Q9UPW6 (SATB2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-binding protein SATB2

Alternative name(s):
Special AT-rich sequence-binding protein 2

Gene names

Name:	SATB2
Synonyms:	KIAA1034

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	733 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Chromosomal rearrangement
Disease	Disease mutation Mental retardation
Domain	Homeobox Repeat
Ligand	DNA-binding
Molecular function	Chromatin regulator Developmental protein Repressor
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cartilage development Inferred from electronic annotation. Source: Compara cellular response to organic substance Inferred from electronic annotation. Source: Compara chromatin remodeling Inferred from electronic annotation. Source: Compara embryonic pattern specification Inferred from electronic annotation. Source: Compara embryonic skeletal system morphogenesis Inferred from electronic annotation. Source: Compara negative regulation of transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: Compara neuron migration Inferred from electronic annotation. Source: Compara osteoblast development Inferred from electronic annotation. Source: Compara palate development Inferred from electronic annotation. Source: Compara positive regulation of transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: Compara transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from direct assay. Source: HPA histone deacetylase complex Inferred from electronic annotation. Source: Compara nuclear matrix Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from direct assay. Source: HPA transcription factor complex Inferred from electronic annotation. Source: Compara
Molecular_function	chromatin binding Inferred from electronic annotation. Source: Compara sequence-specific DNA binding Inferred from electronic annotation. Source: Compara sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 733

733

DNA-binding protein SATB2

PRO_0000202400

Regions

DNA binding

350 – 437

88

CUT 1

DNA binding

473 – 560

88

CUT 2

DNA binding

615 – 674

60

Homeobox

Amino acid modifications

Cross-link

233

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable

Cross-link

350

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable

Natural variations

Natural variant

263

1

S → P.
Corresponds to variant rs12619995 [ dbSNP | Ensembl ].

VAR_059320

Experimental info

Mutagenesis

233

1

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

Mutagenesis

350

1

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

Secondary structure

1

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733

Helix Strand Turn

Details...

Helix

364 – 375

12

Helix

379 – 387

9

Helix

391 – 399

9

Turn

404 – 406

3

Helix

409 – 421

13

Helix

426 – 437

12

Helix

486 – 498

13

Helix

502 – 508

7

Helix

514 – 523

10

Helix

532 – 545

14

Helix

549 – 559

11

Helix

624 – 636

13

Helix

642 – 651

10

Helix

656 – 669

14

Sequences

	Sequence		Length	Mass (Da)
	Q9UPW6 [UniParc]. Last modified April 27, 2001. Version 2. Checksum: 1FE1FCBD34F11E9E	FASTA	733	82,555
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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.

IPI

IPI00010433.

RefSeq

NP_001165980.1. NM_001172509.1.
NP_001165988.1. NM_001172517.1.
NP_056080.1. NM_015265.3.

UniGene

Hs.516617.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WI3	NMR	-	A	615-672	[»]
1WIZ	NMR	-	A	350-437	[»]
2CSF	NMR	-	A	473-560	[»]

ProteinModelPortal

Q9UPW6.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000260926.

PTM databases

PhosphoSite

Q9UPW6.

Polymorphism databases

DMDM

13634020.

Proteomic databases

PaxDb

Q9UPW6.

PRIDE

Q9UPW6.

Protocols and materials databases

DNASU

23314.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000260926; ENSP00000260926; ENSG00000119042.
ENST00000417098; ENSP00000401112; ENSG00000119042.
ENST00000457245; ENSP00000405420; ENSG00000119042.

GeneID

23314.

KEGG

hsa:23314.

UCSC

uc002uuy.2. human.

Organism-specific databases

CTD

23314.

GeneCards

GC02M200098.

HGNC

HGNC:21637. SATB2.

HPA

CAB023669.
HPA001042.
HPA029543.

MIM

119540. phenotype.
608148. gene.

neXtProt

NX_Q9UPW6.

Orphanet

251019. 2q32q33 microdeletion syndrome.
251028. 2q33.1 microdeletion syndrome.
199306. Cleft lip/palate.

PharmGKB

PA128394624.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG313826.

HOVERGEN

HBG054240.

InParanoid

Q9UPW6.

OMA

PPAEDSC.

OrthoDB

EOG4DBTD9.

PhylomeDB

Q9UPW6.

Gene expression databases

ArrayExpress

Q9UPW6.

Bgee

Q9UPW6.

CleanEx

HS_SATB2.

Genevestigator

Q9UPW6.

GermOnline

ENSG00000119042. Homo sapiens.

Family and domain databases

Gene3D

1.10.10.60. 1 hit.
1.10.260.40. 2 hits.

InterPro

IPR003350. Hmoeo_CUT.
IPR001356. Homeodomain.
IPR009057. Homeodomain-like.
IPR010982. Lambda_DNA-bd_dom.
[Graphical view]

Pfam

PF02376. CUT. 2 hits.
PF00046. Homeobox. 1 hit.
[Graphical view]

SMART

SM00389. HOX. 1 hit.
[Graphical view]

SUPFAM

SSF46689. Homeodomain_like. 1 hit.
SSF47413. Lambda_like_DNA. 2 hits.

PROSITE

PS51042. CUT. 2 hits.
PS00027. HOMEOBOX_1. False negative.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

SATB2. human.

EvolutionaryTrace

Q9UPW6.

GenomeRNAi

23314.

NextBio

45192.

SOURCE

Search...

Entry information

Entry name

SATB2_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 117 of the entry and version 2 of the sequence. [Complete history]

Entry status

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.