The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro		Contains 3 AT-hook domain, a CXXC domain, and a possible C2H2 domain.

Description

Description:	lysine methyltransferase 2A [Source:HGNC Symbol;Acc:HGNC:7132]
Entrez Summary	TBA
Ensembl ID:	ENSG00000118058
External Link:
Interpro	IPR001214; IPR001487; IPR001965; IPR002857; IPR003616; IPR003888; IPR003889; IPR011011; IPR016569; IPR019787;
Protein Domain:
Protein: ENSP00000374157	DBD: CxxC	Other: Bromodomain, FYRC, FYRN, PHD, PHD_2, SET, zf-HC5HC
Protein: ENSP00000376612	DBD: CxxC	Other: PHD, PHD_2, PHD_4, zf-PHD-like
Protein: ENSP00000436786	DBD: CxxC	Other: Bromodomain, FYRC, FYRN, PHD, PHD_2, SET, zf-HC5HC
Protein: ENSP00000436564	DBD: CxxC	Other:
Protein: ENSP00000432391	DBD: CxxC	Other:
Protein: ENSP00000434618	DBD: CxxC	Other:
Protein: ENSP00000436700	DBD: CxxC	Other:
Protein: ENSP00000432652	DBD: CxxC	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:12453418
Vaquerizas 2009 TF classification "a" Has direct evidence of TF function; "b" Has evidence for an orthologous TF; "c" contains likely DBDs, but has no functional evidence; "x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription; "other" category contains proteins without clear DBDs they curated from external sources.	c
CisBP considers it as a TF?	Yes
TFclass considers it as a TF?	Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	Yes
GO-Info	GO:0003700 sequence-specific DNA binding transcription factor activity NAS - PMID:10821850
Initial Assessment 1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding; 1a2 There is high confidence data for a close ortholog (as defined in CisBP); 2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model; 2a2 There is lower confidence evidence for an close ortholog; 3a There is decent circumstantial evidence for its role as a TF or not; 4a Two or more datasets predict it as a TF; 5a One of the source datasets predicts is as a TF	1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
PBM	Zoo_01		Direct

Structure

Structure	PDB	Not_Covered

Experimental History

Method	Constructs
Tried in PBM? (Whether the protein was tried in PBM or not)
Tried in HT-SELEX (Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information? (Tried with another method and failed?)

External Contribution

Name
Email
Comment
Reference

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Structural comparisons show that the mono-CXXC is homologous  to the structural-zinc binding domain of medium chain  dehydrogenases [4].", "database": "PfamA", "aliStart": 1148, "scoreName": "E-value", "accession": "PF02008.18", "start": 1147, "score": 3.7e-13, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 1194}}, {"startStyle": "straight", "end": 3748, "endStyle": "straight", "aliStart": 3669, "text": "FYRC", "colour": "#9999ff", "aliEnd": 3748, "start": 3666, "href": "http://pfam.xfam.org/family/PF05965.12", "type": "pfama", "display": "true", "metadata": {"end": 3748, "description": "This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.", "database": "PfamA", "aliStart": 3669, "scoreName": "E-value", "accession": "PF05965.12", "start": 3666, "score": 8.300000000000001e-22, "identifier": "F/Y rich C-terminus", "type": "DBD", "aliEnd": 3748}}, {"startStyle": "straight", "end": 3945, "endStyle": "straight", "aliStart": 3840, "text": "SET", "colour": "#9999ff", "aliEnd": 3944, "start": 3840, "href": "http://pfam.xfam.org/family/PF00856.26", "type": "pfama", "display": "true", "metadata": {"end": 3945, "description": "SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases) [2].  A subset of SET domains have been called PR domains.  These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction [3].  The SET domain consists of two regions known as SET-N and SET-C.  SET-C forms an unusual and conserved knot-like structure of probably functional importance.  Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure [5].", "database": "PfamA", "aliStart": 3840, "scoreName": "E-value", "accession": "PF00856.26", "start": 3840, "score": 1.5999999999999999e-21, "identifier": "SET domain", "type": "DBD", "aliEnd": 3944}}, {"startStyle": "straight", "end": 1482, "endStyle": "straight", "aliStart": 1434, "text": "PHD", "colour": "#9999ff", "aliEnd": 1482, "start": 1433, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1482, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 1434, "scoreName": "E-value", "accession": "PF00628.27", "start": 1433, "score": 1.7000000000000002e-17, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1482}}, {"startStyle": "straight", "end": 1533, "endStyle": "straight", "aliStart": 1481, "text": "PHD", "colour": "#9999ff", "aliEnd": 1533, "start": 1481, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1533, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  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Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 1569, "scoreName": "E-value", "accession": "PF00628.27", "start": 1568, "score": 1.7000000000000002e-17, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1626}}, {"startStyle": "straight", "end": 2071, "endStyle": "straight", "aliStart": 2024, "text": "FYRN", "colour": "#9999ff", "aliEnd": 2071, "start": 2024, "href": "http://pfam.xfam.org/family/PF05964.12", "type": "pfama", "display": "true", "metadata": {"end": 2071, "description": "This region is normally found in the trithorax/ALL1 family proteins. 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It is similar to SMART:SM00542.", "database": "PfamA", "aliStart": 3672, "scoreName": "E-value", "accession": "PF05965.12", "start": 3669, "score": 8.300000000000001e-22, "identifier": "F/Y rich C-terminus", "type": "DBD", "aliEnd": 3751}}, {"startStyle": "straight", "end": 3948, "endStyle": "straight", "aliStart": 3843, "text": "SET", "colour": "#9999ff", "aliEnd": 3947, "start": 3843, "href": "http://pfam.xfam.org/family/PF00856.26", "type": "pfama", "display": "true", "metadata": {"end": 3948, "description": "SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases) [2].  A subset of SET domains have been called PR domains.  These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction [3].  The SET domain consists of two regions known as SET-N and SET-C.  SET-C forms an unusual and conserved knot-like structure of probably functional importance.  Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure [5].", "database": "PfamA", "aliStart": 3843, "scoreName": "E-value", "accession": "PF00856.26", "start": 3843, "score": 1.5999999999999999e-21, "identifier": "SET domain", "type": "DBD", "aliEnd": 3947}}, {"startStyle": "straight", "end": 2074, "endStyle": "straight", "aliStart": 2027, "text": "FYRN", "colour": "#9999ff", "aliEnd": 2074, "start": 2027, "href": "http://pfam.xfam.org/family/PF05964.12", "type": "pfama", "display": "true", "metadata": {"end": 2074, "description": "This region is normally found in the trithorax/ALL1 family proteins. 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Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 1481, "scoreName": "E-value", "accession": "PF00628.27", "start": 1481, "score": 5.599999999999999e-16, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1533}}, {"startStyle": "straight", "end": 1630, "endStyle": "straight", "aliStart": 1569, "text": "PHD", "colour": "#9999ff", "aliEnd": 1629, "start": 1568, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1630, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 1569, "scoreName": "E-value", "accession": "PF00628.27", "start": 1568, "score": 5.599999999999999e-16, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1629}}, {"startStyle": "straight", "end": 1981, "endStyle": "straight", "aliStart": 1903, "text": "zf-HC5HC2H", "colour": "#9999ff", "aliEnd": 1981, "start": 1903, "href": "http://pfam.xfam.org/family/PF13771.4", "type": "pfama", "display": "true", "metadata": {"end": 1981, "description": "The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains.  The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.", "database": "PfamA", "aliStart": 1903, "scoreName": "E-value", "accession": "PF13771.4", "start": 1903, "score": 3.8e-10, "identifier": "PHD-like zinc-binding domain", "type": "DBD", "aliEnd": 1981}}, {"startStyle": "straight", "end": 1980, "endStyle": "jagged", "aliStart": 1889, "text": "zf-HC5HC2H_2", "colour": "#9999ff", "aliEnd": 1969, "start": 1874, "href": "http://pfam.xfam.org/family/PF13832.4", "type": "pfama", "display": "true", "metadata": {"end": 1980, "description": NaN, "database": "PfamA", "aliStart": 1889, "scoreName": "E-value", "accession": "PF13832.4", "start": 1874, "score": 1.3e-08, "identifier": "PHD-zinc-finger like domain", "type": "DBD", "aliEnd": 1969}}, {"startStyle": "jagged", "end": 1480, "endStyle": "straight", "aliStart": 1445, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 1480, "start": 1444, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 1480, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 1445, "scoreName": "E-value", "accession": "PF13831.4", "start": 1444, "score": 0.00011999999999999999, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1480}}, {"startStyle": "straight", "end": 1531, "endStyle": "straight", "aliStart": 1494, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 1530, "start": 1492, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 1531, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 1494, "scoreName": "E-value", "accession": "PF13831.4", "start": 1492, "score": 0.00011999999999999999, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1530}}, {"startStyle": "straight", "end": 1609, "endStyle": "jagged", "aliStart": 1583, "text": "PHD_2", "colour": "#9999ff", "aliEnd": 1599, "start": 1582, "href": "http://pfam.xfam.org/family/PF13831.4", "type": "pfama", "display": "true", "metadata": {"end": 1609, "description": "PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2].  Several PHD fingers have been identified as binding modules of methylated histone H3 [3].", "database": "PfamA", "aliStart": 1583, "scoreName": "E-value", "accession": "PF13831.4", "start": 1582, "score": 0.00011999999999999999, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1599}}, {"startStyle": "jagged", "end": 1754, "endStyle": "jagged", "aliStart": 1697, "text": "Bromodomain", "colour": "#9999ff", "aliEnd": 1742, "start": 1692, "href": "http://pfam.xfam.org/family/PF00439.23", "type": "pfama", "display": "true", "metadata": {"end": 1754, "description": "Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].", "database": "PfamA", "aliStart": 1697, "scoreName": "E-value", "accession": "PF00439.23", "start": 1692, "score": 0.0047, "identifier": "Bromodomain", "type": "DBD", "aliEnd": 1742}}], "length": 3973}

{"regions": [{"startStyle": "curved", "end": 1227, "endStyle": "curved", "aliStart": 1181, "text": "zfCXXC", "colour": "#009900", "aliEnd": 1227, "start": 1180, "href": "http://pfam.xfam.org/family/PF02008.18", "type": "pfama", "display": "true", "metadata": {"end": 1227, "description": "This domain contains eight conserved cysteine residues that bind to two zinc ions.  The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [3], and shows a peculiar internal duplication in which the second unit is inserted into the first one [4]. Each of these units is  characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been  identified by NMR [3]. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess  a mono-CXXC domain that is present in distinct chromatin proteins  [4]. Structural comparisons show that the mono-CXXC is homologous  to the structural-zinc binding domain of medium chain  dehydrogenases [4].", "database": "PfamA", "aliStart": 1181, "scoreName": "E-value", "accession": "PF02008.18", "start": 1180, "score": 5.1e-14, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 1227}}], "length": 1439}

{"regions": [{"startStyle": "curved", "end": 268, "endStyle": "curved", "aliStart": 226, "text": "zfCXXC", "colour": "#009900", "aliEnd": 268, "start": 225, "href": "http://pfam.xfam.org/family/PF02008.18", "type": "pfama", "display": "true", "metadata": {"end": 268, "description": "This domain contains eight conserved cysteine residues that bind to two zinc ions.  The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats [3], and shows a peculiar internal duplication in which the second unit is inserted into the first one [4]. Each of these units is  characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been  identified by NMR [3]. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess  a mono-CXXC domain that is present in distinct chromatin proteins  [4]. Structural comparisons show that the mono-CXXC is homologous  to the structural-zinc binding domain of medium chain  dehydrogenases [4].", "database": "PfamA", "aliStart": 226, "scoreName": "E-value", "accession": "PF02008.18", "start": 225, "score": 7.6e-13, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 268}}], "length": 268}

TF Info Page for KMT2A (CxxC; AT hook)