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Protein

Inactive serine/threonine-protein kinase VRK3

Gene

VRK3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Inactive kinase that suppresses ERK activity by promoting phosphatase activity of DUSP3 which specifically dephosphorylates and inactivates ERK in the nucleus.By similarity2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:HS02672-MONOMER.
SignaLinkiQ8IV63.

Names & Taxonomyi

Protein namesi
Recommended name:
Inactive serine/threonine-protein kinase VRK3
Alternative name(s):
Serine/threonine-protein pseudokinase VRK3
Vaccinia-related kinase 3
Gene namesi
Name:VRK3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:18996. VRK3.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • cytoplasm Source: GO_Central
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000105053.
PharmGKBiPA134923990.

Chemistry databases

ChEMBLiCHEMBL3430761.

Polymorphism and mutation databases

BioMutaiVRK3.
DMDMi45593724.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000868081 – 474Inactive serine/threonine-protein kinase VRK3Add BLAST474

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei54PhosphoserineCombined sources1
Modified residuei55PhosphoserineCombined sources1
Modified residuei59PhosphoserineCombined sources1
Modified residuei82PhosphoserineCombined sources1
Modified residuei83PhosphoserineCombined sources1
Modified residuei90PhosphoserineCombined sources1
Modified residuei115PhosphoserineCombined sources1
Modified residuei122PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8IV63.
MaxQBiQ8IV63.
PaxDbiQ8IV63.
PeptideAtlasiQ8IV63.
PRIDEiQ8IV63.
TopDownProteomicsiQ8IV63-1. [Q8IV63-1]

PTM databases

iPTMnetiQ8IV63.
PhosphoSitePlusiQ8IV63.

Expressioni

Gene expression databases

BgeeiENSG00000105053.
CleanExiHS_VRK3.
ExpressionAtlasiQ8IV63. baseline and differential.
GenevisibleiQ8IV63. HS.

Organism-specific databases

HPAiHPA016040.
HPA056489.

Interactioni

Subunit structurei

Interacts with DUSP3 (By similarity). Interacts with RAN.By similarity1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
MAXP612442EBI-1058605,EBI-751711

GO - Molecular functioni

  • protein phosphatase binding Source: MGI

Protein-protein interaction databases

BioGridi119394. 11 interactors.
IntActiQ8IV63. 11 interactors.
MINTiMINT-8247443.
STRINGi9606.ENSP00000324636.

Structurei

Secondary structure

1474
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi157 – 159Combined sources3
Beta strandi165 – 175Combined sources11
Beta strandi178 – 185Combined sources8
Beta strandi200 – 206Combined sources7
Helixi211 – 221Combined sources11
Helixi224 – 233Combined sources10
Beta strandi246 – 250Combined sources5
Turni251 – 253Combined sources3
Beta strandi254 – 260Combined sources7
Helixi266 – 272Combined sources7
Helixi274 – 276Combined sources3
Helixi280 – 299Combined sources20
Beta strandi311 – 315Combined sources5
Beta strandi318 – 324Combined sources7
Helixi327 – 329Combined sources3
Helixi335 – 337Combined sources3
Turni354 – 356Combined sources3
Helixi359 – 362Combined sources4
Helixi369 – 385Combined sources17
Helixi391 – 393Combined sources3
Helixi397 – 409Combined sources13
Helixi426 – 436Combined sources11
Helixi446 – 459Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JIIX-ray2.00A/B146-474[»]
ProteinModelPortaliQ8IV63.
SMRiQ8IV63.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8IV63.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini166 – 457Protein kinasePROSITE-ProRule annotationAdd BLAST292

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi49 – 64Nuclear localization signal1 PublicationAdd BLAST16

Sequence similaritiesi

Contains 1 protein kinase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1164. Eukaryota.
ENOG410XPGP. LUCA.
GeneTreeiENSGT00850000132311.
HOGENOMiHOG000293191.
HOVERGENiHBG047756.
InParanoidiQ8IV63.
KOiK08816.
OMAiYEEKPPY.
OrthoDBiEOG091G05V5.
PhylomeDBiQ8IV63.
TreeFamiTF106473.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR026870. Zinc_ribbon_dom.
[Graphical view]
PfamiPF00069. Pkinase. 1 hit.
PF13240. zinc_ribbon_2. 1 hit.
[Graphical view]
SMARTiSM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS50011. PROTEIN_KINASE_DOM. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8IV63-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MISFCPDCGK SIQAAFKFCP YCGNSLPVEE HVGSQTFVNP HVSSFQGSKR
60 70 80 90 100
GLNSSFETSP KKVKWSSTVT SPRLSLFSDG DSSESEDTLS SSERSKGSGS
110 120 130 140 150
RPPTPKSSPQ KTRKSPQVTR GSPQKTSCSP QKTRQSPQTL KRSRVTTSLE
160 170 180 190 200
ALPTGTVLTD KSGRQWKLKS FQTRDNQGIL YEAAPTSTLT CDSGPQKQKF
210 220 230 240 250
SLKLDAKDGR LFNEQNFFQR AAKPLQVNKW KKLYSTPLLA IPTCMGFGVH
260 270 280 290 300
QDKYRFLVLP SLGRSLQSAL DVSPKHVLSE RSVLQVACRL LDALEFLHEN
310 320 330 340 350
EYVHGNVTAE NIFVDPEDQS QVTLAGYGFA FRYCPSGKHV AYVEGSRSPH
360 370 380 390 400
EGDLEFISMD LHKGCGPSRR SDLQSLGYCM LKWLYGFLPW TNCLPNTEDI
410 420 430 440 450
MKQKQKFVDK PGPFVGPCGH WIRPSETLQK YLKVVMALTY EEKPPYAMLR
460 470
NNLEALLQDL RVSPYDPIGL PMVP
Length:474
Mass (Da):52,881
Last modified:October 10, 2003 - v2
Checksum:i86B9B91050A7F0CC
GO
Isoform 2 (identifier: Q8IV63-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     407-412: FVDKPG → LPWDSF
     413-474: Missing.

Note: No experimental confirmation available.
Show »
Length:412
Mass (Da):45,904
Checksum:iB8EA8340E4FB9824
GO
Isoform 3 (identifier: Q8IV63-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     47-96: Missing.

Note: No experimental confirmation available.
Show »
Length:424
Mass (Da):47,501
Checksum:iD17A379F153ED44E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti161K → E in AAP47180 (Ref. 2) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04129559S → F.1 PublicationCorresponds to variant rs2033262dbSNPEnsembl.1
Natural variantiVAR_041296105P → T.1 PublicationCorresponds to variant rs11547882dbSNPEnsembl.1
Natural variantiVAR_051682170S → P.Corresponds to variant rs11547881dbSNPEnsembl.1
Natural variantiVAR_041297171F → L.1 PublicationCorresponds to variant rs11547883dbSNPEnsembl.1
Natural variantiVAR_051683188T → A.Corresponds to variant rs11879620dbSNPEnsembl.1
Natural variantiVAR_041298268S → L.1 PublicationCorresponds to variant rs10410075dbSNPEnsembl.1
Natural variantiVAR_041299288C → Y.1 PublicationCorresponds to variant rs10409482dbSNPEnsembl.1
Natural variantiVAR_051684304H → L.Corresponds to variant rs35261919dbSNPEnsembl.1
Natural variantiVAR_041300370R → C.1 PublicationCorresponds to variant rs35331034dbSNPEnsembl.1
Natural variantiVAR_041301371S → G.1 PublicationCorresponds to variant rs56407496dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_04340947 – 96Missing in isoform 3. 1 PublicationAdd BLAST50
Alternative sequenceiVSP_008544407 – 412FVDKPG → LPWDSF in isoform 2. 1 Publication6
Alternative sequenceiVSP_008545413 – 474Missing in isoform 2. 1 PublicationAdd BLAST62

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS12791.1. [Q8IV63-1]
CCDS33076.1. [Q8IV63-3]
CCDS77334.1. [Q8IV63-2]
RefSeqiNP_001020949.1. NM_001025778.1. [Q8IV63-3]
NP_001295349.1. NM_001308420.1. [Q8IV63-2]
NP_057524.3. NM_016440.3. [Q8IV63-1]
XP_005259028.1. XM_005258971.3. [Q8IV63-1]
XP_005259029.1. XM_005258972.3. [Q8IV63-3]
XP_006723300.1. XM_006723237.3. [Q8IV63-1]
XP_006723301.1. XM_006723238.3. [Q8IV63-3]
XP_011525325.1. XM_011527023.2. [Q8IV63-2]
UniGeneiHs.443330.

Genome annotation databases

EnsembliENST00000316763; 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]
GeneIDi51231.
KEGGihsa:51231.
UCSCiuc002prg.3. human. [Q8IV63-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS12791.1. [Q8IV63-1]
CCDS33076.1. [Q8IV63-3]
CCDS77334.1. [Q8IV63-2]
RefSeqiNP_001020949.1. NM_001025778.1. [Q8IV63-3]
NP_001295349.1. NM_001308420.1. [Q8IV63-2]
NP_057524.3. NM_016440.3. [Q8IV63-1]
XP_005259028.1. XM_005258971.3. [Q8IV63-1]
XP_005259029.1. XM_005258972.3. [Q8IV63-3]
XP_006723300.1. XM_006723237.3. [Q8IV63-1]
XP_006723301.1. XM_006723238.3. [Q8IV63-3]
XP_011525325.1. XM_011527023.2. [Q8IV63-2]
UniGeneiHs.443330.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2JIIX-ray2.00A/B146-474[»]
ProteinModelPortaliQ8IV63.
SMRiQ8IV63.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119394. 11 interactors.
IntActiQ8IV63. 11 interactors.
MINTiMINT-8247443.
STRINGi9606.ENSP00000324636.

Chemistry databases

ChEMBLiCHEMBL3430761.

PTM databases

iPTMnetiQ8IV63.
PhosphoSitePlusiQ8IV63.

Polymorphism and mutation databases

BioMutaiVRK3.
DMDMi45593724.

Proteomic databases

EPDiQ8IV63.
MaxQBiQ8IV63.
PaxDbiQ8IV63.
PeptideAtlasiQ8IV63.
PRIDEiQ8IV63.
TopDownProteomicsiQ8IV63-1. [Q8IV63-1]

Protocols and materials databases

DNASUi51231.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000316763; 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]
GeneIDi51231.
KEGGihsa:51231.
UCSCiuc002prg.3. human. [Q8IV63-1]

Organism-specific databases

CTDi51231.
GeneCardsiVRK3.
HGNCiHGNC:18996. VRK3.
HPAiHPA016040.
HPA056489.
neXtProtiNX_Q8IV63.
OpenTargetsiENSG00000105053.
PharmGKBiPA134923990.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1164. Eukaryota.
ENOG410XPGP. LUCA.
GeneTreeiENSGT00850000132311.
HOGENOMiHOG000293191.
HOVERGENiHBG047756.
InParanoidiQ8IV63.
KOiK08816.
OMAiYEEKPPY.
OrthoDBiEOG091G05V5.
PhylomeDBiQ8IV63.
TreeFamiTF106473.

Enzyme and pathway databases

BioCyciZFISH:HS02672-MONOMER.
SignaLinkiQ8IV63.

Miscellaneous databases

ChiTaRSiVRK3. human.
EvolutionaryTraceiQ8IV63.
GenomeRNAii51231.
PROiQ8IV63.

Gene expression databases

BgeeiENSG00000105053.
CleanExiHS_VRK3.
ExpressionAtlasiQ8IV63. baseline and differential.
GenevisibleiQ8IV63. HS.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR026870. Zinc_ribbon_dom.
[Graphical view]
PfamiPF00069. Pkinase. 1 hit.
PF13240. zinc_ribbon_2. 1 hit.
[Graphical view]
SMARTiSM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS50011. PROTEIN_KINASE_DOM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVRK3_HUMAN
AccessioniPrimary (citable) accession number: Q8IV63
Secondary accession number(s): A6NEG5
, A8KA53, Q502Y2, Q9P2V8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: October 10, 2003
Last modified: November 2, 2016
This is version 138 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Caution

Inactive as a kinase due to its inability to bind ATP.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human and mouse protein kinases
    Human and mouse protein kinases: classification and index
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.