The name of this superfamily has been modified since the most recent official CATH+ release (v4_3_0). At the point of the last release, this superfamily was named:

"
Zinc/RING finger domain, C3HC4 (zinc finger)
".

Functional Families

Overview of the Structural Clusters (SC) and Functional Families within this CATH Superfamily. Clusters with a representative structure are represented by a filled circle.
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FunFam 193: lysine-specific demethylase PHF2 isoform X1

Please note: GO annotations are assigned to the full protein sequence rather than individual protein domains. Since a given protein can contain multiple domains, it is possible that some of the annotations below come from additional domains that occur in the same protein, but have been classified elsewhere in CATH.

There are 31 GO terms relating to "molecular function"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Iron ion binding GO:0005506
Interacting selectively and non-covalently with iron (Fe) ions.
4 E6ZGB4 (/ISS) Q3UWM4 (/ISS) Q6P949 (/ISS) Q9WTU0 (/ISS)
Methylated histone binding GO:0035064
Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
4 E6ZGB4 (/ISS) Q3UWM4 (/ISS) Q6P949 (/ISS) Q9WTU0 (/ISS)
Transcription factor binding GO:0008134
Interacting selectively and non-covalently with a transcription factor, a protein required to initiate or regulate transcription.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Zinc ion binding GO:0008270
Interacting selectively and non-covalently with zinc (Zn) ions.
3 Q3UWM4 (/ISS) Q6P949 (/ISS) Q9WTU0 (/ISS)
Histone demethylase activity (H3-K9 specific) GO:0032454
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
3 E6ZGB4 (/ISS) Q6P949 (/ISS) Q9WTU0 (/ISS)
Sequence-specific DNA binding GO:0043565
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Iron ion binding GO:0005506
Interacting selectively and non-covalently with iron (Fe) ions.
2 O75151 (/IDA) Q6ZMT4 (/IDA)
Iron ion binding GO:0005506
Interacting selectively and non-covalently with iron (Fe) ions.
2 Q3UWM4 (/ISO) Q9WTU0 (/ISO)
Zinc ion binding GO:0008270
Interacting selectively and non-covalently with zinc (Zn) ions.
2 O75151 (/IDA) Q6ZMT4 (/IDA)
Zinc ion binding GO:0008270
Interacting selectively and non-covalently with zinc (Zn) ions.
2 Q3UWM4 (/ISO) Q9WTU0 (/ISO)
Histone demethylase activity (H3-K9 specific) GO:0032454
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
2 O75151 (/IDA) Q6ZMT4 (/IDA)
Histone demethylase activity (H3-K9 specific) GO:0032454
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
2 Q3UWM4 (/ISO) Q9WTU0 (/ISO)
Methylated histone binding GO:0035064
Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
2 O75151 (/IDA) Q6ZMT4 (/IDA)
Methylated histone binding GO:0035064
Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
2 Q3UWM4 (/ISO) Q9WTU0 (/ISO)
Iron ion binding GO:0005506
Interacting selectively and non-covalently with iron (Fe) ions.
1 Q6ZMT4 (/TAS)
Protein binding GO:0005515
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
1 O75151 (/IPI)
2-oxoglutarate-dependent dioxygenase activity GO:0016706
Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
1 Q6ZMT4 (/IDA)
2-oxoglutarate-dependent dioxygenase activity GO:0016706
Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
1 Q3UWM4 (/ISO)
2-oxoglutarate-dependent dioxygenase activity GO:0016706
Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
1 Q3UWM4 (/ISS)
Histone demethylase activity (H3-K9 specific) GO:0032454
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
1 Q3UWM4 (/IMP)
Histone demethylase activity (H3-K9 specific) GO:0032454
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
1 Q9WTU0 (/TAS)
Histone demethylase activity (H4-K20 specific) GO:0035575
Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein.
1 Q6ZMT4 (/IDA)
Histone demethylase activity (H4-K20 specific) GO:0035575
Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein.
1 Q3UWM4 (/ISO)
Histone demethylase activity (H4-K20 specific) GO:0035575
Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein.
1 Q3UWM4 (/ISS)
Sequence-specific DNA binding GO:0043565
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
1 Q6P9L3 (/ISS)
Histone demethylase activity (H3-K36 specific) GO:0051864
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
1 Q6ZMT4 (/IDA)
Histone demethylase activity (H3-K36 specific) GO:0051864
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
1 Q3UWM4 (/ISO)
Histone demethylase activity (H3-K36 specific) GO:0051864
Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
1 Q3UWM4 (/ISS)
Histone demethylase activity (H3-K27 specific) GO:0071558
Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
1 Q6ZMT4 (/IDA)
Histone demethylase activity (H3-K27 specific) GO:0071558
Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
1 Q3UWM4 (/IMP)
Histone demethylase activity (H3-K27 specific) GO:0071558
Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
1 Q3UWM4 (/ISO)

There are 32 GO terms relating to "biological process"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Negative regulation of transcription by RNA polymerase II GO:0000122
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Embryonic placenta development GO:0001892
The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
3 Q3TMJ3 (/IMP) Q6P9L3 (/IMP) Q8VDN7 (/IMP)
Chromatin remodeling GO:0006338
Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Regulation of transcription by RNA polymerase II GO:0006357
Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Protein demethylation GO:0006482
The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
3 E6ZGB4 (/ISS) Q6P949 (/ISS) Q9WTU0 (/ISS)
Brain development GO:0007420
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Endoderm development GO:0007492
The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
3 Q3TMJ3 (/IMP) Q6P9L3 (/IMP) Q8VDN7 (/IMP)
Anterior/posterior pattern specification GO:0009952
The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
3 Q3TMJ3 (/IMP) Q6P9L3 (/IMP) Q8VDN7 (/IMP)
Positive regulation of transcription by RNA polymerase II GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Midbrain development GO:0030901
The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
2 Q3UWM4 (/ISS) Q6ZMT4 (/ISS)
Histone H3-K9 demethylation GO:0033169
The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
2 Q6ZMT4 (/IDA) Q9WTU0 (/IDA)
Negative regulation of chromatin silencing at rDNA GO:0061188
Any process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
2 Q6P949 (/ISS) Q9WTU0 (/ISS)
Liver development GO:0001889
The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
1 O75151 (/TAS)
Chromatin remodeling GO:0006338
Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
1 Q6P9L3 (/ISS)
Regulation of transcription by RNA polymerase II GO:0006357
Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.
1 Q6P9L3 (/ISS)
Protein demethylation GO:0006482
The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
1 O75151 (/IDA)
Protein demethylation GO:0006482
The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
1 Q9WTU0 (/ISO)
Brain development GO:0007420
The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
1 Q6P9L3 (/ISS)
Histone H3-K9 demethylation GO:0033169
The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
1 Q3UWM4 (/IMP)
Histone H3-K9 demethylation GO:0033169
The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
1 Q3UWM4 (/ISO)
Histone H4-K20 demethylation GO:0035574
The modification of histone H4 by the removal of a methyl group from lysine at position 20 of the histone.
1 Q6ZMT4 (/IDA)
Histone H4-K20 demethylation GO:0035574
The modification of histone H4 by the removal of a methyl group from lysine at position 20 of the histone.
1 Q3UWM4 (/ISO)
Histone H4-K20 demethylation GO:0035574
The modification of histone H4 by the removal of a methyl group from lysine at position 20 of the histone.
1 Q3UWM4 (/ISS)
Positive regulation of transcription, DNA-templated GO:0045893
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
1 Q3UWM4 (/IMP)
Negative regulation of chromatin silencing at rDNA GO:0061188
Any process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
1 O75151 (/IMP)
Negative regulation of chromatin silencing at rDNA GO:0061188
Any process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
1 Q9WTU0 (/ISO)
Histone H3-K36 demethylation GO:0070544
The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
1 Q6ZMT4 (/IDA)
Histone H3-K36 demethylation GO:0070544
The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
1 Q3UWM4 (/ISO)
Histone H3-K36 demethylation GO:0070544
The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
1 Q3UWM4 (/ISS)
Histone H3-K27 demethylation GO:0071557
The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
1 Q6ZMT4 (/IDA)
Histone H3-K27 demethylation GO:0071557
The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
1 Q3UWM4 (/IMP)
Histone H3-K27 demethylation GO:0071557
The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
1 Q3UWM4 (/ISO)

There are 20 GO terms relating to "cellular component"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
4 Q3TMJ3 (/ISO) Q3UWM4 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Kinetochore GO:0000776
A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
3 E6ZGB4 (/ISS) Q6P949 (/ISS) Q9WTU0 (/ISS)
Nuclear chromatin GO:0000790
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Cytoplasm GO:0005737
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
NURF complex GO:0016589
An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Dendrite GO:0030425
A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Neuron projection GO:0043005
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Cell body GO:0044297
The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Perinuclear region of cytoplasm GO:0048471
Cytoplasm situated near, or occurring around, the nucleus.
3 Q3TMJ3 (/ISO) Q6P9L3 (/ISO) Q8VDN7 (/ISO)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
2 O75151 (/TAS) Q6ZMT4 (/TAS)
Nucleolus GO:0005730
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
2 O75151 (/IDA) Q6ZMT4 (/IDA)
Nucleolus GO:0005730
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
2 Q3UWM4 (/ISO) Q9WTU0 (/ISO)
Nucleolus GO:0005730
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
2 Q6P949 (/ISS) Q9WTU0 (/ISS)
Kinetochore GO:0000776
A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
1 O75151 (/IDA)
Kinetochore GO:0000776
A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
1 Q9WTU0 (/ISO)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
1 Q6ZMT4 (/IC)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
1 Q6P9L3 (/ISS)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
1 O75151 (/TAS)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
1 Q6ZMT4 (/IDA)