Heterogeneous nuclear ribonucleoprotein K

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Reviewed, UniProtKB/Swiss-Prot P61978 (HNRPK_HUMAN)

Last modified June 10, 2008. Version 70. History...

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Names and origin · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Heterogeneous nuclear ribonucleoprotein K
Also known as:
     hnRNP K
     Transformation up-regulated nuclear protein
     TUNP

Gene names

Name:	HNRNPK
Synonyms:	HNRPK

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 existence

Evidence at protein level.

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General annotation (Comments)

Function	One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single-stranded DNA.
Subunit structure	Interacts with ZIK1 By similarity. 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, HNRPA1, HNRPA2B1, HNRPA3, HNRPC, HNRPF, HNRPH1, HNRNPK, HNRPM, HNRPR, HNRPU, 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. Interacts with HCV core protein. Interacts with ANKRD28.
Subcellular location	Cytoplasm. Nucleus, nucleoplasm.
Post-translational modification	Arg-296 and Arg-299 are dimethylated, probably to asymmetric dimethylarginine.
Sequence similarities	Contains 3 KH domains.
Mass spectrometry	Molecular weight is 50976.25 Da from positions 1 - 463 (P61978-1). Determined by MALDI. Ref.8

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Ontologies

Keywords
Biological process	Host-virus interaction mRNA processing mRNA splicing
Cellular component	Cytoplasm Nucleus Spliceosome
Coding sequence diversity	Alternative splicing
Domain	Repeat
Ligand	DNA-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 signal transduction Traceable author statement. Source: ProtInc
Cellular component	cytoplasm Traceable author statement. Source: ProtInc heterogeneous nuclear ribonucleoprotein complex Ref.2 Traceable author statement. Source: ProtInc nucleoplasm Ref.1 Traceable author statement. Source: ProtInc
Molecular function	RNA binding Ref.2 Traceable author statement. Source: ProtInc protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
HCK	P08631	1	EBI-304185,EBI-346340
QKI	Q96PU8	1	EBI-304185,EBI-945792

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Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: P61978-1)
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 2 (identifier: P61978-2)
The sequence of this isoform differs from the canonical sequence as follows:
459-463 SGKFF → ADVEGF

Isoform 3 (identifier: P61978-3)
The sequence of this isoform differs from the canonical sequence as follows:
111-134: Missing.
459-463 SGKFF → ADVEGF
Notes: No experimental confirmation available.

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Molecule processing

Chain

1 – 463

463

Heterogeneous nuclear ribonucleoprotein K

Regions

Domain

42 – 104

KH 1

Repeat

54 – 76

1-1

Repeat

59 – 62

3-1

Domain

144 – 209

KH 2

Repeat

245 – 250

2-1

Repeat

257 – 260

3-2

Repeat

267 – 270

3-3

Repeat

295 – 298

3-4

Repeat

324 – 329

2-2

Domain

387 – 451

KH 3

Repeat

399 – 421

1-2

Repeat

404 – 407

3-5

Region

54 – 421

368

2 X 22 AA approximate repeats

Region

59 – 407

349

5 X 4 AA repeats of G-X-G-G

Region

209 – 337

129

Interaction with ZIK1 By similarity

Region

236 – 273

RNA-binding RGG-box

Region

245 – 329

2 X 6 AA approximate repeats

Compositional bias

289 – 294

Poly-Pro

Compositional bias

310 – 315

Poly-Pro

Amino acid modifications

Modified residue

N-acetylmethionine

Modified residue

Phosphothreonine

Modified residue

Phosphoserine

Modified residue

116

Phosphoserine

Modified residue

214

Phosphoserine

Modified residue

216

Phosphoserine

Modified residue

284

Phosphoserine

Modified residue

296

Omega-N-methylated arginine

Modified residue

299

Omega-N-methylated arginine

Modified residue

379

Phosphoserine

Natural variations

Alternative sequence

111 – 134

Missing in isoform 3.

Alternative sequence

459 – 463

SGKFF → ADVEGF in isoform 2 and isoform 3.

Experimental info

Sequence conflict

A → D in CAA51267. Ref.2

Secondary structure

463

Helix Strand Turn

Details...

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Sequences

Sequence		Length	Mass (Da)
Isoform 1 [UniParc]. Last modified June 7, 2004. Version 1. Checksum: 0F70EE169B2A064A Show »	FASTA	463	50,976
10 20 30 40 50 60 METEQPEETF PNTETNGEFG KRPAEDMEEE QAFKRSRNTD EMVELRILLQ SKNAGAVIGK 70 80 90 100 110 120 GGKNIKALRT DYNASVSVPD SSGPERILSI SADIETIGEI LKKIIPTLEE GLQLPSPTAT 130 140 150 160 170 180 SQLPLESDAV ECLNYQHYKG SDFDCELRLL IHQSLAGGII GVKGAKIKEL RENTQTTIKL 190 200 210 220 230 240 FQECCPHSTD RVVLIGGKPD RVVECIKIIL DLISESPIKG RAQPYDPNFY DETYDYGGFT 250 260 270 280 290 300 MMFDDRRGRP VGFPMRGRGG FDRMPPGRGG RPMPPSRRDY DDMSPRRGPP PPPPGRGGRG 310 320 330 340 350 360 GSRARNLPLP PPPPPRGGDL MAYDRRGRPG DRYDGMVGFS ADETWDSAID TWSPSEWQMA 370 380 390 400 410 420 YEPQGGSGYD YSYAGGRGSY GDLGGPIITT QVTIPKDLAG SIIGKGGQRI KQIRHESGAS 430 440 450 460 IKIDEPLEGS EDRIITITGT QDQIQNAQYL LQNSVKQYSG KFF « Hide
Isoform 2 [UniParc]. Checksum: 0B4EC22FE4534A06 Show »		464	51,028
10 20 30 40 50 60 METEQPEETF PNTETNGEFG KRPAEDMEEE QAFKRSRNTD EMVELRILLQ SKNAGAVIGK 70 80 90 100 110 120 GGKNIKALRT DYNASVSVPD SSGPERILSI SADIETIGEI LKKIIPTLEE GLQLPSPTAT 130 140 150 160 170 180 SQLPLESDAV ECLNYQHYKG SDFDCELRLL IHQSLAGGII GVKGAKIKEL RENTQTTIKL 190 200 210 220 230 240 FQECCPHSTD RVVLIGGKPD RVVECIKIIL DLISESPIKG RAQPYDPNFY DETYDYGGFT 250 260 270 280 290 300 MMFDDRRGRP VGFPMRGRGG FDRMPPGRGG RPMPPSRRDY DDMSPRRGPP PPPPGRGGRG 310 320 330 340 350 360 GSRARNLPLP PPPPPRGGDL MAYDRRGRPG DRYDGMVGFS ADETWDSAID TWSPSEWQMA 370 380 390 400 410 420 YEPQGGSGYD YSYAGGRGSY GDLGGPIITT QVTIPKDLAG SIIGKGGQRI KQIRHESGAS 430 440 450 460 IKIDEPLEGS EDRIITITGT QDQIQNAQYL LQNSVKQYAD VEGF « Hide
Isoform 3 [UniParc]. Checksum: C98A78A7462BF776 Show »		440	48,562
10 20 30 40 50 60 METEQPEETF PNTETNGEFG KRPAEDMEEE QAFKRSRNTD EMVELRILLQ SKNAGAVIGK 70 80 90 100 110 120 GGKNIKALRT DYNASVSVPD SSGPERILSI SADIETIGEI LKKIIPTLEE YQHYKGSDFD 130 140 150 160 170 180 CELRLLIHQS LAGGIIGVKG AKIKELRENT QTTIKLFQEC CPHSTDRVVL IGGKPDRVVE 190 200 210 220 230 240 CIKIILDLIS ESPIKGRAQP YDPNFYDETY DYGGFTMMFD DRRGRPVGFP MRGRGGFDRM 250 260 270 280 290 300 PPGRGGRPMP PSRRDYDDMS PRRGPPPPPP GRGGRGGSRA RNLPLPPPPP PRGGDLMAYD 310 320 330 340 350 360 RRGRPGDRYD GMVGFSADET WDSAIDTWSP SEWQMAYEPQ GGSGYDYSYA GGRGSYGDLG 370 380 390 400 410 420 GPIITTQVTI PKDLAGSIIG KGGQRIKQIR HESGASIKID EPLEGSEDRI ITITGTQDQI 430 440 QNAQYLLQNS VKQYADVEGF « Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization and primary structure of the poly(C)-binding heterogeneous nuclear ribonucleoprotein complex K protein." Matunis M.J., Michael W.M., Dreyfuss G. Mol. Cell. Biol. 12:164-171(1992) [PubMed: 1729596] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION.
[2]	"Identification, molecular cloning, expression and chromosome mapping of a family of transformation upregulated hnRNP-K proteins derived by alternative splicing." Dejgaard K., Leffers H., Rasmussen H.H., Madsen P., Kruse T.A., Gesser B., Nielsen H., Celis J.E. J. Mol. Biol. 236:33-48(1994) [PubMed: 8107114] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PHOSPHORYLATION.
[3]	Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S., Ohara O., Nagase T., Kikuno R.F. Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3). Tissue: Brain.
[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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Muscle.
[5]	Bienvenut W.V., Vousden K.H., Lukashchuk N. Submitted (MAR-2008) to UniProtKB Cited for: PROTEIN SEQUENCE OF 1-52; 70-103; 149-163; 192-201; 208-219; 317-325; 378-405 AND 423-456, ACETYLATION AT MET-1, MASS SPECTROMETRY. Tissue: Lung carcinoma.
[6]	Lubec G., Afjehi-Sadat L. Submitted (MAR-2007) to UniProtKB Cited for: PROTEIN SEQUENCE OF 149-163, MASS SPECTROMETRY. Tissue: Brain and Cajal-Retzius cell.
[7]	"Hepatitis C virus core protein interacts with heterogeneous nuclear ribonucleoprotein K." Hsieh T.-Y., Matsumoto M., Chou H.-C., Schneider R., Hwang S.B., Lee A.S., Lai M.M.C. J. Biol. Chem. 273:17651-17659(1998) [PubMed: 9651361] [Abstract] Cited for: INTERACTION WITH HCV CORE PROTEIN.
[8]	"Cluster analysis of an extensive human breast cancer cell line protein expression map database." Harris R.A., Yang A., Stein R.C., Lucy K., Brusten L., Herath A., Parekh R., Waterfield M.D., O'Hare M.J., Neville M.A., Page M.J., Zvelebil M.J. Proteomics 2:212-223(2002) [PubMed: 11840567] [Abstract] Cited for: MASS SPECTROMETRY. Tissue: Mammary cancer.
[9]	"Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis." Jurica M.S., Licklider L.J., Gygi S.R., 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.
[10]	"Global phosphoproteome of HT-29 human colon adenocarcinoma cells." Kim J.-E., Tannenbaum S.R., White F.M. J. Proteome Res. 4:1339-1346(2005) [PubMed: 16083285] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-284, MASS SPECTROMETRY.
[11]	"PITK, a PP1 targeting subunit that modulates the phosphorylation of the transcriptional regulator hnRNP K." Kwiek N.C., Thacker D.F., Datto M.B., Megosh H.B., Haystead T.A.J. Cell. Signal. 18:1769-1778(2006) [PubMed: 16564677] [Abstract] Cited for: INTERACTION WITH ANKRD28, PHOSPHORYLATION AT SER-284.
[12]	"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-296 AND ARG-299, MASS SPECTROMETRY.
[13]	"Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-3; SER-116 AND SER-284, MASS SPECTROMETRY. Tissue: Epithelium.
[14]	"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-36; SER-216 AND SER-284, MASS SPECTROMETRY. Tissue: Epithelium.
[15]	"A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P. Nat. Biotechnol. 24:1285-1292(2006) [PubMed: 16964243] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-216; SER-284 AND SER-379, MASS SPECTROMETRY. Tissue: Epithelium.
[16]	"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-214; SER-216 AND SER-379, MASS SPECTROMETRY. Tissue: Epithelium.
[17]	"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-116 AND SER-284, MASS SPECTROMETRY.
[18]	"Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column." Imami K., Sugiyama N., Kyono Y., Tomita M., Ishihama Y. Anal. Sci. 24:161-166(2008) [PubMed: 18187866] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-216, MASS SPECTROMETRY.
[19]	"High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor." Baber J.L., Libutti D., Levens D., Tjandra N. J. Mol. Biol. 289:949-962(1999) [PubMed: 10369774] [Abstract] Cited for: STRUCTURE BY NMR OF 375-463.
[20]	"Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA." Braddock D.T., Baber J.L., Levens D., Clore G.M. EMBO J. 21:3476-3485(2002) [PubMed: 12093748] [Abstract] Cited for: STRUCTURE BY NMR OF 379-463 IN COMPLEX WITH SINGLE STRANDED DNA.

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Cross-references

Sequence databases

S74678 mRNA. Translation: AAB20770.1.
X72727 mRNA. Translation: CAA51267.1.
AB209562 mRNA. Translation: BAD92799.1. Different initiation.
BC000355 mRNA. Translation: AAH00355.1.
BC014980 mRNA. Translation: AAH14980.1.

PIR

S43363.

RefSeq

NP_112552.1.

UniGene

Hs.695973

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1J5K	NMR	-	A	379-463	[»]
1KHM	NMR	-	A	379-463	[»]
1ZZI	X-ray	1.80	A/B	385-463	[»]
1ZZJ	X-ray	2.30	A/B/C	385-463	[»]
1ZZK	X-ray	0.95	A	385-463	[»]