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Q9UPS6 (SET1B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 97. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone-lysine N-methyltransferase SETD1B

EC=2.1.1.43
Alternative name(s):
Lysine N-methyltransferase 2G
SET domain-containing protein 1B
Short name=hSET1B
Gene names
Name:SETD1B
Synonyms:KIAA1076, KMT2G, SET1B
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1966 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Histone methyltransferase that specifically methylates 'Lys-4' of histone H3, when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. The non-overalpping localization with SETD1A suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. Specifically tri-methylates 'Lys-4' of histone H3 in vitro.

Catalytic activity

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]. Ref.4

Subunit structure

Component of the SET1 complex, at least composed of the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30. Interacts with HCFC1 and ASH2L/ASH2. Interacts (via the RRM domain) with WDR82. Interacts (via the RRM domain) with hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A) only in the presence of WDR82. Binds specifically to CTD heptad repeats phosphorylated on 'Ser-5' of each heptad. Interacts with RBM15. Ref.1 Ref.4 Ref.5 Ref.6

Subcellular location

Nucleus speckle. Chromosome. Note: Localizes to a largely non-overlapping set of euchromatic nuclear speckles with SETD1A, suggesting that SETD1A and SET1B each bind to a unique set of target genes. Ref.4

Sequence similarities

Belongs to the class V-like SAM-binding methyltransferase superfamily.

Contains 1 post-SET domain.

Contains 1 RRM (RNA recognition motif) domain.

Contains 1 SET domain.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9UPS6-1)

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.
Isoform 2 (identifier: Q9UPS6-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1043-1068: Missing.
     1088-1104: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 19661966Histone-lysine N-methyltransferase SETD1B
PRO_0000316993

Regions

Domain93 – 18189RRM
Domain1827 – 1944118SET
Domain1950 – 196617Post-SET
Coiled coil1173 – 120432 Potential
Compositional bias366 – 16711306Pro-rich
Compositional bias1040 – 1175136Ser-rich
Compositional bias1068 – 1312245Glu-rich
Compositional bias1103 – 113836Asp-rich

Sites

Binding site19431S-adenosyl-L-methionine By similarity

Amino acid modifications

Modified residue16591Phosphoserine Ref.8
Modified residue16631Phosphoserine Ref.8

Natural variations

Alternative sequence1043 – 106826Missing in isoform 2.
VSP_053875
Alternative sequence1088 – 110417Missing in isoform 2.
VSP_053876

Experimental info

Mutagenesis5771L → A: Abolishes interaction with RBM15. Ref.1
Mutagenesis5791D → A: Abolishes interaction with RBM15. Ref.1

Secondary structure

... 1966
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 19, 2014. Version 3.
Checksum: 164F81BC84EAD2C2

FASTA1,966212,803
        10         20         30         40         50         60 
MENSHPPHHH HQQPPPQPGP SGERRNHHWR SYKLMIDPAL KKGHHKLYRY DGQHFSLAMS 

        70         80         90        100        110        120 
SNRPVEIVED PRVVGIWTKN KELELSVPKF KIDEFYVGPV PPKQVTFAKL NDNIRENFLR 

       130        140        150        160        170        180 
DMCKKYGEVE EVEILYNPKT KKHLGIAKVV FATVRGAKDA VQHLHSTSVM GNIIHVELDT 

       190        200        210        220        230        240 
KGETRMRFYE LLVTGRYTPQ TLPVGELDAV SPIVNETLQL SDALKRLKDG GLSAGCGSGS 

       250        260        270        280        290        300 
SSVTPNSGGT PFSQDTAYSS CRLDTPNSYG QGTPLTPRLG TPFSQDSSYS SRQPTPSYLF 

       310        320        330        340        350        360 
SQDPAVTFKA RRHESKFTDA YNRRHEHHYV HNSPAVTAVA GATAAFRGSS DLPFGAVGGT 

       370        380        390        400        410        420 
GGSSGPPFKA QPQDSATFAH TPPPAQATPA PGFKSAFSPY QTPVAHFPPP PEEPTATAAF 

       430        440        450        460        470        480 
GARDSGEFRR APAPPPLPPA EPLAKEKPGT PPGPPPPDTN SMELGGRPTF GWSPEPCDSP 

       490        500        510        520        530        540 
GTPTLESSPA GPEKPHDSLD SRIEMLLKEQ RTKLLFLREP DSDTELQMEG SPISSSSSQL 

       550        560        570        580        590        600 
SPLAPFGTNS QPGFRGPTPP SSRPSSTGLE DISPTPLPDS DEDEELDLGL GPRPPPEPGP 

       610        620        630        640        650        660 
PDPAGLLSQT AEVALDLVGD RTPTSEKMDE GQQSSGEDME ISDDEMPSAP ITSADCPKPM 

       670        680        690        700        710        720 
VVTPGAAAVA APSVLAPTLP LPPPPGFPPL PPPPPPPPPQ PGFPMPPPLP PPPPPPPPAH 

       730        740        750        760        770        780 
PAVTVPPPPL PAPPGVPPPP ILPPLPPFPP GLFPVMQVDM SHVLGGQWGG MPMSFQMQTQ 

       790        800        810        820        830        840 
VLSRLMTGQG ACPYPPFMAA AAAAASAGLQ FVNLPPYRGP FSLSNSGPGR GQHWPPLPKF 

       850        860        870        880        890        900 
DPSVPPPGYM PRQEDPHKAT VDGVLLVVLK ELKAIMKRDL NRKMVEVVAF RAFDEWWDKK 

       910        920        930        940        950        960 
ERMAKASLTP VKSGEHKDED RPKPKDRIAS CLLESWGKGE GLGYEGLGLG IGLRGAIRLP 

       970        980        990       1000       1010       1020 
SFKVKRKEPP DTTSSGDQKR LRPSTSVDEE DEESERERDR DMADTPCELA KRDPKGVGVR 

      1030       1040       1050       1060       1070       1080 
RRPARPLELD SGGEEDEKES LSASSSSSAS SSSGSSTTSP SSSASDKEEE QESTEEEEEA 

      1090       1100       1110       1120       1130       1140 
EEEEEEEVPR SQLSSSSTSS TSDKDDDDDD SDDRDESEND DEDTALSEAS EKDEGDSDEE 

      1150       1160       1170       1180       1190       1200 
ETVSIVTSKA EATSSSESSE SSEFESSSES SPSSSEDEEE VVAREEEEEE EEEEMVAEES 

      1210       1220       1230       1240       1250       1260 
MASAGPEDFE QDGEEAALAP GAPAVDSLGM EEEVDIETEA VAPEERPSML DEPPLPVGVE 

      1270       1280       1290       1300       1310       1320 
EPADSREPPE EPGLSQEGAM LLSPEPPAKE VEARPPLSPE RAPEHDLEVE PEPPMMLPLP 

      1330       1340       1350       1360       1370       1380 
LQPPLPPPRP PRPPSPPPEP ETTDASHPSV PPEPLAEDHP PHTPGLCGSL AKSQSTETVP 

      1390       1400       1410       1420       1430       1440 
ATPGGEPPLS GGSSGLSLSS PQVPGSPFSY PAPSPSLSSG GLPRTPGRDF SFTPTFSEPS 

      1450       1460       1470       1480       1490       1500 
GPLLLPVCPL PTGRRDERSG PLASPVLLET GLPLPLPLPL PLPLALPAVL RAQARAPTPL 

      1510       1520       1530       1540       1550       1560 
PPLLPAPLAS CPPPMKRKPG RPRRSPPSML SLDGPLVRPP AGAALGRELL LLPGQPQTPV 

      1570       1580       1590       1600       1610       1620 
FPSTHDPRTV TLDFRNAGIP APPPPLPPQP PPPPPPPPVE PTKLPFKELD NQWPSEAIPP 

      1630       1640       1650       1660       1670       1680 
GPRGRDEVTE EYMELAKSRG PWRRPPKKRH EDLVPPAGSP ELSPPQPLFR PRSEFEEMTI 

      1690       1700       1710       1720       1730       1740 
LYDIWNGGID EEDIRFLCVT YERLLQQDNG MDWLNDTLWV YHPSTSLSSA KKKKRDDGIR 

      1750       1760       1770       1780       1790       1800 
EHVTGCARSE GFYTIDKKDK LRYLNSSRAS TDEPPADTQG MSIPAQPHAS TRAGSERRSE 

      1810       1820       1830       1840       1850       1860 
QRRLLSSFTG SCDSDLLKFN QLKFRKKKLK FCKSHIHDWG LFAMEPIAAD EMVIEYVGQN 

      1870       1880       1890       1900       1910       1920 
IRQVIADMRE KRYEDEGIGS SYMFRVDHDT IIDATKCGNF ARFINHSCNP NCYAKVITVE 

      1930       1940       1950       1960 
SQKKIVIYSK QHINVNEEIT YDYKFPIEDV KIPCLCGSEN CRGTLN 

« Hide

Isoform 2 [UniParc].

Checksum: 057CD0948D670243
Show »

FASTA1,923208,732

References

« Hide 'large scale' references
[1]"Rbm15-Mkl1 interacts with the Setd1b histone H3-Lys4 methyltransferase via a SPOC domain that is required for cytokine-independent proliferation."
Lee J.H., Skalnik D.G.
PLoS ONE 7:E42965-E42965(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH RBM15, MUTAGENESIS OF LEU-577 AND ASP-579.
[2]"The finished DNA sequence of human chromosome 12."
Scherer S.E., Muzny D.M., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J., Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R. expand/collapse author list , Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Montgomery K.T., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Lovering R.C., Wheeler D.A., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clerc-Blankenburg K.P., Davis C., Delgado O., Dinh H.H., Draper H., Gonzalez-Garay M.L., Havlak P., Jackson L.R., Jacob L.S., Kelly S.H., Li L., Li Z., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Pasternak S., Perez L.M., Plopper F.J.H., Santibanez J., Shen H., Tabor P.E., Verduzco D., Waldron L., Wang Q., Williams G.A., Zhang J., Zhou J., Allen C.C., Amin A.G., Anyalebechi V., Bailey M., Barbaria J.A., Bimage K.E., Bryant N.P., Burch P.E., Burkett C.E., Burrell K.L., Calderon E., Cardenas V., Carter K., Casias K., Cavazos I., Cavazos S.R., Ceasar H., Chacko J., Chan S.N., Chavez D., Christopoulos C., Chu J., Cockrell R., Cox C.D., Dang M., Dathorne S.R., David R., Davis C.M., Davy-Carroll L., Deshazo D.R., Donlin J.E., D'Souza L., Eaves K.A., Egan A., Emery-Cohen A.J., Escotto M., Flagg N., Forbes L.D., Gabisi A.M., Garza M., Hamilton C., Henderson N., Hernandez O., Hines S., Hogues M.E., Huang M., Idlebird D.G., Johnson R., Jolivet A., Jones S., Kagan R., King L.M., Leal B., Lebow H., Lee S., LeVan J.M., Lewis L.C., London P., Lorensuhewa L.M., Loulseged H., Lovett D.A., Lucier A., Lucier R.L., Ma J., Madu R.C., Mapua P., Martindale A.D., Martinez E., Massey E., Mawhiney S., Meador M.G., Mendez S., Mercado C., Mercado I.C., Merritt C.E., Miner Z.L., Minja E., Mitchell T., Mohabbat F., Mohabbat K., Montgomery B., Moore N., Morris S., Munidasa M., Ngo R.N., Nguyen N.B., Nickerson E., Nwaokelemeh O.O., Nwokenkwo S., Obregon M., Oguh M., Oragunye N., Oviedo R.J., Parish B.J., Parker D.N., Parrish J., Parks K.L., Paul H.A., Payton B.A., Perez A., Perrin W., Pickens A., Primus E.L., Pu L.-L., Puazo M., Quiles M.M., Quiroz J.B., Rabata D., Reeves K., Ruiz S.J., Shao H., Sisson I., Sonaike T., Sorelle R.P., Sutton A.E., Svatek A.F., Svetz L.A., Tamerisa K.S., Taylor T.R., Teague B., Thomas N., Thorn R.D., Trejos Z.Y., Trevino B.K., Ukegbu O.N., Urban J.B., Vasquez L.I., Vera V.A., Villasana D.M., Wang L., Ward-Moore S., Warren J.T., Wei X., White F., Williamson A.L., Wleczyk R., Wooden H.S., Wooden S.H., Yen J., Yoon L., Yoon V., Zorrilla S.E., Nelson D., Kucherlapati R., Weinstock G., Gibbs R.A.
Nature 440:346-351(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
Kikuno R., Nagase T., Ishikawa K., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
DNA Res. 6:197-205(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1163-1966 (ISOFORM 1/2).
Tissue: Brain.
[4]"Identification and characterization of the human Set1B histone H3-Lys4 methyltransferase complex."
Lee J.-H., Tate C.M., You J.-S., Skalnik D.G.
J. Biol. Chem. 282:13419-13428(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME ACTIVITY, SUBCELLULAR LOCATION, IDENTIFICATION IN THE SET1 COMPLEX.
[5]"Wdr82 is a C-terminal domain-binding protein that recruits the Setd1A Histone H3-Lys4 methyltransferase complex to transcription start sites of transcribed human genes."
Lee J.H., Skalnik D.G.
Mol. Cell. Biol. 28:609-618(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN SET1 COMPLEX, INTERACTION WITH WDR82; ASH2L AND POLR2A.
[6]"Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS."
Wu M., Wang P.F., Lee J.S., Martin-Brown S., Florens L., Washburn M., Shilatifard A.
Mol. Cell. Biol. 28:7337-7344(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN SET1 COMPLEX.
[7]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[8]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1659 AND SER-1663, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
JF813787 mRNA. Translation: AEG67286.1.
AC079360 Genomic DNA. No translation available.
AC084018 Genomic DNA. No translation available.
AB028999 mRNA. Translation: BAA83028.1.
CCDSCCDS53838.1.
RefSeqNP_055863.1. NM_015048.1. [Q9UPS6-2]
XP_005253915.1. XM_005253858.2. [Q9UPS6-1]
XP_006719358.1. XM_006719295.1. [Q9UPS6-1]
XP_006719359.1. XM_006719296.1. [Q9UPS6-1]
UniGeneHs.507122.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3UVOX-ray2.20B1745-1755[»]
4ES0X-ray1.82C1741-1754[»]
ProteinModelPortalQ9UPS6.
SMRQ9UPS6. Positions 98-203.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116702. 10 interactions.
STRING9606.ENSP00000267197.

PTM databases

PhosphoSiteQ9UPS6.

Polymorphism databases

DMDM166977692.

Proteomic databases

MaxQBQ9UPS6.
PaxDbQ9UPS6.
PRIDEQ9UPS6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000267197; ENSP00000267197; ENSG00000139718.
ENST00000542440; ENSP00000442924; ENSG00000139718.
ENST00000604567; ENSP00000474253; ENSG00000139718.
GeneID23067.
KEGGhsa:23067.
UCSCuc001ubi.3. human. [Q9UPS6-1]

Organism-specific databases

CTD23067.
GeneCardsGC12P122243.
H-InvDBHIX0011090.
HGNCHGNC:29187. SETD1B.
HPAHPA021667.
MIM611055. gene.
neXtProtNX_Q9UPS6.
PharmGKBPA143485611.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG2940.
HOGENOMHOG000168216.
HOVERGENHBG055596.
InParanoidQ9UPS6.
KOK11422.
OMAQHWPPLP.
OrthoDBEOG7GQXTT.
TreeFamTF106436.

Gene expression databases

ArrayExpressQ9UPS6.
BgeeQ9UPS6.
CleanExHS_SETD1B.
GenevestigatorQ9UPS6.

Family and domain databases

Gene3D3.30.70.330. 2 hits.
InterProIPR024657. COMPASS_Set1_N-SET.
IPR012677. Nucleotide-bd_a/b_plait.
IPR003616. Post-SET_dom.
IPR000504. RRM_dom.
IPR001214. SET_dom.
[Graphical view]
PfamPF11764. N-SET. 1 hit.
PF00076. RRM_1. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
SMARTSM00508. PostSET. 1 hit.
SM00360. RRM. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
PROSITEPS50868. POST_SET. 1 hit.
PS50102. RRM. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi23067.
NextBio35510195.
PROQ9UPS6.
SOURCESearch...

Entry information

Entry nameSET1B_HUMAN
AccessionPrimary (citable) accession number: Q9UPS6
Secondary accession number(s): F6MFW1
Entry history
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: March 19, 2014
Last modified: July 9, 2014
This is version 97 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 12

Human chromosome 12: entries, gene names and cross-references to MIM