UniProtKB - Q5T5X7 (BEND3_HUMAN)
Protein
BEN domain-containing protein 3
Gene
BEND3
Organism
Homo sapiens (Human)
Status
Functioni
Transcriptional repressor which associates with the NoRC (nucleolar remodeling complex) complex and plays a key role in repressing rDNA transcription. The sumoylated form modulates the stability of the NoRC complex component BAZ2A/TIP5 by controlling its USP21-mediated deubiquitination (PubMed:21914818, PubMed:26100909). Binds to unmethylated major satellite DNA and is involved in the recruitment of the Polycomb repressive complex 2 (PRC2) to major satellites (By similarity). Stimulates the ERCC6L translocase and ATPase activities (PubMed:28977671).By similarity3 Publications
GO - Molecular functioni
- rDNA binding Source: UniProtKB
GO - Biological processi
- DNA methylation Source: UniProtKB
- histone H3-K27 trimethylation Source: UniProtKB
- histone H3-K4 trimethylation Source: UniProtKB
- histone H3-K9 trimethylation Source: UniProtKB
- histone H4 acetylation Source: UniProtKB
- histone H4-K20 trimethylation Source: UniProtKB
- negative regulation of transcription by RNA polymerase II Source: UniProtKB
- positive regulation of ATP metabolic process Source: UniProtKB
- protein homooligomerization Source: UniProtKB
- rDNA heterochromatin assembly Source: UniProtKB
Keywordsi
Molecular function | Chromatin regulator, DNA-binding, Repressor |
Biological process | Transcription, Transcription regulation |
Enzyme and pathway databases
PathwayCommonsi | Q5T5X7 |
Names & Taxonomyi
Protein namesi | Recommended name: BEN domain-containing protein 3 |
Gene namesi | Name:BEND3 Synonyms:KIAA1553 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
EuPathDBi | HostDB:ENSG00000178409.13 |
HGNCi | HGNC:23040, BEND3 |
MIMi | 616374, gene |
neXtProti | NX_Q5T5X7 |
Subcellular locationi
Nucleus
Note: In the nucleus, observed in heterochromatic foci containing CBX1, CBX3, CBX5 and histone H3 trimethylated at 'Lys-9'. Released from chromatin during decondensation. Association with heterochromatin does not depend on sumoylation.1 Publication
Nucleus
- nuclear heterochromatin Source: UniProtKB
- nucleolus Source: UniProtKB
- nucleoplasm Source: HPA
Keywords - Cellular componenti
NucleusPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 20 | K → R: Partial loss of sumoylation. Almost complete loss of sumoylation, partial loss of transcription repression, no effect on subcellular location, loss of rDNA silencing; when associated with R-512. 2 Publications | 1 | |
Mutagenesisi | 56 | K → A: Loss of nuclear localization. 1 Publication | 1 | |
Mutagenesisi | 57 | R → A: Loss of nuclear localization. 1 Publication | 1 | |
Mutagenesisi | 58 | K → A: Loss of nuclear localization. 1 Publication | 1 | |
Mutagenesisi | 512 | K → R: Partial loss of sumoylation. Almost complete loss of sumoylation, partial loss of transcription repression, no effect on subcellular location, loss of rDNA silencing; when associated with R-20. 2 Publications | 1 |
Organism-specific databases
DisGeNETi | 57673 |
OpenTargetsi | ENSG00000178409 |
PharmGKBi | PA164716540 |
Miscellaneous databases
Pharosi | Q5T5X7, Tbio |
Polymorphism and mutation databases
BioMutai | BEND3 |
DMDMi | 74745144 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000290200 | 1 – 828 | BEN domain-containing protein 3Add BLAST | 828 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Cross-linki | 20 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate1 Publication | ||
Cross-linki | 20 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources | ||
Cross-linki | 20 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources | ||
Cross-linki | 41 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 56 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 58 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 73 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 128 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 129 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 137 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 142 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 158 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Modified residuei | 164 | PhosphoserineCombined sources | 1 | |
Cross-linki | 176 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Modified residuei | 379 | PhosphoserineCombined sources | 1 | |
Cross-linki | 427 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Modified residuei | 489 | PhosphoserineCombined sources | 1 | |
Cross-linki | 512 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate1 Publication | ||
Cross-linki | 512 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources | ||
Cross-linki | 528 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 700 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources |
Post-translational modificationi
Sumoylated at Lys-20 by SUMO1 and at Lys-512 by SUMO1, SUMO2 and SUMO3. Sumoylation probably occurs sequentially, with that of Lys-20 preceding that of Lys-512. It does not alter association with heterochromatin, but is required for the repression of transcription.1 Publication
Keywords - PTMi
Isopeptide bond, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | Q5T5X7 |
jPOSTi | Q5T5X7 |
MassIVEi | Q5T5X7 |
MaxQBi | Q5T5X7 |
PaxDbi | Q5T5X7 |
PeptideAtlasi | Q5T5X7 |
PRIDEi | Q5T5X7 |
ProteomicsDBi | 64557 |
PTM databases
iPTMneti | Q5T5X7 |
PhosphoSitePlusi | Q5T5X7 |
Expressioni
Tissue specificityi
Expressed at least in heart, kidney, liver, ovary and spleen, with highest levels in spleen and lowest in heart. Expressed on the surface of T-cells.2 Publications
Gene expression databases
Bgeei | ENSG00000178409, Expressed in metanephros and 176 other tissues |
Genevisiblei | Q5T5X7, HS |
Organism-specific databases
HPAi | ENSG00000178409, Tissue enhanced (pancreas) |
Interactioni
Subunit structurei
Homooligomer, probably a homooctamer (PubMed:28977671).
Interacts with HDAC2 and HDAC3, but not HDAC1.
Interacts with SALL4 (PubMed:21914818).
Interacts with SMARCA5/SNF2H, BAZ2A/TIP5 and USP21 (PubMed:26100909).
Interacts with the nucleosome remodeling and histone deacetylase (NuRD) repressor complex (By similarity).
Interacts (via BEN domains 1 and 3) with ERCC6L (via N-terminal TPR repeat); the interaction is direct (PubMed:28977671).
By similarity3 PublicationsBinary interactionsi
Hide detailsQ5T5X7
Protein-protein interaction databases
BioGRIDi | 121704, 30 interactors |
IntActi | Q5T5X7, 23 interactors |
MINTi | Q5T5X7 |
STRINGi | 9606.ENSP00000411268 |
Miscellaneous databases
RNActi | Q5T5X7, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q5T5X7 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 242 – 343 | BEN 1PROSITE-ProRule annotationAdd BLAST | 102 | |
Domaini | 387 – 487 | BEN 2PROSITE-ProRule annotationAdd BLAST | 101 | |
Domaini | 548 – 650 | BEN 3PROSITE-ProRule annotationAdd BLAST | 103 | |
Domaini | 715 – 816 | BEN 4PROSITE-ProRule annotationAdd BLAST | 102 |
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 56 – 58 | Nuclear localization signal1 Publication | 3 |
Domaini
The BEN domain 4 is necessary and sufficient for the localization of BEND3 to heterochromatic regions.1 Publication
Keywords - Domaini
RepeatPhylogenomic databases
eggNOGi | ENOG502QQWG, Eukaryota |
GeneTreei | ENSGT00390000010827 |
HOGENOMi | CLU_017582_0_0_1 |
InParanoidi | Q5T5X7 |
OMAi | KMFYTLN |
OrthoDBi | 168652at2759 |
PhylomeDBi | Q5T5X7 |
TreeFami | TF300204 |
Family and domain databases
InterProi | View protein in InterPro IPR018379, BEN_domain IPR033583, BEND3 |
PANTHERi | PTHR28665, PTHR28665, 1 hit |
Pfami | View protein in Pfam PF10523, BEN, 4 hits |
SMARTi | View protein in SMART SM01025, BEN, 4 hits |
PROSITEi | View protein in PROSITE PS51457, BEN, 4 hits |
i Sequence
Sequence statusi: Complete.
Q5T5X7-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MNSTEFTEDV EEVLKSITVK VETEAEDAAL DCSVNSRTSE KHSVDSVLTA
60 70 80 90 100
LQDSSKRKQL VSDGLLDSVP GVKRRRLIPE ALLAGMRNRE NSSPCQGNGE
110 120 130 140 150
QAGRGRSLGN VWPGEEEPCN DATTPSYKKP LYGISHKIME KKNPPSGDLL
160 170 180 190 200
NVYELFEKAN ASNSPSSLRL LNEPQKRDCG STGAGTDNDP NIYFLIQKMF
210 220 230 240 250
YMLNTLTSNM SQLHSKVDLL SLEVSRIKKQ VSPTEMVAKF QPPPEYQLTA
260 270 280 290 300
AELKQIVDQS LSGGDLACRL LVQLFPELFS DVDFSRGCSA CGFAAKRKLE
310 320 330 340 350
SLHLQLIRNY VEVYYPSVKD TAVWQAECLP QLNDFFSRFW AQREMEDSQP
360 370 380 390 400
SGQVASFFEA EQVDPGHFLD NKDQEEALSL DRSSTIASDH VVDTQDLTEF
410 420 430 440 450
LDEASSPGEF AVFLLHRLFP ELFDHRKLGE QYSCYGDGGK QELDPQRLQI
460 470 480 490 500
IRNYTEIYFP DMQEEEAWLQ QCAQRINDEL EGLGLDAGSE GDPPRDDCYD
510 520 530 540 550
SSSLPDDISV VKVEDSFEGE RPGRRSKKIW LVPIDFDKLE IPQPDFEVPG
560 570 580 590 600
ADCLLSKEQL RSIYESSLSI GNFASRLLVH LFPELFTHEN LRKQYNCSGS
610 620 630 640 650
LGKKQLDPSR IKLIRHYVQL LYPRAKNDRV WTLEFVGKLD ERCRRRDTEQ
660 670 680 690 700
RRSYQQQRKV HVPGPECRDL TSYAINPERF REEFEGPPLP PERSSKDFCK
710 720 730 740 750
IPLDELVVPS PDFPVPSPYL LSDKEVREIV QQSLSVGNFA ARLLVRLFPE
760 770 780 790 800
LFTAENLRLQ YNHSGACNKK QLDPTRLRLI RHYVEAVYPV EKMEEVWHYE
810 820
CIPSIDERCR RPNRKKCDIL KKAKKVEK
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 409 | E → D in BAB13379 (PubMed:10997877).Curated | 1 | |
Sequence conflicti | 596 | N → S in AAI31629 (PubMed:15489334).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AL355586 Genomic DNA No translation available. BC131628 mRNA Translation: AAI31629.1 AB046773 mRNA Translation: BAB13379.1 |
CCDSi | CCDS34507.1 |
RefSeqi | NP_001073919.1, NM_001080450.2 XP_005267136.1, XM_005267079.3 XP_005267137.1, XM_005267080.3 XP_011534307.1, XM_011536005.2 XP_016866627.1, XM_017011138.1 |
Genome annotation databases
Ensembli | ENST00000369042; ENSP00000358038; ENSG00000178409 ENST00000429433; ENSP00000411268; ENSG00000178409 |
GeneIDi | 57673 |
KEGGi | hsa:57673 |
UCSCi | uc003prs.3, human |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AL355586 Genomic DNA No translation available. BC131628 mRNA Translation: AAI31629.1 AB046773 mRNA Translation: BAB13379.1 |
CCDSi | CCDS34507.1 |
RefSeqi | NP_001073919.1, NM_001080450.2 XP_005267136.1, XM_005267079.3 XP_005267137.1, XM_005267080.3 XP_011534307.1, XM_011536005.2 XP_016866627.1, XM_017011138.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
5JNO | X-ray | 2.20 | A | 236-347 | [»] | |
SMRi | Q5T5X7 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 121704, 30 interactors |
IntActi | Q5T5X7, 23 interactors |
MINTi | Q5T5X7 |
STRINGi | 9606.ENSP00000411268 |
PTM databases
iPTMneti | Q5T5X7 |
PhosphoSitePlusi | Q5T5X7 |
Polymorphism and mutation databases
BioMutai | BEND3 |
DMDMi | 74745144 |
Proteomic databases
EPDi | Q5T5X7 |
jPOSTi | Q5T5X7 |
MassIVEi | Q5T5X7 |
MaxQBi | Q5T5X7 |
PaxDbi | Q5T5X7 |
PeptideAtlasi | Q5T5X7 |
PRIDEi | Q5T5X7 |
ProteomicsDBi | 64557 |
Protocols and materials databases
Antibodypediai | 2976, 119 antibodies |
Genome annotation databases
Ensembli | ENST00000369042; ENSP00000358038; ENSG00000178409 ENST00000429433; ENSP00000411268; ENSG00000178409 |
GeneIDi | 57673 |
KEGGi | hsa:57673 |
UCSCi | uc003prs.3, human |
Organism-specific databases
CTDi | 57673 |
DisGeNETi | 57673 |
EuPathDBi | HostDB:ENSG00000178409.13 |
GeneCardsi | BEND3 |
HGNCi | HGNC:23040, BEND3 |
HPAi | ENSG00000178409, Tissue enhanced (pancreas) |
MIMi | 616374, gene |
neXtProti | NX_Q5T5X7 |
OpenTargetsi | ENSG00000178409 |
PharmGKBi | PA164716540 |
HUGEi | Search... |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | ENOG502QQWG, Eukaryota |
GeneTreei | ENSGT00390000010827 |
HOGENOMi | CLU_017582_0_0_1 |
InParanoidi | Q5T5X7 |
OMAi | KMFYTLN |
OrthoDBi | 168652at2759 |
PhylomeDBi | Q5T5X7 |
TreeFami | TF300204 |
Enzyme and pathway databases
PathwayCommonsi | Q5T5X7 |
Miscellaneous databases
BioGRID-ORCSi | 57673, 18 hits in 843 CRISPR screens |
ChiTaRSi | BEND3, human |
GenomeRNAii | 57673 |
Pharosi | Q5T5X7, Tbio |
PROi | PR:Q5T5X7 |
RNActi | Q5T5X7, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000178409, Expressed in metanephros and 176 other tissues |
Genevisiblei | Q5T5X7, HS |
Family and domain databases
InterProi | View protein in InterPro IPR018379, BEN_domain IPR033583, BEND3 |
PANTHERi | PTHR28665, PTHR28665, 1 hit |
Pfami | View protein in Pfam PF10523, BEN, 4 hits |
SMARTi | View protein in SMART SM01025, BEN, 4 hits |
PROSITEi | View protein in PROSITE PS51457, BEN, 4 hits |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | BEND3_HUMAN | |
Accessioni | Q5T5X7Primary (citable) accession number: Q5T5X7 Secondary accession number(s): A2RRH2, Q9HCL9 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | June 12, 2007 |
Last sequence update: | December 21, 2004 | |
Last modified: | December 2, 2020 | |
This is version 126 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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, Reference proteomeDocuments
- Human chromosome 6
Human chromosome 6: entries, gene names and cross-references to MIM - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references