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Q9UPW6 (SATB2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 125. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA-binding protein SATB2
Alternative name(s):
Special AT-rich sequence-binding protein 2
Gene names
Name:SATB2
Synonyms:KIAA1034
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length733 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Binds to DNA, at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcription factor controlling nuclear gene expression, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Required for the initiation of the upper-layer neurons (UL1) specific genetic program and for the inactivation of deep-layer neurons (DL) and UL2 specific genes, probably by modulating BCL11B expression. Repressor of Ctip2 and regulatory determinant of corticocortical connections in the developing cerebral cortex. May play an important role in palate formation. Acts as a molecular node in a transcriptional network regulating skeletal development and osteoblast differentiation. Ref.6

Subunit structure

Interacts with ATF4 and RUNX2; resulting in enhanced DNA binding and transactivation by these transcription factors By similarity. Interacts with PIAS1. Ref.6

Subcellular location

Nucleus matrix Ref.6.

Tissue specificity

High expression in adult brain, moderate expression in fetal brain, and weak expression in adult liver, kidney, and spinal cord and in select brain regions, including amygdala, corpus callosum, caudate nucleus, and hippocampus. Ref.6

Post-translational modification

Sumoylated by PIAS1. Sumoylation promotes nuclear localization, but represses transcription factor activity. Ref.6

Involvement in disease

Chromosomal aberrations involving SATB2 are found in isolated cleft palate. Translocation t(2;7); translocation t(2;11).

Cleft palate isolated (CPI) [MIM:119540]: A congenital fissure of the soft and/or hard palate, due to faulty fusion. Isolated cleft palate is not associated with cleft lips. Some patients may manifest other craniofacial dysmorphic features, mental retardation, and osteoporosis.
Note: The disease may be caused by mutations affecting the gene represented in this entry. Ref.7 Ref.8

A chromosomal aberration involving SATB2 is found in a patient with classical features of Toriello-Carey syndrome. Translocation t(2;14)(q33;q22).

Sequence similarities

Belongs to the CUT homeobox family.

Contains 2 CUT DNA-binding domains.

Contains 1 homeobox DNA-binding domain.

Sequence caution

The sequence BAA82986.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityChromosomal rearrangement
   DiseaseDisease mutation
Mental retardation
   DomainHomeobox
Repeat
   LigandDNA-binding
   Molecular functionChromatin regulator
Developmental protein
Repressor
   PTMIsopeptide bond
Ubl conjugation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcartilage development

Inferred from electronic annotation. Source: Ensembl

cellular response to organic substance

Inferred from electronic annotation. Source: Ensembl

chromatin remodeling

Inferred from electronic annotation. Source: Ensembl

embryonic pattern specification

Inferred from electronic annotation. Source: Ensembl

embryonic skeletal system morphogenesis

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Ensembl

neuron migration

Inferred from electronic annotation. Source: Ensembl

osteoblast development

Inferred from electronic annotation. Source: Ensembl

palate development

Inferred from electronic annotation. Source: Ensembl

positive regulation of transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from direct assay. Source: HPA

histone deacetylase complex

Inferred from electronic annotation. Source: Ensembl

nuclear matrix

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay. Source: HPA

transcription factor complex

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionchromatin binding

Inferred from electronic annotation. Source: Ensembl

sequence-specific DNA binding

Inferred from electronic annotation. Source: Ensembl

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

TP63Q9H3D4-25EBI-8298169,EBI-6481107

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 733733DNA-binding protein SATB2
PRO_0000202400

Regions

DNA binding350 – 43788CUT 1
DNA binding473 – 56088CUT 2
DNA binding615 – 67460Homeobox

Amino acid modifications

Cross-link233Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable
Cross-link350Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable

Natural variations

Natural variant2631S → P.
Corresponds to variant rs12619995 [ dbSNP | Ensembl ].
VAR_059320

Experimental info

Mutagenesis2331K → R: Reduced sumoylation, impaired nuclear localization, but enhanced transcription factor activity. Ref.6
Mutagenesis3501K → R: Reduced sumoylation, impaired nuclear localization, but enhanced transcription factor activity. Ref.6

Secondary structure

............................. 733
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9UPW6 [UniParc].

Last modified April 27, 2001. Version 2.
Checksum: 1FE1FCBD34F11E9E

FASTA73382,555
        10         20         30         40         50         60 
MERRSESPCL RDSPDRRSGS PDVKGPPPVK VARLEQNGSP MGARGRPNGA VAKAVGGLMI 

        70         80         90        100        110        120 
PVFCVVEQLD GSLEYDNREE HAEFVLVRKD VLFSQLVETA LLALGYSHSS AAQAQGIIKL 

       130        140        150        160        170        180 
GRWNPLPLSY VTDAPDATVA DMLQDVYHVV TLKIQLQSCS KLEDLPAEQW NHATVRNALK 

       190        200        210        220        230        240 
ELLKEMNQST LAKECPLSQS MISSIVNSTY YANVSATKCQ EFGRWYKKYK KIKVERVERE 

       250        260        270        280        290        300 
NLSDYCVLGQ RPMHLPNMNQ LASLGKTNEQ SPHSQIHHST PIRNQVPALQ PIMSPGLLSP 

       310        320        330        340        350        360 
QLSPQLVRQQ IAMAHLINQQ IAVSRLLAHQ HPQAINQQFL NHPPIPRAVK PEPTNSSVEV 

       370        380        390        400        410        420 
SPDIYQQVRD ELKRASVSQA VFARVAFNRT QGLLSEILRK EEDPRTASQS LLVNLRAMQN 

       430        440        450        460        470        480 
FLNLPEVERD RIYQDERERS MNPNVSMVSS ASSSPSSSRT PQAKTSTPTT DLPIKVDGAN 

       490        500        510        520        530        540 
INITAAIYDE IQQEMKRAKV SQALFAKVAA NKSQGWLCEL LRWKENPSPE NRTLWENLCT 

       550        560        570        580        590        600 
IRRFLNLPQH ERDVIYEEES RHHHSERMQH VVQLPPEPVQ VLHRQQSQPA KESSPPREEA 

       610        620        630        640        650        660 
PPPPPPTEDS CAKKPRSRTK ISLEALGILQ SFIHDVGLYP DQEAIHTLSA QLDLPKHTII 

       670        680        690        700        710        720 
KFFQNQRYHV KHHGKLKEHL GSAVDVAEYK DEELLTESEE NDSEEGSEEM YKVEAEEENA 

       730 
DKSKAAPAEI DQR 

« Hide

References

« Hide 'large scale' references
[1]"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].
Tissue: Brain.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Brain.
[3]"Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. expand/collapse author list , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]"SUMO modification of a novel MAR-binding protein, SATB2, modulates immunoglobulin mu gene expression."
Dobreva G., Dambacher J., Grosschedl R.
Genes Dev. 17:3048-3061(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH PIAS1, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-233 AND LYS-350, SUMOYLATION.
[7]"Identification of SATB2 as the cleft palate gene on 2q32-q33."
FitzPatrick D.R., Carr I.M., McLaren L., Leek J.P., Wightman P., Williamson K., Gautier P., McGill N., Hayward C., Firth H., Markham A.F., Fantes J.A., Bonthron D.T.
Hum. Mol. Genet. 12:2491-2501(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN CPI.
[8]"Heterozygous nonsense mutation SATB2 associated with cleft palate, osteoporosis, and cognitive defects."
Leoyklang P., Suphapeetiporn K., Siriwan P., Desudchit T., Chaowanapanja P., Gahl W.A., Shotelersuk V.
Hum. Mutat. 28:732-738(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN CPI.
[9]"Toriello-Carey syndrome in a patient with a de novo balanced translocation [46,XY,t(2;14)(q33;q22)] interrupting SATB2."
Tegay D.H., Chan K.K., Leung L., Wang C., Burkett S., Stone G., Stanyon R., Toriello H.V., Hatchwell E.
Clin. Genet. 75:259-264(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: CHROMOSOMAL TRANSLOCATION.
[10]"Solution structure of the homeodomain of KIAA1034 protein."
RIKEN structural genomics initiative (RSGI)
Submitted (FEB-2009) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 615-674.
[11]"Solution structure of the first CUT domain of KIAA1034 protein."
RIKEN structural genomics initiative (RSGI)
Submitted (FEB-2009) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 350-437.
[12]"Solution structure of the second CUT domain of human SATB2."
RIKEN structural genomics initiative (RSGI)
Submitted (FEB-2009) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 473-560.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB028957 mRNA. Translation: BAA82986.1. Different initiation.
AK291463 mRNA. Translation: BAF84152.1.
AC016746 Genomic DNA. No translation available.
AC017096 Genomic DNA. No translation available.
CH471063 Genomic DNA. Translation: EAW70180.1.
BC098136 mRNA. Translation: AAH98136.1.
BC099723 mRNA. Translation: AAH99723.1.
BC103500 mRNA. Translation: AAI03501.1.
RefSeqNP_001165980.1. NM_001172509.1.
NP_001165988.1. NM_001172517.1.
NP_056080.1. NM_015265.3.
UniGeneHs.516617.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1WI3NMR-A615-672[»]
1WIZNMR-A350-437[»]
2CSFNMR-A473-560[»]
ProteinModelPortalQ9UPW6.
SMRQ9UPW6. Positions 57-157, 165-231, 350-437, 473-674.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116905. 4 interactions.
DIPDIP-60551N.
IntActQ9UPW6. 1 interaction.
MINTMINT-2822679.
STRING9606.ENSP00000260926.

PTM databases

PhosphoSiteQ9UPW6.

Polymorphism databases

DMDM13634020.

Proteomic databases

PaxDbQ9UPW6.
PRIDEQ9UPW6.

Protocols and materials databases

DNASU23314.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000260926; ENSP00000260926; ENSG00000119042.
ENST00000417098; ENSP00000401112; ENSG00000119042.
ENST00000457245; ENSP00000405420; ENSG00000119042.
GeneID23314.
KEGGhsa:23314.
UCSCuc002uuy.2. human.

Organism-specific databases

CTD23314.
GeneCardsGC02M200098.
HGNCHGNC:21637. SATB2.
HPACAB023669.
CAB062562.
HPA001042.
HPA029543.
MIM119540. phenotype.
608148. gene.
neXtProtNX_Q9UPW6.
Orphanet251019. 2q32q33 microdeletion syndrome.
251028. 2q33.1 microdeletion syndrome.
199306. Cleft lip/palate.
PharmGKBPA128394624.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG313826.
HOVERGENHBG054240.
InParanoidQ9UPW6.
OMAPPAEDSC.
OrthoDBEOG7FBRH5.
PhylomeDBQ9UPW6.
TreeFamTF332714.

Gene expression databases

ArrayExpressQ9UPW6.
BgeeQ9UPW6.
CleanExHS_SATB2.
GenevestigatorQ9UPW6.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
1.10.260.40. 2 hits.
InterProIPR003350. Hmoeo_CUT.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR010982. Lambda_DNA-bd_dom.
[Graphical view]
PfamPF02376. CUT. 2 hits.
PF00046. Homeobox. 1 hit.
[Graphical view]
SMARTSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
SSF47413. SSF47413. 2 hits.
PROSITEPS51042. CUT. 2 hits.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSATB2. human.
EvolutionaryTraceQ9UPW6.
GeneWikiSATB2.
GenomeRNAi23314.
NextBio45192.
PROQ9UPW6.
SOURCESearch...

Entry information

Entry nameSATB2_HUMAN
AccessionPrimary (citable) accession number: Q9UPW6
Secondary accession number(s): A8K5Z8, Q4V763
Entry history
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: April 27, 2001
Last modified: March 19, 2014
This is version 125 of the entry and version 2 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 polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM