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Protein

BEN domain-containing protein 3

Gene

BEND3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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).By similarity2 Publications

GO - Molecular functioni

  • rDNA binding Source: UniProtKB

GO - Biological processi

  • chromatin silencing at rDNA Source: UniProtKB
  • 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 from RNA polymerase II promoter Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
BEN domain-containing protein 3
Gene namesi
Name:BEND3
Synonyms:KIAA1553
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:23040. BEND3.

Subcellular locationi

GO - Cellular componenti

  • nuclear heterochromatin Source: UniProtKB
  • nucleolus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi20 – 201K → 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
Mutagenesisi56 – 561K → A: Loss of nuclear localization. 1 Publication
Mutagenesisi57 – 571R → A: Loss of nuclear localization. 1 Publication
Mutagenesisi58 – 581K → A: Loss of nuclear localization. 1 Publication
Mutagenesisi512 – 5121K → 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

Organism-specific databases

PharmGKBiPA164716540.

Polymorphism and mutation databases

BioMutaiBEND3.
DMDMi74745144.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 828828BEN domain-containing protein 3PRO_0000290200Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki20 – 20Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate1 Publication
Cross-linki20 – 20Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1); alternateCombined sources
Cross-linki20 – 20Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki56 – 56Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki129 – 129Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki142 – 142Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei164 – 1641PhosphoserineCombined sources
Modified residuei379 – 3791PhosphoserineCombined sources
Cross-linki427 – 427Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei489 – 4891PhosphoserineCombined sources
Cross-linki512 – 512Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication

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 conjugation

Proteomic databases

EPDiQ5T5X7.
MaxQBiQ5T5X7.
PaxDbiQ5T5X7.
PeptideAtlasiQ5T5X7.
PRIDEiQ5T5X7.

PTM databases

iPTMnetiQ5T5X7.
PhosphoSiteiQ5T5X7.

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

BgeeiENSG00000178409.
CleanExiHS_BEND3.
GenevisibleiQ5T5X7. HS.

Organism-specific databases

HPAiHPA017891.

Interactioni

Subunit structurei

Interacts with HDAC2 and HDAC3, but not HDAC1. Interacts with SALL4. Interacts with SMARCA5/SNF2H, BAZ2A/TIP5 and USP21. Interacts with the nucleosome remodeling and histone deacetylase (NuRD) repressor complex (By similarity).By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
FAM161AQ3B8203EBI-1211496,EBI-719941
MORN4Q8NDC43EBI-1211496,EBI-10269566

Protein-protein interaction databases

BioGridi121704. 21 interactions.
IntActiQ5T5X7. 14 interactions.
MINTiMINT-8173827.
STRINGi9606.ENSP00000358038.

Structurei

3D structure databases

ProteinModelPortaliQ5T5X7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini242 – 343102BEN 1PROSITE-ProRule annotationAdd
BLAST
Domaini387 – 487101BEN 2PROSITE-ProRule annotationAdd
BLAST
Domaini548 – 650103BEN 3PROSITE-ProRule annotationAdd
BLAST
Domaini715 – 816102BEN 4PROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi56 – 583Nuclear localization signal1 Publication

Domaini

The BEN domain 4 is necessary and sufficient for the localization of BEND3 to heterochromatic regions.1 Publication

Sequence similaritiesi

Contains 4 BEN domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410IHA7. Eukaryota.
ENOG410Y8FH. LUCA.
GeneTreeiENSGT00390000010827.
HOGENOMiHOG000082471.
HOVERGENiHBG091074.
InParanoidiQ5T5X7.
OMAiPPRDDCY.
OrthoDBiEOG091G025S.
PhylomeDBiQ5T5X7.
TreeFamiTF300204.

Family and domain databases

InterProiIPR018379. BEN_domain.
IPR033583. BEND3.
[Graphical view]
PANTHERiPTHR28665. PTHR28665. 1 hit.
PfamiPF10523. BEN. 4 hits.
[Graphical view]
SMARTiSM01025. BEN. 4 hits.
[Graphical view]
PROSITEiPS51457. BEN. 4 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5T5X7-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:828
Mass (Da):94,475
Last modified:December 21, 2004 - v1
Checksum:i28D8F39112DB7EAE
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti409 – 4091E → D in BAB13379 (PubMed:10997877).Curated
Sequence conflicti596 – 5961N → S in AAI31629 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL355586 Genomic DNA. Translation: CAI16110.1.
BC131628 mRNA. Translation: AAI31629.1.
AB046773 mRNA. Translation: BAB13379.1.
CCDSiCCDS34507.1.
RefSeqiNP_001073919.1. NM_001080450.2.
XP_005267136.1. XM_005267079.3.
XP_005267137.1. XM_005267080.3.
XP_011534307.1. XM_011536005.2.
UniGeneiHs.418045.

Genome annotation databases

EnsembliENST00000369042; ENSP00000358038; ENSG00000178409.
ENST00000429433; ENSP00000411268; ENSG00000178409.
GeneIDi57673.
KEGGihsa:57673.
UCSCiuc003prs.3. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL355586 Genomic DNA. Translation: CAI16110.1.
BC131628 mRNA. Translation: AAI31629.1.
AB046773 mRNA. Translation: BAB13379.1.
CCDSiCCDS34507.1.
RefSeqiNP_001073919.1. NM_001080450.2.
XP_005267136.1. XM_005267079.3.
XP_005267137.1. XM_005267080.3.
XP_011534307.1. XM_011536005.2.
UniGeneiHs.418045.

3D structure databases

ProteinModelPortaliQ5T5X7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121704. 21 interactions.
IntActiQ5T5X7. 14 interactions.
MINTiMINT-8173827.
STRINGi9606.ENSP00000358038.

PTM databases

iPTMnetiQ5T5X7.
PhosphoSiteiQ5T5X7.

Polymorphism and mutation databases

BioMutaiBEND3.
DMDMi74745144.

Proteomic databases

EPDiQ5T5X7.
MaxQBiQ5T5X7.
PaxDbiQ5T5X7.
PeptideAtlasiQ5T5X7.
PRIDEiQ5T5X7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369042; ENSP00000358038; ENSG00000178409.
ENST00000429433; ENSP00000411268; ENSG00000178409.
GeneIDi57673.
KEGGihsa:57673.
UCSCiuc003prs.3. human.

Organism-specific databases

CTDi57673.
GeneCardsiBEND3.
H-InvDBHIX0006107.
HIX0021350.
HIX0170379.
HGNCiHGNC:23040. BEND3.
HPAiHPA017891.
MIMi616374. gene.
neXtProtiNX_Q5T5X7.
PharmGKBiPA164716540.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IHA7. Eukaryota.
ENOG410Y8FH. LUCA.
GeneTreeiENSGT00390000010827.
HOGENOMiHOG000082471.
HOVERGENiHBG091074.
InParanoidiQ5T5X7.
OMAiPPRDDCY.
OrthoDBiEOG091G025S.
PhylomeDBiQ5T5X7.
TreeFamiTF300204.

Miscellaneous databases

GenomeRNAii57673.
PROiQ5T5X7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000178409.
CleanExiHS_BEND3.
GenevisibleiQ5T5X7. HS.

Family and domain databases

InterProiIPR018379. BEN_domain.
IPR033583. BEND3.
[Graphical view]
PANTHERiPTHR28665. PTHR28665. 1 hit.
PfamiPF10523. BEN. 4 hits.
[Graphical view]
SMARTiSM01025. BEN. 4 hits.
[Graphical view]
PROSITEiPS51457. BEN. 4 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiBEND3_HUMAN
AccessioniPrimary (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: September 7, 2016
This is version 91 of the entry and version 1 of the sequence. [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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.