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Protein

Lethal(3)malignant brain tumor-like protein 1

Gene

L3MBTL1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Polycomb group (PcG) protein that specifically recognizes and binds mono- and dimethyllysine residues on target proteins, therey acting as a 'reader' of a network of post-translational modifications. PcG proteins maintain the transcriptionally repressive state of genes: acts as a chromatin compaction factor by recognizing and binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condense chromatin and repress transcription. Recognizes and binds p53/TP53 monomethylated at 'Lys-382', leading to repress p53/TP53-target genes. Also recognizes and binds RB1/RB monomethylated at 'Lys-860'. Participates in the ETV6-mediated repression. Probably plays a role in cell proliferation. Overexpression induces multinucleated cells, suggesting that it is required to accomplish normal mitosis.4 Publications

Miscellaneous

The L3MBTL1 locus is imprinted. Paternal inherited gene is expressed, while the maternal inherited gene is silenced.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei423Mediates recognition of monomethylated and dimethylated peptides1
Sitei426Positioned at the entrance of MBT 2 and is required for recognition of monomethylated and dimethylated peptides1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri613 – 656CCHHC-typePROSITE-ProRule annotationAdd BLAST44

GO - Molecular functioni

  • chromatin binding Source: UniProtKB
  • DNA binding transcription factor activity Source: InterPro
  • histone binding Source: UniProtKB
  • identical protein binding Source: UniProtKB
  • methylated histone binding Source: UniProtKB
  • nucleosomal histone binding Source: UniProtKB
  • nucleosome binding Source: UniProtKB
  • SAM domain binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • chromatin organization Source: UniProtKB
  • hemopoiesis Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • regulation of cell cycle Source: UniProtKB
  • regulation of megakaryocyte differentiation Source: UniProtKB
  • regulation of mitotic nuclear division Source: UniProtKB
  • regulation of signal transduction by p53 class mediator Source: Reactome
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionChromatin regulator, Repressor
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-6804760 Regulation of TP53 Activity through Methylation

Names & Taxonomyi

Protein namesi
Recommended name:
Lethal(3)malignant brain tumor-like protein 1
Short name:
H-l(3)mbt
Short name:
H-l(3)mbt protein
Short name:
L(3)mbt-like
Alternative name(s):
L(3)mbt protein homolog
L3MBTL1
Gene namesi
Name:L3MBTL1
Synonyms:KIAA0681, L3MBT, L3MBTL
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

EuPathDBiHostDB:ENSG00000185513.14
HGNCiHGNC:15905 L3MBTL1
MIMi608802 gene
neXtProtiNX_Q9Y468

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi316D → N: Does not affect binding to monomethylated and dimethylated peptides. 1 Publication1
Mutagenesisi340F → A: Does not affect binding to monomethylated and dimethylated peptides. 1 Publication1
Mutagenesisi423D → A: Abolishes binding to monomethylated and dimethylated peptides. 4 Publications1
Mutagenesisi423D → N: Strongly impairs binding to monomethylated and dimethylated peptides. Abolishes binding to p53/TP53 monomethylated at 'Lys-382'. 4 Publications1
Mutagenesisi426N → A: Abolishes binding to monomethylated and dimethylated peptides. 2 Publications1
Mutagenesisi426N → Q: Strongly impairs binding to monomethylated and dimethylated peptides. Abolishes binding to p53/TP53 monomethylated at 'Lys-382'. 2 Publications1
Mutagenesisi431C → F or R: Strongly impairs binding to monomethylated and dimethylated peptides. 1 Publication1
Mutagenesisi447F → A: Abolishes binding to monomethylated and dimethylated peptides. Abolishes binding to p53/TP53 monomethylated at 'Lys-382'. 2 Publications1
Mutagenesisi450W → L: Abolishes binding to p53/TP53 monomethylated at 'Lys-382'. 1 Publication1
Mutagenesisi454Y → L: Abolishes binding to p53/TP53 monomethylated at 'Lys-382'. 1 Publication1
Mutagenesisi527D → N: Does not affect binding to monomethylated and dimethylated peptides. 1 Publication1
Mutagenesisi551F → A: Does not affect binding to monomethylated and dimethylated peptides. 1 Publication1

Organism-specific databases

DisGeNETi26013
OpenTargetsiENSG00000185513
PharmGKBiPA30260

Chemistry databases

ChEMBLiCHEMBL1287622
DrugBankiDB03814 2-(N-Morpholino)-Ethanesulfonic Acid

Polymorphism and mutation databases

BioMutaiL3MBTL1
DMDMi325511398

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000844521 – 840Lethal(3)malignant brain tumor-like protein 1Add BLAST840

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei117PhosphoserineCombined sources1

Post-translational modificationi

Ubiquitinated in a VCP/p97-dependent way following DNA damage, leading to its removal from DNA damage sites, promoting accessibility of H4K20me2 mark for DNA repair protein TP53BP1, which is then recruited to DNA damage sites.1 Publication

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9Y468
PaxDbiQ9Y468
PeptideAtlasiQ9Y468
PRIDEiQ9Y468
ProteomicsDBi86115
86116 [Q9Y468-1]
86117 [Q9Y468-2]
86118 [Q9Y468-3]
86119 [Q9Y468-5]

PTM databases

iPTMnetiQ9Y468
PhosphoSitePlusiQ9Y468

Expressioni

Tissue specificityi

Widely expressed. Expression is reduced in colorectal cancer cell line SW480 and promyelocytic leukemia cell line HL-60.1 Publication

Developmental stagei

In interphase cells, it is scattered throughout the nucleoplasm. In mitotic cells, it strongly associates with condensed chromosomes from the prophase to telophase.

Gene expression databases

BgeeiENSG00000185513
CleanExiHS_L3MBTL
ExpressionAtlasiQ9Y468 baseline and differential
GenevisibleiQ9Y468 HS

Organism-specific databases

HPAiHPA068051

Interactioni

Subunit structurei

Homodimer. Interacts with RB1/RB (when monomethylated at 'Lys-860'). Interacts with p53/TP53 (when monomethylated at 'Lys-382'). Interacts with CBX3, ETV6, KMT5A and VCP/p97.8 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • histone binding Source: UniProtKB
  • identical protein binding Source: UniProtKB
  • methylated histone binding Source: UniProtKB
  • nucleosomal histone binding Source: UniProtKB
  • SAM domain binding Source: UniProtKB

Protein-protein interaction databases

BioGridi117486, 46 interactors
ComplexPortaliCPX-469 L3MBTL1 complex
DIPiDIP-29628N
IntActiQ9Y468, 64 interactors
MINTiQ9Y468
STRINGi9606.ENSP00000398516

Chemistry databases

BindingDBiQ9Y468

Structurei

Secondary structure

1840
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi276 – 283Combined sources8
Helixi290 – 292Combined sources3
Helixi295 – 298Combined sources4
Beta strandi311 – 316Combined sources6
Beta strandi319 – 332Combined sources14
Beta strandi335 – 340Combined sources6
Helixi345 – 347Combined sources3
Beta strandi349 – 352Combined sources4
Beta strandi356 – 359Combined sources4
Helixi363 – 367Combined sources5
Helixi379 – 381Combined sources3
Helixi384 – 391Combined sources8
Helixi398 – 400Combined sources3
Beta strandi418 – 422Combined sources5
Turni424 – 427Combined sources4
Beta strandi430 – 439Combined sources10
Beta strandi442 – 447Combined sources6
Helixi452 – 454Combined sources3
Beta strandi456 – 458Combined sources3
Helixi470 – 474Combined sources5
Helixi487 – 489Combined sources3
Helixi492 – 499Combined sources8
Helixi506 – 508Combined sources3
Beta strandi522 – 526Combined sources5
Beta strandi528 – 530Combined sources3
Beta strandi534 – 542Combined sources9
Beta strandi544 – 551Combined sources8
Helixi556 – 558Combined sources3
Beta strandi560 – 563Combined sources4
Helixi574 – 578Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OYXX-ray1.85A/B/C265-595[»]
1OZ2X-ray1.55A265-595[»]
1OZ3X-ray1.85A/B/C265-595[»]
2PQWX-ray2.00A268-590[»]
2RHIX-ray1.66A265-594[»]
2RHUX-ray1.90A274-587[»]
2RHXX-ray2.10A265-594[»]
2RHYX-ray1.90A274-587[»]
2RHZX-ray2.20A274-587[»]
2RI2X-ray2.20A274-587[»]
2RI3X-ray2.00A274-587[»]
2RI5X-ray2.00A274-587[»]
2RJCX-ray2.00A/B/C268-598[»]
2RJDX-ray1.65A268-598[»]
2RJEX-ray1.86A/B/C268-598[»]
2RJFX-ray2.05A/C/E268-598[»]
3OQ5X-ray2.50A/B/C259-598[»]
3P8HX-ray2.55A/B/C268-590[»]
3UWNX-ray2.15A268-598[»]
6BYBX-ray1.74A200-522[»]
ProteinModelPortaliQ9Y468
SMRiQ9Y468
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y468

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati274 – 374MBT 1Add BLAST101
Repeati382 – 481MBT 2Add BLAST100
Repeati490 – 585MBT 3Add BLAST96
Domaini751 – 824SAMPROSITE-ProRule annotationAdd BLAST74

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni447 – 454Interaction with monomethylated and dimethylated peptides8

Domaini

The MBT repeat 2 specifically recognizes and binds monomethylated and dimethylated proteins. In contrast, it does not bind trimethylated proteins. The MBT repeat 1 does not bind methylated peptides but inserts a proline ring in a Pro-Ser-Ser/Thr sequence context.1 Publication

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri613 – 656CCHHC-typePROSITE-ProRule annotationAdd BLAST44

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG3766 Eukaryota
ENOG410Y4AQ LUCA
GeneTreeiENSGT00760000119024
HOVERGENiHBG071375
InParanoidiQ9Y468
OMAiRFTAHYC
OrthoDBiEOG091G01BW
PhylomeDBiQ9Y468
TreeFamiTF316498

Family and domain databases

InterProiView protein in InterPro
IPR004092 Mbt
IPR002515 Znf_C2HC
IPR036060 Znf_C2HC_sf
PfamiView protein in Pfam
PF02820 MBT, 3 hits
PF01530 zf-C2HC, 1 hit
SMARTiView protein in SMART
SM00561 MBT, 3 hits
SUPFAMiSSF103637 SSF103637, 1 hit
PROSITEiView protein in PROSITE
PS51079 MBT, 3 hits
PS50105 SAM_DOMAIN, 1 hit
PS51802 ZF_CCHHC, 1 hit

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 5 (identifier: Q9Y468-5) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MHLVAGDSPG SGPHLPATAF IIPASSATLG LPSSALDVSC FPREPIHVGA
60 70 80 90 100
PEQVAGCEPV SATVLPQLSA GPASSSTSTV RLLEWTEAAA PPPGGGLRFR
110 120 130 140 150
ISEYKPLNMA GVEQPPSPEL RQEGVTEYED GGAPAGDGEA GPQQAEDHPQ
160 170 180 190 200
NPPEDPNQDP PEDDSTCQCQ ACGPHQAAGP DLGSSNDGCP QLFQERSVIV
210 220 230 240 250
ENSSGSTSAS ELLKPMKKRK RREYQSPSEE ESEPEAMEKQ EEGKDPEGQP
260 270 280 290 300
TASTPESEEW SSSQPATGEK KECWSWESYL EEQKAITAPV SLFQDSQAVT
310 320 330 340 350
HNKNGFKLGM KLEGIDPQHP SMYFILTVAE VCGYRLRLHF DGYSECHDFW
360 370 380 390 400
VNANSPDIHP AGWFEKTGHK LQPPKGYKEE EFSWSQYLRS TRAQAAPKHL
410 420 430 440 450
FVSQSHSPPP LGFQVGMKLE AVDRMNPSLV CVASVTDVVD SRFLVHFDNW
460 470 480 490 500
DDTYDYWCDP SSPYIHPVGW CQKQGKPLTP PQDYPDPDNF CWEKYLEETG
510 520 530 540 550
ASAVPTWAFK VRPPHSFLVN MKLEAVDRRN PALIRVASVE DVEDHRIKIH
560 570 580 590 600
FDGWSHGYDF WIDADHPDIH PAGWCSKTGH PLQPPLGPRE PSSASPGGCP
610 620 630 640 650
PLSYRSLPHT RTSKYSFHHR KCPTPGCDGS GHVTGKFTAH HCLSGCPLAE
660 670 680 690 700
RNQSRLKAEL SDSEASARKK NLSGFSPRKK PRHHGRIGRP PKYRKIPQED
710 720 730 740 750
FQTLTPDVVH QSLFMSALSA HPDRSLSVCW EQHCKLLPGV AGISASTVAK
760 770 780 790 800
WTIDEVFGFV QTLTGCEDQA RLFKDEARIV RVTHVSGKTL VWTVAQLGDL
810 820 830 840
VCSDHLQEGK GILETGVHSL LCSLPTHLLA KLSFASDSQY
Length:840
Mass (Da):92,297
Last modified:March 28, 2018 - v4
Checksum:i70004D458897CB24
GO
Isoform 1 (identifier: Q9Y468-1) [UniParc]FASTAAdd to basket
Also known as: mbt-I

The sequence of this isoform differs from the canonical sequence as follows:
     1-98: MHLVAGDSPG...AAPPPGGGLR → MRRREGHGTDSEMGQGPVRESQSSDPPALQ

Show »
Length:772
Mass (Da):85,917
Checksum:i117B03A628826B29
GO
Isoform 2 (identifier: Q9Y468-2) [UniParc]FASTAAdd to basket
Also known as: mbt-II

The sequence of this isoform differs from the canonical sequence as follows:
     1-98: MHLVAGDSPG...AAPPPGGGLR → MRRREGHGTDSEMGQGPVRESQSSDPPALQ
     777-840: ARIVRVTHVS...KLSFASDSQY → VRCKCRVGDRAGVTVLKTAGSRCPPQRHFC

Show »
Length:738
Mass (Da):82,318
Checksum:i091F0E829CE6665D
GO
Isoform 3 (identifier: Q9Y468-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-416: Missing.
     777-840: ARIVRVTHVS...KLSFASDSQY → VRCKCRVGDRAGVTVLKTAGSRCPPQRHFC

Show »
Length:390
Mass (Da):43,766
Checksum:i8C720B89B9DD6388
GO
Isoform 4 (identifier: Q9Y468-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-98: MHLVAGDSPG...AAPPPGGGLR → MRRREGHGTDSEMGQGPVRESQSSDPPALQ
     777-840: ARIVRVTHVS...KLSFASDSQY → MIDGEAFLLL...MFKNADDTLK

Note: No experimental confirmation available.
Show »
Length:752
Mass (Da):83,884
Checksum:i6B92FF852FF98CB4
GO

Sequence cautioni

The sequence EAW75958 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence EAW75961 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence EAW75962 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti254T → A in BAG61241 (PubMed:14702039).Curated1
Sequence conflicti373P → L in AAC69438 (PubMed:10445843).Curated1
Sequence conflicti388 – 389LR → MC in AAC69438 (PubMed:10445843).Curated2
Sequence conflicti400L → M in AAC69438 (PubMed:10445843).Curated1
Sequence conflicti561W → R in BAG61241 (PubMed:14702039).Curated1
Sequence conflicti663S → P in AAC69438 (PubMed:10445843).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_051097117S → T1 PublicationCorresponds to variant dbSNP:rs17857202Ensembl.1
Natural variantiVAR_051098547I → M. Corresponds to variant dbSNP:rs6017104Ensembl.1
Isoform 1 (identifier: Q9Y468-1)
Natural varianti759H → R DbSNP:rs6030948. 1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0039011 – 416Missing in isoform 3. 1 PublicationAdd BLAST416
Alternative sequenceiVSP_0594581 – 98MHLVA…GGGLR → MRRREGHGTDSEMGQGPVRE SQSSDPPALQ in isoform 1, isoform 2 and isoform 4. 3 PublicationsAdd BLAST98
Alternative sequenceiVSP_059459777 – 840ARIVR…SDSQY → VRCKCRVGDRAGVTVLKTAG SRCPPQRHFC in isoform 2 and isoform 3. 2 PublicationsAdd BLAST64
Alternative sequenceiVSP_059460777 – 840ARIVR…SDSQY → MIDGEAFLLLTQADIVKIMS VKLGPALKIYNAILMFKNAD DTLK in isoform 4. 1 PublicationAdd BLAST64

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89358 mRNA Translation: AAC69438.1
AK299199 mRNA Translation: BAG61241.1
AL110279 mRNA Translation: CAB53714.1
AL031681 Genomic DNA No translation available.
Z98752 Genomic DNA No translation available.
CH471077 Genomic DNA Translation: EAW75958.1 Sequence problems.
CH471077 Genomic DNA Translation: EAW75961.1 Sequence problems.
CH471077 Genomic DNA Translation: EAW75962.1 Sequence problems.
BC039820 mRNA Translation: AAH39820.1
AB014581 mRNA Translation: BAA31656.1
CCDSiCCDS13319.1 [Q9Y468-1]
CCDS46602.2 [Q9Y468-5]
PIRiT14794
RefSeqiNP_056293.4, NM_015478.6 [Q9Y468-1]
NP_115479.4, NM_032107.4 [Q9Y468-5]
UniGeneiHs.709356
Hs.736988

Genome annotation databases

EnsembliENST00000373135; ENSP00000362227; ENSG00000185513 [Q9Y468-1]
ENST00000418998; ENSP00000398516; ENSG00000185513 [Q9Y468-5]
GeneIDi26013
KEGGihsa:26013
UCSCiuc002xkl.4 human [Q9Y468-5]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiLMBL1_HUMAN
AccessioniPrimary (citable) accession number: Q9Y468
Secondary accession number(s): B4DRC9
, E1P5W7, Q5H8Y8, Q5H8Y9, Q8IUV7, Q9H1E6, Q9H1G5, Q9UG06, Q9UJB9, Q9Y4C9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: March 28, 2018
Last modified: June 20, 2018
This is version 188 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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