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P17480 (UBF1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 158. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nucleolar transcription factor 1
Alternative name(s):
Autoantigen NOR-90
Upstream-binding factor 1
Short name=UBF-1
Gene names
Name:UBTF
Synonyms:UBF, UBF1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length764 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. Ref.5

Subunit structure

Homodimer. Interacts with TBP. Interacts with RASL11A, TAF1A and TAF1D. Binds to IRS1 and PIK3CA By similarity. Interacts with DHX33. Interacts with PHF6. Ref.5 Ref.6 Ref.11 Ref.14

Subcellular location

Nucleusnucleolus By similarity Ref.14.

Post-translational modification

Phosphorylated and activated by PIK3CA By similarity.

Sequence similarities

Contains 6 HMG box DNA-binding domains.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainRepeat
   LigandDNA-binding
   Molecular functionActivator
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processchromatin silencing at rDNA

Inferred from electronic annotation. Source: Ensembl

gene expression

Traceable author statement. Source: Reactome

positive regulation of transcription from RNA polymerase I promoter

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of transcription from RNA polymerase I promoter

Traceable author statement Ref.1. Source: ProtInc

termination of RNA polymerase I transcription

Traceable author statement. Source: Reactome

transcription elongation from RNA polymerase I promoter

Traceable author statement. Source: Reactome

transcription from RNA polymerase I promoter

Traceable author statement. Source: Reactome

transcription initiation from RNA polymerase I promoter

Traceable author statement. Source: Reactome

   Cellular_componentnucleolus

Inferred from sequence or structural similarity. Source: UniProtKB

nucleoplasm

Traceable author statement. Source: Reactome

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

poly(A) RNA binding

Inferred from direct assay PubMed 22681889. Source: UniProtKB

protein binding

Inferred from physical interaction PubMed 16777843PubMed 19174463PubMed 20208542Ref.11. Source: UniProtKB

Complete GO annotation...

Binary interactions

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform UBF1 (identifier: P17480-1)

Also known as: Long;

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.
Isoform UBF2 (identifier: P17480-2)

Also known as: Short;

The sequence of this isoform differs from the canonical sequence as follows:
     221-257: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 764764Nucleolar transcription factor 1
PRO_0000048625

Regions

DNA binding112 – 18069HMG box 1
DNA binding196 – 26469HMG box 2
DNA binding298 – 36265HMG box 3
DNA binding407 – 47569HMG box 4
DNA binding482 – 54968HMG box 5
DNA binding568 – 63467HMG box 6
Compositional bias675 – 76490Asp/Glu/Ser-rich (acidic)

Amino acid modifications

Modified residue11N-acetylmethionine Ref.8
Modified residue2011Phosphothreonine Ref.7
Modified residue2731Phosphoserine By similarity
Modified residue3361Phosphoserine By similarity
Modified residue3641Phosphoserine By similarity
Modified residue3891Phosphoserine By similarity
Modified residue4121Phosphoserine Ref.7 Ref.9
Modified residue4331Phosphoserine By similarity
Modified residue4841Phosphoserine Ref.9 Ref.12
Modified residue4951Phosphoserine Ref.9
Modified residue5461Phosphoserine By similarity
Modified residue5841Phosphoserine By similarity
Modified residue6381Phosphoserine Ref.7

Natural variations

Alternative sequence221 – 25737Missing in isoform UBF2.
VSP_002193

Secondary structure

.................... 764
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform UBF1 (Long) [UniParc].

Last modified August 1, 1990. Version 1.
Checksum: D4F0F8BB180E757D

FASTA76489,406
        10         20         30         40         50         60 
MNGEADCPTD LEMAAPKGQD RWSQEDMLTL LECMKNNLPS NDSSKFKTTE SHMDWEKVAF 

        70         80         90        100        110        120 
KDFSGDMCKL KWVEISNEVR KFRTLTELIL DAQEHVKNPY KGKKLKKHPD FPKKPLTPYF 

       130        140        150        160        170        180 
RFFMEKRAKY AKLHPEMSNL DLTKILSKKY KELPEKKKMK YIQDFQREKQ EFERNLARFR 

       190        200        210        220        230        240 
EDHPDLIQNA KKSDIPEKPK TPQQLWYTHE KKVYLKVRPD ATTKEVKDSL GKQWSQLSDK 

       250        260        270        280        290        300 
KRLKWIHKAL EQRKEYEEIM RDYIQKHPEL NISEEGITKS TLTKAERQLK DKFDGRPTKP 

       310        320        330        340        350        360 
PPNSYSLYCA ELMANMKDVP STERMVLCSQ QWKLLSQKEK DAYHKKCDQK KKDYEVELLR 

       370        380        390        400        410        420 
FLESLPEEEQ QRVLGEEKML NINKKQATSP ASKKPAQEGG KGGSEKPKRP VSAMFIFSEE 

       430        440        450        460        470        480 
KRRQLQEERP ELSESELTRL LARMWNDLSE KKKAKYKARE AALKAQSERK PGGEREERGK 

       490        500        510        520        530        540 
LPESPKRAEE IWQQSVIGDY LARFKNDRVK ALKAMEMTWN NMEKKEKLMW IKKAAEDQKR 

       550        560        570        580        590        600 
YERELSEMRA PPAATNSSKK MKFQGEPKKP PMNGYQKFSQ ELLSNGELNH LPLKERMVEI 

       610        620        630        640        650        660 
GSRWQRISQS QKEHYKKLAE EQQKQYKVHL DLWVKSLSPQ DRAAYKEYIS NKRKSMTKLR 

       670        680        690        700        710        720 
GPNPKSSRTT LQSKSESEED DEEDEDDEDE DEEEEDDENG DSSEDGGDSS ESSSEDESED 

       730        740        750        760 
GDENEEDDED EDDDEDDDED EDNESEGSSS SSSSSGDSSD SDSN 

« Hide

Isoform UBF2 (Short) [UniParc].

Checksum: 9E5ECB321567DB64
Show »

FASTA72784,937

References

« Hide 'large scale' references
[1]"Nucleolar transcription factor hUBF contains a DNA-binding motif with homology to HMG proteins."
Jantzen H.M., Admon A., Bell S.P., Tjian R.
Nature 344:830-836(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM UBF1).
[2]"Human autoantibody to RNA polymerase I transcription factor hUBF. Molecular identity of nucleolus organizer region autoantigen NOR-90 and ribosomal RNA transcription upstream binding factor."
Chan E.K.L., Imai H., Hamel J.C., Tan E.M.
J. Exp. Med. 174:1239-1244(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM UBF2).
[3]"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] (ISOFORM UBF1).
Tissue: Placenta and Testis.
[4]"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] (ISOFORM UBF2).
Tissue: Testis.
[5]"The RNA polymerase I transcription factor, upstream binding factor, interacts directly with the TATA box-binding protein."
Kwon H., Green M.R.
J. Biol. Chem. 269:30140-30146(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH TBP.
[6]"Coactivator and promoter-selective properties of RNA polymerase I TAFs."
Beckmann H., Chen J.L., O'Brien T., Tjian R.
Science 270:1506-1509(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH TAF1A.
[7]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-201; SER-412 AND SER-638, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[8]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-412; SER-484 AND SER-495, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Identification of DHX33 as a mediator of rRNA synthesis and cell growth."
Zhang Y., Forys J.T., Miceli A.P., Gwinn A.S., Weber J.D.
Mol. Cell. Biol. 31:4676-4691(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH DHX33.
[12]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-484, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"PHF6 regulates cell cycle progression by suppressing ribosomal RNA synthesis."
Wang J., Leung J.W., Gong Z., Feng L., Shi X., Chen J.
J. Biol. Chem. 288:3174-3183(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, INTERACTION WITH PHF6.
[15]"Solution structure of the first HMG box domain in human upstream binding factor."
Xu Y., Yang W., Wu J., Shi Y.
Biochemistry 41:5415-5420(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 103-192.
[16]"Solution structure and DNA binding property of the fifth HMG box domain in comparison with the first HMG box domain in human upstream binding factor."
Yang W., Xu Y., Wu J., Zeng W., Shi Y.
Biochemistry 42:1930-1938(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 479-560.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X53390 mRNA. Translation: CAA37469.1.
X53461 mRNA. Translation: CAA37548.1.
X56687 mRNA. Translation: CAA40016.1.
AK291733 mRNA. Translation: BAF84422.1.
AK292518 mRNA. Translation: BAF85207.1.
BC042297 mRNA. Translation: AAH42297.1.
CCDSCCDS11480.1. [P17480-1]
CCDS42346.1. [P17480-2]
PIRS09318.
S18193.
RefSeqNP_001070151.1. NM_001076683.1. [P17480-2]
NP_001070152.1. NM_001076684.2. [P17480-2]
NP_055048.1. NM_014233.3. [P17480-1]
XP_006722122.1. XM_006722059.1. [P17480-1]
XP_006722123.1. XM_006722060.1. [P17480-1]
XP_006722124.1. XM_006722061.1. [P17480-1]
UniGeneHs.89781.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1K99NMR-A103-192[»]
1L8YNMR-A479-560[»]
1L8ZNMR-A479-560[»]
2HDZX-ray2.00A479-560[»]
ProteinModelPortalP17480.
SMRP17480. Positions 103-192, 288-383, 394-472, 481-546, 567-655.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid113190. 43 interactions.
DIPDIP-640N.
IntActP17480. 10 interactions.
MINTMINT-1348764.
STRING9606.ENSP00000302640.

PTM databases

PhosphoSiteP17480.

Polymorphism databases

DMDM136652.

Proteomic databases

MaxQBP17480.
PaxDbP17480.
PRIDEP17480.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000302904; ENSP00000302640; ENSG00000108312. [P17480-1]
ENST00000343638; ENSP00000345297; ENSG00000108312. [P17480-2]
ENST00000393606; ENSP00000377231; ENSG00000108312. [P17480-2]
ENST00000436088; ENSP00000390669; ENSG00000108312. [P17480-1]
ENST00000526094; ENSP00000432925; ENSG00000108312. [P17480-2]
ENST00000529383; ENSP00000435708; ENSG00000108312. [P17480-1]
ENST00000533177; ENSP00000437180; ENSG00000108312. [P17480-2]
GeneID7343.
KEGGhsa:7343.
UCSCuc002igc.3. human. [P17480-2]
uc010czs.3. human. [P17480-1]

Organism-specific databases

CTD7343.
GeneCardsGC17M042282.
HGNCHGNC:12511. UBTF.
HPACAB004611.
HPA006385.
MIM600673. gene.
neXtProtNX_P17480.
PharmGKBPA37158.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG327891.
HOGENOMHOG000232068.
HOVERGENHBG008708.
InParanoidP17480.
KOK09273.
OMACSQRWKL.
OrthoDBEOG7P2XTJ.
PhylomeDBP17480.
TreeFamTF328989.

Enzyme and pathway databases

ReactomeREACT_1788. Transcription.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpressP17480.
BgeeP17480.
CleanExHS_UBTF.
GenevestigatorP17480.

Family and domain databases

Gene3D1.10.30.10. 6 hits.
InterProIPR029215. HMG_box_5.
IPR009071. HMG_box_dom.
[Graphical view]
PfamPF00505. HMG_box. 3 hits.
PF09011. HMG_box_2. 1 hit.
PF14887. HMG_box_5. 1 hit.
[Graphical view]
SMARTSM00398. HMG. 6 hits.
[Graphical view]
SUPFAMSSF47095. SSF47095. 6 hits.
PROSITEPS50118. HMG_BOX_2. 6 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSUBTF. human.
EvolutionaryTraceP17480.
GeneWikiUBTF.
GenomeRNAi7343.
NextBio28746.
PROP17480.
SOURCESearch...

Entry information

Entry nameUBF1_HUMAN
AccessionPrimary (citable) accession number: P17480
Secondary accession number(s): A8K6R8
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: August 1, 1990
Last modified: July 9, 2014
This is version 158 of the entry and version 1 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 chromosome 17

Human chromosome 17: entries, gene names and cross-references to MIM