Reviewed, UniProtKB/Swiss-Prot Q00839 (HNRPU_HUMAN)

Names and origin

Protein names

Recommended name:
    Heterogeneous nuclear ribonucleoprotein U
      Short name=hnRNP U
Alternative name(s):
    Scaffold attachment factor A
      Short name=SAF-A
    p120
    pp120

Gene names

Name:	HNRNPU
Synonyms:	HNRPU, SAFA, U21.1

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	824 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Binds to pre-mRNA. Has high affinity for scaffold-attached region (SAR) DNA. Bind to double- and single-stranded DNA and RNA.
Subunit structure	Identified in the spliceosome C complex, at least composed of AQR, ASCC3L1, C19orf29, CDC40, CDC5L, CRNKL1, DDX23, DDX41, DDX48, DDX5, DGCR14, DHX35, DHX38, DHX8, EFTUD2, FRG1, GPATC1, HNRNPA1, HNRNPA2B1, HNRPA3, HNRNPC, HNRPF, HNRPH1, HNRPK, HNRPM, HNRNPR, HNRNPU, KIAA1160, KIAA1604, LSM2, LSM3, MAGOH, MORG1, PABPC1, PLRG1, PNN, PPIE, PPIL1, PPIL3, PPWD1, PRPF19, PRPF4B, PRPF6, PRPF8, RALY, RBM22, RBM8A, RBMX, SART1, SF3A1, SF3A2, SF3A3, SF3B1, SF3B2, SF3B3, SFRS1, SKIV2L2, SNRPA1, SNRPB, SNRPB2, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, SNW1, SRRM1, SRRM2, SYF2, SYNCRIP, TFIP11, THOC4, U2AF1, WDR57, XAB2 and ZCCHC8. Ligand for CR2.
Subcellular location	Nucleus. Cell surface. Note= Component of ribonucleosomes. Also found associated with the cell surface.
Post-translational modification	Extensively phosphorylated. Arg-732 and Arg-738 are dimethylated, probably to asymmetric dimethylarginine.
Sequence similarities	Contains 1 B30.2/SPRY domain. Contains 1 SAP domain.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Coding sequence diversity	Alternative splicing Polymorphism
Ligand	ATP-binding DNA-binding Nucleotide-binding RNA-binding
Molecular function	Ribonucleoprotein
PTM	Acetylation Methylation Phosphoprotein
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	nuclear mRNA splicing, via spliceosome Inferred from Experiment. Source: Reactome
Cellular component	cell surface Inferred from electronic annotation. Source: UniProtKB-SubCell heterogeneous nuclear ribonucleoprotein complex Ref.2 Traceable author statement. Source: ProtInc spliceosome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Ref.1 Traceable author statement. Source: ProtInc RNA binding Ref.1 Traceable author statement. Source: ProtInc protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NDRG1	Q92597	1	EBI-351126,EBI-716486

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform Long (identifier: Q00839-1)

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 Short (identifier: Q00839-2)

The sequence of this isoform differs from the canonical sequence as follows:
     213-230: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 824

823

Heterogeneous nuclear ribonucleoprotein U

PRO_0000081872

Regions

Domain

8 – 42

35

SAP

Domain

267 – 463

197

B30.2/SPRY

Nucleotide binding

503 – 510

8

ATP Potential

Region

713 – 738

26

RNA-binding RGG-box

Compositional bias

2 – 160

159

Asp/Glu-rich (acidic)

Compositional bias

84 – 94

11

Poly-Glu

Compositional bias

161 – 209

49

Gln-rich

Compositional bias

702 – 824

123

Gly-rich

Compositional bias

739 – 749

11

Poly-Gly

Amino acid modifications

Modified residue

2

1

N-acetylserine

Modified residue

4

1

Phosphoserine

Modified residue

26

1

Phosphoserine

Modified residue

50

1

Omega-N-methylarginine

Modified residue

59

1

Phosphoserine

Modified residue

66

1

Phosphoserine

Modified residue

188

1

Phosphoserine

Modified residue

270

1

Phosphoserine

Modified residue

472

1

Phosphotyrosine

Modified residue

732

1

Omega-N-methylated arginine

Modified residue

738

1

Omega-N-methylated arginine

Natural variations

Alternative sequence

213 – 230

18

Missing in isoform Short.

VSP_005846

Natural variant

711

1

F → L: dbSNP rs1052660.

VAR_014712

Experimental info

Sequence conflict

602

1

A → V in AAH07950. Ref.5

Secondary structure

1

.

.

.

824

Helix Strand Turn

Details...

Turn

24 – 25

2

Sequences

	Sequence		Length	Mass (Da)
	Isoform Long [UniParc]. Last modified February 20, 2007. Version 5. Checksum: 57D7FD3C9371393A	FASTA	824	90,513
	10 20 30 40 50 60 MSSSPVNVKK LKVSELKEEL KKRRLSDKGL KAELMERLQA ALDDEEAGGR PAMEPGNGSL 70 80 90 100 110 120 DLGGDSAGRS GAGLEQEAAA GGDEEEEEEE EEEEGISALD GDQMELGEEN GAAGAADSGP 130 140 150 160 170 180 MEEEEAASED ENGDDQGFQE GEDELGDEEE GAGDENGHGE QQPQPPATQQ QQPQQQRGAA 190 200 210 220 230 240 KEAAGKSSGP TSLFAVTVAP PGARQGQQQA GGKKKAEGGG GGGRPGAPAG DGKTEQKGGD 250 260 270 280 290 300 KKRGVKRPRE DHGRGYFEYI EENKYSRAKS PQPPVEEEDE HFDDTVVCLD TYNCDLHFKI 310 320 330 340 350 360 SRDRLSASSL TMESFAFLWA GGRASYGVSK GKVCFEMKVT EKIPVRHLYT KDIDIHEVRI 370 380 390 400 410 420 GWSLTTSGML LGEEEFSYGY SLKGIKTCNC ETEDYGEKFD ENDVITCFAN FESDEVELSY 430 440 450 460 470 480 AKNGQDLGVA FKISKEVLAG RPLFPHVLCH NCAVEFNFGQ KEKPYFPIPE EYTFIQNVPL 490 500 510 520 530 540 EDRVRGPKGP EEKKDCEVVM MIGLPGAGKT TWVTKHAAEN PGKYNILGTN TIMDKMMVAG 550 560 570 580 590 600 FKKQMADTGK LNTLLQRAPQ CLGKFIEIAA RKKRNFILDQ TNVSAAAQRR KMCLFAGFQR 610 620 630 640 650 660 KAVVVCPKDE DYKQRTQKKA EVEGKDLPEH AVLKMKGNFT LPEVAECFDE ITYVELQKEE 670 680 690 700 710 720 AQKLLEQYKE ESKKALPPEK KQNTGSKKSN KNKSGKNQFN RGGGHRGRGG FNMRGGNFRG 730 740 750 760 770 780 GAPGNRGGYN RRGNMPQRGG GGGGSGGIGY PYPRAPVFPG RGSYSNRGNY NRGGMPNRGN 790 800 810 820 YNQNFRGRGN NRGYKNQSQG YNQWQQGQFW GQKPWSQHYH QGYY
	Isoform Short [UniParc]. Checksum: BCE1AD365501EDC1		806	88,980
	10 20 30 40 50 60 MSSSPVNVKK LKVSELKEEL KKRRLSDKGL KAELMERLQA ALDDEEAGGR PAMEPGNGSL 70 80 90 100 110 120 DLGGDSAGRS GAGLEQEAAA GGDEEEEEEE EEEEGISALD GDQMELGEEN GAAGAADSGP 130 140 150 160 170 180 MEEEEAASED ENGDDQGFQE GEDELGDEEE GAGDENGHGE QQPQPPATQQ QQPQQQRGAA 190 200 210 220 230 240 KEAAGKSSGP TSLFAVTVAP PGARQGQQQA GGDGKTEQKG GDKKRGVKRP REDHGRGYFE 250 260 270 280 290 300 YIEENKYSRA KSPQPPVEEE DEHFDDTVVC LDTYNCDLHF KISRDRLSAS SLTMESFAFL 310 320 330 340 350 360 WAGGRASYGV SKGKVCFEMK VTEKIPVRHL YTKDIDIHEV RIGWSLTTSG MLLGEEEFSY 370 380 390 400 410 420 GYSLKGIKTC NCETEDYGEK FDENDVITCF ANFESDEVEL SYAKNGQDLG VAFKISKEVL 430 440 450 460 470 480 AGRPLFPHVL CHNCAVEFNF GQKEKPYFPI PEEYTFIQNV PLEDRVRGPK GPEEKKDCEV 490 500 510 520 530 540 VMMIGLPGAG KTTWVTKHAA ENPGKYNILG TNTIMDKMMV AGFKKQMADT GKLNTLLQRA 550 560 570 580 590 600 PQCLGKFIEI AARKKRNFIL DQTNVSAAAQ RRKMCLFAGF QRKAVVVCPK DEDYKQRTQK 610 620 630 640 650 660 KAEVEGKDLP EHAVLKMKGN FTLPEVAECF DEITYVELQK EEAQKLLEQY KEESKKALPP 670 680 690 700 710 720 EKKQNTGSKK SNKNKSGKNQ FNRGGGHRGR GGFNMRGGNF RGGAPGNRGG YNRRGNMPQR 730 740 750 760 770 780 GGGGGGSGGI GYPYPRAPVF PGRGSYSNRG NYNRGGMPNR GNYNQNFRGR GNNRGYKNQS 790 800 QGYNQWQQGQ FWGQKPWSQH YHQGYY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box." Kiledjian M., Dreyfuss G. EMBO J. 11:2655-2664(1992) [PubMed: 1628625] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM SHORT), RNA-BINDING DOMAIN, VARIANT LEU-711.
[2]	"hnRNP-U/SAF-A is encoded by two differentially polyadenylated mRNAs in human cells." Fackelmayer F.O., Richter A. Biochim. Biophys. Acta 1217:232-234(1994) [PubMed: 7509195] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM SHORT).
[3]	"A variant of human scaffold attachment factor A (SAF-A), also known as heterogeneous nuclear ribonucleoprotein U (hnRNP-U)." Fackelmayer F.O. Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM LONG), VARIANT LEU-711.
[4]	"The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R. Nature 441:315-321(2006) [PubMed: 16710414] [Abstract] 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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM SHORT). Tissue: Eye, Lymph, Placenta and Skin.
[6]	Bienvenut W.V., Kanor S., Tissot J.-D., Quadroni M. Submitted (MAY-2006) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-9; 186-194; 318-329; 398-408; 422-431; 451-460; 463-474 AND 523-534, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2, MASS SPECTROMETRY. Tissue: T-cell.
[7]	"Major cell surface-located protein substrates of an ecto-protein kinase are homologs of known nuclear proteins." Jordan P., Heid H., Kinzel V., Kubler D. Biochemistry 33:14696-14706(1994) [PubMed: 7993898] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-7; 255-264 AND 462-475, PHOSPHORYLATION, SUBCELLULAR LOCATION.
[8]	"Purification of two isoforms of hnRNP-U and characterization of their nucleic acid binding activity." Fackelmayer F.O., Richter A. Biochemistry 33:10416-10422(1994) [PubMed: 8068679] [Abstract] Cited for: CHARACTERIZATION.
[9]	"Binding sites of the Epstein-Barr virus and C3d receptor (CR2, CD21) for its three intracellular ligands, the p53 anti-oncoprotein, the p68 calcium binding protein and the nuclear p120 ribonucleoprotein." Barel M., Balbo M., Gauffre A., Frade R. Mol. Immunol. 32:389-397(1995) [PubMed: 7753047] [Abstract] Cited for: INTERACTION WITH CR2.
[10]	"Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis." Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J. RNA 8:426-439(2002) [PubMed: 11991638] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPICEOSOMAL C COMPLEX.
[11]	"Identifying and quantifying in vivo methylation sites by heavy methyl SILAC." Ong S.E., Mittler G., Mann M. Nat. Methods 1:119-126(2004) [PubMed: 15782174] [Abstract] Cited for: METHYLATION [LARGE SCALE ANALYSIS] AT ARG-50; ARG-732 AND ARG-738, MASS SPECTROMETRY.
[12]	"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells." Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J. Nat. Biotechnol. 23:94-101(2005) [PubMed: 15592455] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-472, MASS SPECTROMETRY.
[13]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-4; SER-59 AND SER-270, MASS SPECTROMETRY. Tissue: Epithelium.
[14]	"Toward a global characterization of the phosphoproteome in prostate cancer cells: identification of phosphoproteins in the LNCaP cell line." Giorgianni F., Zhao Y., Desiderio D.M., Beranova-Giorgianni S. Electrophoresis 28:2027-2034(2007) [PubMed: 17487921] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-270, MASS SPECTROMETRY.
[15]	"Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra." Yu L.-R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D. J. Proteome Res. 6:4150-4162(2007) [PubMed: 17924679] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-270, MASS SPECTROMETRY. Tissue: Epithelium.
[16]	"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry." Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A. Proc. Natl. Acad. Sci. U.S.A. 104:2199-2204(2007) [PubMed: 17287340] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-26, MASS SPECTROMETRY.
[17]	"Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis." Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III J. Proteome Res. 7:1346-1351(2008) [PubMed: 18220336] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59; SER-66 AND SER-188, MASS SPECTROMETRY.
[18]	"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: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59; SER-66 AND SER-270, MASS SPECTROMETRY.
[19]	"Solution structure of the SAP domain of human E1B-55kDa-associated protein 5 isoform C." RIKEN structural genomics initiative (RSGI) Submitted (JAN-2008) to the PDB data bank Cited for: STRUCTURE BY NMR OF 23-42.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X65488 mRNA. Translation: CAA46472.1.
AF068846 mRNA. Translation: AAC19382.1.
BX323046 Genomic DNA. Translation: CAI11058.1.
BC003367 mRNA. Translation: AAH03367.1.
BC003621 mRNA. Translation: AAH03621.1.
BC007950 mRNA. Translation: AAH07950.2.
BC024767 mRNA. Translation: AAH24767.1.
BC034925 mRNA. Translation: AAH34925.1.

PIR

S22765.

RefSeq

NP_004492.2.
NP_114032.2.

UniGene

Hs.166463

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZRJ	NMR	-	A	23-42	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:684N.

IntAct

Q00839.

PTM databases

PhosphoSite

Q00839.

Genome annotation databases

Ensembl

ENSG00000153187. Homo sapiens. [Contig view]

GeneID

3192.

KEGG

hsa:3192.

Organism-specific databases

H-InvDB

HIX0001754.

HGNC

HGNC:5048. HNRNPU.

HPA

CAB011532.

MIM

602869. gene.

PharmGKB

PA29372.

GenAtlas

Search...

GeneCards

Search...

Phylogenomic databases

HOGENOM

Q00839.

HOVERGEN

Q00839.

Enzyme and pathway databases

Reactome

REACT_1675. mRNA Processing.
REACT_6167. Influenza Infection.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

Q00839.

CleanEx

HS_HNRNPU.

GermOnline

ENSG00000153187. Homo sapiens.

Family and domain databases

InterPro

IPR001870. B302.
IPR003034. SAP_DNA_bd.
IPR003877. SPRY_rcpt.
[Graphical view]

Pfam

PF02037. SAP. 1 hit.
PF00622. SPRY. 1 hit.
[Graphical view]

SMART

SM00513. SAP. 1 hit.
SM00449. SPRY. 1 hit.
[Graphical view]

PROSITE

PS50188. B302_SPRY. 1 hit.
PS50800. SAP. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

12700.

SOURCE

Search...

Entry information

Entry name	HNRPU_HUMAN
Accession	Primary (citable) accession number: Q00839 Secondary accession number(s): O75507