57820) acts at the DNA methylation-histone interface to maintain centromeric heterochromatin
Title: VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001333806.1

Supported by ESTs:

NM_104576.6

Supported by ESTs:

NM_202316.2

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded methylated DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IPI Inferred from Physical Interaction more info	PubMed
enables methyl-CpG binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpG binding	ISS Inferred from Sequence or Structural Similarity more info
enables methyl-CpNpG binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpNpG binding	ISS Inferred from Sequence or Structural Similarity more info
enables methyl-CpNpN binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpNpN binding	ISS Inferred from Sequence or Structural Similarity more info
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell division	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within chromatin organization	IPI Inferred from Physical Interaction more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pericentric heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromocenter	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: Zinc finger (C3HC4-type RING finger) family protein

NP_001319260.1

VARIANT IN METHYLATION 1 (VIM1); CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type, conserved site (InterPro:IPR017907), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, PHD-type (InterPro:IPR001965), SRA-YDG (InterPro:IPR003105), Zinc finger, C3HC4 RING-type (InterPro:IPR018957), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: zinc finger (C3HC4-type RING finger) family protein (TAIR:AT1G57800.1); Has 4294 Blast hits to 3626 proteins in 667 species: Archae - 0; Bacteria - 14; Metazoa - 3221; Fungi - 261; Plants - 573; Viruses - 10; Other Eukaryotes - 215 (source: NCBI BLink).

NP_974045.1

VARIANT IN METHYLATION 1 (VIM1); CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type, conserved site (InterPro:IPR017907), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, PHD-type (InterPro:IPR001965), SRA-YDG (InterPro:IPR003105), Zinc finger, C3HC4 RING-type (InterPro:IPR018957), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: zinc finger (C3HC4-type RING finger) family protein (TAIR:AT1G57800.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003070.9 Reference assembly

Range

21413981..21418115 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001333806.1 → NP_001319260.1 Zinc finger (C3HC4-type RING finger) family protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q3ECM8, Q8VYZ0, Q9FVS3

UniProtKB/TrEMBL

A0A5S9WMM2
NM_104576.6 → NP_176092.2 Zinc finger (C3HC4-type RING finger) family protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_176092.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q3ECM8, Q8VYZ0, Q9FVS3

UniProtKB/TrEMBL

A0A5S9WMM2

Conserved Domains (3) summary

smart00249
Location:14 → 60

PHD; PHD zinc finger

cd00162
Location:145 → 188

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam02182
Location:262 → 424

SAD_SRA; SAD/SRA domain
NM_202316.2 → NP_974045.1 Zinc finger (C3HC4-type RING finger) family protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_974045.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9WMM2

Conserved Domains (3) summary

smart00249
Location:14 → 60

PHD; PHD zinc finger

cd00162
Location:145 → 188

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam02182
Location:262 → 421

SAD_SRA; SAD/SRA domain