Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Likely to be sequence specific TF
1 Monomer or homomultimer
No motif
Structural evidence shows direct DNA-binding (PDB:4PZI) and KMT2B appears to make specific contacts with methylated DNA.
Description
Description:
lysine methyltransferase 2B [Source:HGNC Symbol;Acc:HGNC:15840]
Entrez Summary
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This gene encodes a protein which contains multiple domains
including a CXXC zinc finger, three PHD zinc fingers, two FY-rich domains,
and a SET (suppressor of variegation, enhancer of zeste, and trithorax)
domain. The SET domain is a conserved C-terminal domain that characterizes
proteins of the MLL (mixed-lineage leukemia) family. This gene is
ubiquitously expressed in adult tissues. It is also amplified in solid tumor
cell lines, and may be involved in human cancer. Two alternatively spliced
transcript variants encoding distinct isoforms have been reported for this
gene, however, the full length nature of the shorter transcript is not known.
[provided by RefSeq, Jul 2008]
Ensembl ID:
ENSG00000272333
External Link:
CisBP
Interpro
IPR001214 ; IPR001965 ; IPR002857 ; IPR003616 ; IPR003888 ; IPR003889 ; IPR011011 ; IPR016569 ; IPR019787 ;
Protein Domain:
ENSP00000398837
Domain:
Protein: ENSP00000398837DBD: CxxCOther: FYRC, FYRN, PHD, SET, zf-HC5HC2H, zf-HC5HC2H_2
Previous Annotations
Source
Annotation
TF-CAT classification
No PMIDS:
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.
No
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:10409430
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
Structure
Experimental History
{"regions": [{"startStyle": "curved", "end": 1005, "endStyle": "curved", "aliStart": 960, "text": "zfCXXC", "colour": "#009900", "aliEnd": 1005, "start": 958, "href": "http://pfam.xfam.org/family/PF02008.18", "type": "pfama", "display": "true", "metadata": {"end": 1005, "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": 960, "scoreName": "E-value", "accession": "PF02008.18", "start": 958, "score": 5.5999999999999996e-12, "identifier": "CXXC zinc finger domain", "type": "DBD", "aliEnd": 1005}}, {"startStyle": "straight", "end": 2691, "endStyle": "straight", "aliStart": 2586, "text": "SET", "colour": "#9999ff", "aliEnd": 2690, "start": 2586, "href": "http://pfam.xfam.org/family/PF00856.26", "type": "pfama", "display": "true", "metadata": {"end": 2691, "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": 2586, "scoreName": "E-value", "accession": "PF00856.26", "start": 2586, "score": 8.800000000000001e-23, "identifier": "SET domain", "type": "DBD", "aliEnd": 2690}}, {"startStyle": "straight", "end": 2493, "endStyle": "straight", "aliStart": 2411, "text": "FYRC", "colour": "#9999ff", "aliEnd": 2493, "start": 2411, "href": "http://pfam.xfam.org/family/PF05965.12", "type": "pfama", "display": "true", "metadata": {"end": 2493, "description": "This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.", "database": "PfamA", "aliStart": 2411, "scoreName": "E-value", "accession": "PF05965.12", "start": 2411, "score": 2.3e-22, "identifier": "F/Y rich C-terminus", "type": "DBD", "aliEnd": 2493}}, {"startStyle": "straight", "end": 1251, "endStyle": "straight", "aliStart": 1204, "text": "PHD", "colour": "#9999ff", "aliEnd": 1250, "start": 1203, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1251, "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": 1204, "scoreName": "E-value", "accession": "PF00628.27", "start": 1203, "score": 8.8e-17, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1250}}, {"startStyle": "straight", "end": 1303, "endStyle": "straight", "aliStart": 1251, "text": "PHD", "colour": "#9999ff", "aliEnd": 1303, "start": 1251, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1303, "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": 1251, "scoreName": "E-value", "accession": "PF00628.27", "start": 1251, "score": 8.8e-17, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1303}}, {"startStyle": "straight", "end": 1396, "endStyle": "straight", "aliStart": 1337, "text": "PHD", "colour": "#9999ff", "aliEnd": 1394, "start": 1337, "href": "http://pfam.xfam.org/family/PF00628.27", "type": "pfama", "display": "true", "metadata": {"end": 1396, "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": 1337, "scoreName": "E-value", "accession": "PF00628.27", "start": 1337, "score": 8.8e-17, "identifier": "PHD-finger", "type": "DBD", "aliEnd": 1394}}, {"startStyle": "straight", "end": 1780, "endStyle": "straight", "aliStart": 1733, "text": "FYRN", "colour": "#9999ff", "aliEnd": 1780, "start": 1733, "href": "http://pfam.xfam.org/family/PF05964.12", "type": "pfama", "display": "true", "metadata": {"end": 1780, "description": "This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.", "database": "PfamA", "aliStart": 1733, "scoreName": "E-value", "accession": "PF05964.12", "start": 1733, "score": 6.4e-15, "identifier": "F/Y-rich N-terminus", "type": "DBD", "aliEnd": 1780}}, {"startStyle": "straight", "end": 1686, "endStyle": "straight", "aliStart": 1608, "text": "zf-HC5HC2H", "colour": "#9999ff", "aliEnd": 1686, "start": 1608, "href": "http://pfam.xfam.org/family/PF13771.4", "type": "pfama", "display": "true", "metadata": {"end": 1686, "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": 1608, "scoreName": "E-value", "accession": "PF13771.4", "start": 1608, "score": 9.4e-11, "identifier": "PHD-like zinc-binding domain", "type": "DBD", "aliEnd": 1686}}, {"startStyle": "straight", "end": 1686, "endStyle": "jagged", "aliStart": 1580, "text": "zf-HC5HC2H_2", "colour": "#9999ff", "aliEnd": 1677, "start": 1579, "href": "http://pfam.xfam.org/family/PF13832.4", "type": "pfama", "display": "true", "metadata": {"end": 1686, "description": NaN, "database": "PfamA", "aliStart": 1580, "scoreName": "E-value", "accession": "PF13832.4", "start": 1579, "score": 2.1e-08, "identifier": "PHD-zinc-finger like domain", "type": "DBD", "aliEnd": 1677}}], "length": 2716}