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Q8IV63 (VRK3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 114. 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·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Inactive serine/threonine-protein kinase VRK3
Alternative name(s):
Serine/threonine-protein pseudokinase VRK3
Vaccinia-related kinase 3
Gene names
Name:VRK3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length474 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Inactive kinase that suppresses ERK activity by promoting phosphatase activity of DUSP3 which specifically dephosphorylates and inactivates ERK in the nucleus By similarity. Ref.6 Ref.12

Subunit structure

Interacts with DUSP3 By similarity. Interacts with RAN. Ref.7

Subcellular location

Nucleus Ref.6.

Sequence similarities

Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. VRK subfamily.

Contains 1 protein kinase domain.

Caution

Inactive as a kinase due to its inability to bind ATP (Ref.12).

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q8IV63-1)

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: Q8IV63-2)

The sequence of this isoform differs from the canonical sequence as follows:
     407-412: FVDKPG → LPWDSF
     413-474: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q8IV63-3)

The sequence of this isoform differs from the canonical sequence as follows:
     47-96: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 474474Inactive serine/threonine-protein kinase VRK3
PRO_0000086808

Regions

Domain166 – 457292Protein kinase
Motif49 – 6416Nuclear localization signal Ref.6

Amino acid modifications

Modified residue551Phosphoserine Ref.8
Modified residue591Phosphoserine Ref.8
Modified residue821Phosphoserine Ref.9 Ref.10 Ref.11
Modified residue831Phosphoserine Ref.9 Ref.10 Ref.11
Modified residue901Phosphoserine Ref.9
Modified residue1151Phosphoserine Ref.11
Modified residue1221Phosphoserine Ref.11

Natural variations

Alternative sequence47 – 9650Missing in isoform 3.
VSP_043409
Alternative sequence407 – 4126FVDKPG → LPWDSF in isoform 2.
VSP_008544
Alternative sequence413 – 47462Missing in isoform 2.
VSP_008545
Natural variant591S → F. Ref.13
Corresponds to variant rs2033262 [ dbSNP | Ensembl ].
VAR_041295
Natural variant1051P → T. Ref.13
Corresponds to variant rs11547882 [ dbSNP | Ensembl ].
VAR_041296
Natural variant1701S → P.
Corresponds to variant rs11547881 [ dbSNP | Ensembl ].
VAR_051682
Natural variant1711F → L. Ref.13
Corresponds to variant rs11547883 [ dbSNP | Ensembl ].
VAR_041297
Natural variant1881T → A.
Corresponds to variant rs11879620 [ dbSNP | Ensembl ].
VAR_051683
Natural variant2681S → L. Ref.13
Corresponds to variant rs10410075 [ dbSNP | Ensembl ].
VAR_041298
Natural variant2881C → Y. Ref.13
Corresponds to variant rs10409482 [ dbSNP | Ensembl ].
VAR_041299
Natural variant3041H → L.
Corresponds to variant rs35261919 [ dbSNP | Ensembl ].
VAR_051684
Natural variant3701R → C. Ref.13
Corresponds to variant rs35331034 [ dbSNP | Ensembl ].
VAR_041300
Natural variant3711S → G. Ref.13
Corresponds to variant rs56407496 [ dbSNP | Ensembl ].
VAR_041301

Experimental info

Sequence conflict1611K → E in AAP47180. Ref.2

Secondary structure

............................................. 474
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 10, 2003. Version 2.
Checksum: 86B9B91050A7F0CC

FASTA47452,881
        10         20         30         40         50         60 
MISFCPDCGK SIQAAFKFCP YCGNSLPVEE HVGSQTFVNP HVSSFQGSKR GLNSSFETSP 

        70         80         90        100        110        120 
KKVKWSSTVT SPRLSLFSDG DSSESEDTLS SSERSKGSGS RPPTPKSSPQ KTRKSPQVTR 

       130        140        150        160        170        180 
GSPQKTSCSP QKTRQSPQTL KRSRVTTSLE ALPTGTVLTD KSGRQWKLKS FQTRDNQGIL 

       190        200        210        220        230        240 
YEAAPTSTLT CDSGPQKQKF SLKLDAKDGR LFNEQNFFQR AAKPLQVNKW KKLYSTPLLA 

       250        260        270        280        290        300 
IPTCMGFGVH QDKYRFLVLP SLGRSLQSAL DVSPKHVLSE RSVLQVACRL LDALEFLHEN 

       310        320        330        340        350        360 
EYVHGNVTAE NIFVDPEDQS QVTLAGYGFA FRYCPSGKHV AYVEGSRSPH EGDLEFISMD 

       370        380        390        400        410        420 
LHKGCGPSRR SDLQSLGYCM LKWLYGFLPW TNCLPNTEDI MKQKQKFVDK PGPFVGPCGH 

       430        440        450        460        470 
WIRPSETLQK YLKVVMALTY EEKPPYAMLR NNLEALLQDL RVSPYDPIGL PMVP 

« Hide

Isoform 2 [UniParc].

Checksum: B8EA8340E4FB9824
Show »

FASTA41245,904
Isoform 3 [UniParc].

Checksum: D17A379F153ED44E
Show »

FASTA42447,501

References

« Hide 'large scale' references
[1]"Vaccinia related kinase 3 (VRK3)."
Nezu J.
Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Liver.
[2]"Cloning and characterization of a novel human VRK3 gene."
Ni X., Xie Y., Mao Y.
Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[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] (ISOFORMS 1 AND 3).
Tissue: Testis and Trachea.
[4]"The DNA sequence and biology of human chromosome 19."
Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. expand/collapse author list , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
Nature 428:529-535(2004) [PubMed] [Europe PMC] [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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Brain and Skin.
[6]"Characterization of three paralogous members of the Mammalian vaccinia related kinase family."
Nichols R.J., Traktman P.
J. Biol. Chem. 279:7934-7946(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, NUCLEAR LOCALIZATION SIGNAL.
[7]"Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities."
Sanz-Garcia M., Lopez-Sanchez I., Lazo P.A.
Mol. Cell. Proteomics 7:2199-2214(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RAN.
[8]"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 SER-55 AND SER-59, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-82; SER-83 AND SER-90, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[10]"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-82 AND SER-83, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[11]"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-82; SER-83; SER-115 AND SER-122, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Structure of the pseudokinase VRK3 reveals a degraded catalytic site, a highly conserved kinase fold, and a putative regulatory binding site."
Scheeff E.D., Eswaran J., Bunkoczi G., Knapp S., Manning G.
Structure 17:128-138(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 146-474, FUNCTION, LACK OF CATALYTIC ACTIVITY.
[13]"Patterns of somatic mutation in human cancer genomes."
Greenman C., Stephens P., Smith R., Dalgliesh G.L., Hunter C., Bignell G., Davies H., Teague J., Butler A., Stevens C., Edkins S., O'Meara S., Vastrik I., Schmidt E.E., Avis T., Barthorpe S., Bhamra G., Buck G. expand/collapse author list , Choudhury B., Clements J., Cole J., Dicks E., Forbes S., Gray K., Halliday K., Harrison R., Hills K., Hinton J., Jenkinson A., Jones D., Menzies A., Mironenko T., Perry J., Raine K., Richardson D., Shepherd R., Small A., Tofts C., Varian J., Webb T., West S., Widaa S., Yates A., Cahill D.P., Louis D.N., Goldstraw P., Nicholson A.G., Brasseur F., Looijenga L., Weber B.L., Chiew Y.-E., DeFazio A., Greaves M.F., Green A.R., Campbell P., Birney E., Easton D.F., Chenevix-Trench G., Tan M.-H., Khoo S.K., Teh B.T., Yuen S.T., Leung S.Y., Wooster R., Futreal P.A., Stratton M.R.
Nature 446:153-158(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS [LARGE SCALE ANALYSIS] PHE-59; THR-105; LEU-171; LEU-268; TYR-288; CYS-370 AND GLY-371.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB031052 mRNA. Translation: BAA90769.1.
AF514788 mRNA. Translation: AAP47180.1.
AK292918 mRNA. Translation: BAF85607.1.
AK303010 mRNA. Translation: BAG64141.1.
AC011452 Genomic DNA. No translation available.
BC023556 mRNA. Translation: AAH23556.1.
BC095449 mRNA. Translation: AAH95449.1.
CCDSCCDS12791.1. [Q8IV63-1]
CCDS33076.1. [Q8IV63-3]
RefSeqNP_001020949.1. NM_001025778.1. [Q8IV63-3]
NP_057524.3. NM_016440.3. [Q8IV63-1]
XP_005259028.1. XM_005258971.1. [Q8IV63-1]
XP_005259029.1. XM_005258972.1. [Q8IV63-3]
XP_005259031.1. XM_005258974.2. [Q8IV63-2]
XP_006723300.1. XM_006723237.1. [Q8IV63-1]
XP_006723301.1. XM_006723238.1. [Q8IV63-3]
UniGeneHs.443330.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2JIIX-ray2.00A/B146-474[»]
ProteinModelPortalQ8IV63.
SMRQ8IV63. Positions 145-472.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid119394. 5 interactions.
IntActQ8IV63. 5 interactions.
MINTMINT-8247443.
STRING9606.ENSP00000324636.

PTM databases

PhosphoSiteQ8IV63.

Polymorphism databases

DMDM45593724.

Proteomic databases

MaxQBQ8IV63.
PaxDbQ8IV63.
PRIDEQ8IV63.

Protocols and materials databases

DNASU51231.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000316763; ENSP00000324636; ENSG00000105053. [Q8IV63-1]
ENST00000377011; ENSP00000366210; ENSG00000105053. [Q8IV63-3]
ENST00000594092; ENSP00000472541; ENSG00000105053. [Q8IV63-2]
ENST00000594948; ENSP00000473171; ENSG00000105053. [Q8IV63-1]
ENST00000599538; ENSP00000469880; ENSG00000105053. [Q8IV63-1]
ENST00000601341; ENSP00000470156; ENSG00000105053. [Q8IV63-3]
GeneID51231.
KEGGhsa:51231.
UCSCuc002prg.2. human. [Q8IV63-1]
uc002pri.1. human. [Q8IV63-3]
uc002prk.2. human. [Q8IV63-2]

Organism-specific databases

CTD51231.
GeneCardsGC19M050479.
HGNCHGNC:18996. VRK3.
HPAHPA016040.
neXtProtNX_Q8IV63.
PharmGKBPA134923990.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG298316.
HOGENOMHOG000293191.
HOVERGENHBG047756.
InParanoidQ8IV63.
KOK08816.
OMAYEEKPPY.
OrthoDBEOG7KSX83.
PhylomeDBQ8IV63.
TreeFamTF106473.

Enzyme and pathway databases

SignaLinkQ8IV63.

Gene expression databases

ArrayExpressQ8IV63.
BgeeQ8IV63.
CleanExHS_VRK3.
GenevestigatorQ8IV63.

Family and domain databases

InterProIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR026870. Zinc_ribbon_dom.
[Graphical view]
PfamPF00069. Pkinase. 1 hit.
PF13240. zinc_ribbon_2. 1 hit.
[Graphical view]
SUPFAMSSF56112. SSF56112. 1 hit.
PROSITEPS50011. PROTEIN_KINASE_DOM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSVRK3. human.
EvolutionaryTraceQ8IV63.
GenomeRNAi51231.
NextBio54332.
PROQ8IV63.

Entry information

Entry nameVRK3_HUMAN
AccessionPrimary (citable) accession number: Q8IV63
Secondary accession number(s): A6NEG5 expand/collapse secondary AC list , A8KA53, Q502Y2, Q9P2V8
Entry history
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: October 10, 2003
Last modified: July 9, 2014
This is version 114 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

Human and mouse protein kinases

Human and mouse protein kinases: classification and index

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

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 19

Human chromosome 19: entries, gene names and cross-references to MIM