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Protein

Cell growth-regulating nucleolar protein

Gene

LYAR

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

Functioni

Plays a role in the maintenance of the appropriate processing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and their subsequent processing to produce 18S and 28S rRNAs (PubMed:24495227). Also acts at the level of transcription regulation. Along with PRMT5, binds the gamma-globin (HBG1/HBG2) promoter and represses its expression (PubMed:25092918). In neuroblastoma cells, may also repress the expression of oxidative stress genes, including CHAC1, HMOX1, SLC7A11, ULBP1 and SNORD41 that encodes a small nucleolar RNA (PubMed:28686580). Preferentially binds to a DNA motif containing 5'-GGTTAT-3' (PubMed:25092918). Stimulates phagocytosis of photoreceptor outer segments by retinal pigment epithelial cells (By similarity). Prevents nucleolin/NCL self-cleavage, maintaining a normal steady-state level of NCL protein in undifferentiated embryonic stem cells (ESCs), which in turn is essential for ESC self-renewal (By similarity).By similarity3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi6Zinc 1By similarity1
Metal bindingi9Zinc 1By similarity1
Metal bindingi21Zinc 1By similarity1
Metal bindingi25Zinc 1By similarity1
Metal bindingi33Zinc 2By similarity1
Metal bindingi36Zinc 2By similarity1
Metal bindingi48Zinc 2By similarity1
Metal bindingi51Zinc 2By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1 – 26C2HC LYAR-type 1PROSITE-ProRule annotationAdd BLAST26
Zinc fingeri28 – 52C2HC LYAR-type 2PROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

  • DNA binding Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • RNA binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processrRNA processing, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Cell growth-regulating nucleolar protein
Gene namesi
Name:LYAR
ORF Names:PNAS-5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

EuPathDBiHostDB:ENSG00000145220.13
HGNCiHGNC:26021 LYAR
MIMi617684 gene
neXtProtiNX_Q9NX58

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell projection, Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1 – 58Missing : Decreases the production of 28S rRNA and the formation of pre-60S particle. 1 PublicationAdd BLAST58

Organism-specific databases

DisGeNETi55646
PharmGKBiPA162394697

Polymorphism and mutation databases

BioMutaiLYAR
DMDMi71153817

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000845281 – 379Cell growth-regulating nucleolar proteinAdd BLAST379

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki14Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki207Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei215PhosphoserineCombined sources1
Modified residuei244PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9NX58
MaxQBiQ9NX58
PaxDbiQ9NX58
PeptideAtlasiQ9NX58
PRIDEiQ9NX58
ProteomicsDBi83045

2D gel databases

SWISS-2DPAGEiQ9NX58

PTM databases

iPTMnetiQ9NX58
PhosphoSitePlusiQ9NX58
SwissPalmiQ9NX58

Expressioni

Tissue specificityi

Predominantly expressed in testis.1 Publication

Developmental stagei

In an ex vivo erythroid culture system, highly expressed from early (preproerythroblasts) to mid (basophilic normoblasts) maturation. Markedly reduced in more mature erythroblasts (at protein level). The decrease in LYAR protein correlates with the rise of beta-globin (HBB) mRNA levels during erythroid cell differentiation.1 Publication

Inductioni

Induced by MYCN.1 Publication

Gene expression databases

BgeeiENSG00000145220 Expressed in 197 organ(s), highest expression level in secondary oocyte
CleanExiHS_LYAR
ExpressionAtlasiQ9NX58 baseline and differential
GenevisibleiQ9NX58 HS

Organism-specific databases

HPAiHPA035881

Interactioni

Subunit structurei

Interacts with PRMT5; this interaction is direct (PubMed:25092918). Interacts with GNL2 and RPL23A (PubMed:26203195). Interacts with nucleolin/NCL; this interaction is direct (By similarity).By similarity2 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi120780, 76 interactors
CORUMiQ9NX58
IntActiQ9NX58, 50 interactors
MINTiQ9NX58
STRINGi9606.ENSP00000345917

Structurei

3D structure databases

ProteinModelPortaliQ9NX58
SMRiQ9NX58
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili175 – 219Sequence analysisAdd BLAST45

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi168 – 379Lys-richAdd BLAST212

Domaini

The N-terminal zinc-finger domains are required for the appropriate production of 28S rRNA and the formation of pre-60S particles.1 Publication

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1 – 26C2HC LYAR-type 1PROSITE-ProRule annotationAdd BLAST26
Zinc fingeri28 – 52C2HC LYAR-type 2PROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG2186 Eukaryota
ENOG411081U LUCA
HOGENOMiHOG000006633
HOVERGENiHBG006298
InParanoidiQ9NX58
KOiK15263
OrthoDBiEOG091G0L4Z
PhylomeDBiQ9NX58
TreeFamiTF314925

Family and domain databases

InterProiView protein in InterPro
IPR039999 LYAR
IPR014898 Znf_C2H2_LYAR
IPR036236 Znf_C2H2_sf
PANTHERiPTHR13100 PTHR13100, 1 hit
PfamiView protein in Pfam
PF08790 zf-LYAR, 1 hit
SUPFAMiSSF57667 SSF57667, 2 hits
PROSITEiView protein in PROSITE
PS51804 ZF_C2HC_LYAR, 2 hits

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q9NX58-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVFFTCNACG ESVKKIQVEK HVSVCRNCEC LSCIDCGKDF WGDDYKNHVK
60 70 80 90 100
CISEDQKYGG KGYEGKTHKG DIKQQAWIQK ISELIKRPNV SPKVRELLEQ
110 120 130 140 150
ISAFDNVPRK KAKFQNWMKN SLKVHNESIL DQVWNIFSEA SNSEPVNKEQ
160 170 180 190 200
DQRPLHPVAN PHAEISTKVP ASKVKDAVEQ QGEVKKNKRE RKEERQKKRK
210 220 230 240 250
REKKELKLEN HQENSRNQKP KKRKKGQEAD LEAGGEEVPE ANGSAGKRSK
260 270 280 290 300
KKKQRKDSAS EEEAHVGAGK RKRRHSEVET DSKKKKMKLP EHPEGGEPED
310 320 330 340 350
DEAPAKGKFN WKGTIKAILK QAPDNEITIK KLRKKVLAQY YTVTDEHHRS
360 370
EEELLVIFNK KISKNPTFKL LKDKVKLVK
Length:379
Mass (Da):43,615
Last modified:July 19, 2005 - v2
Checksum:i45159F44C22537DB
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D6RDJ1D6RDJ1_HUMAN
Cell growth-regulating nucleolar pr...
LYAR
79Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti21H → R in CAG38579 (Ref. 3) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_023080151D → Y. Corresponds to variant dbSNP:rs2272739Ensembl.1
Natural variantiVAR_023081265H → R5 PublicationsCorresponds to variant dbSNP:rs7376390Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL136750 mRNA Translation: CAB66684.1
AK000432 mRNA Translation: BAA91162.1
CR533548 mRNA Translation: CAG38579.1
CH471131 Genomic DNA Translation: EAW82437.1
CH471131 Genomic DNA Translation: EAW82438.1
CH471131 Genomic DNA Translation: EAW82439.1
BC015796 mRNA Translation: AAH15796.1
AF229835 mRNA Translation: AAF42870.1
CCDSiCCDS3374.1
RefSeqiNP_001139197.1, NM_001145725.1
NP_060286.1, NM_017816.2
XP_011511807.1, XM_011513505.1
XP_011511808.1, XM_011513506.2
UniGeneiHs.425427

Genome annotation databases

EnsembliENST00000343470; ENSP00000345917; ENSG00000145220
ENST00000452476; ENSP00000397367; ENSG00000145220
GeneIDi55646
KEGGihsa:55646
UCSCiuc003ght.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL136750 mRNA Translation: CAB66684.1
AK000432 mRNA Translation: BAA91162.1
CR533548 mRNA Translation: CAG38579.1
CH471131 Genomic DNA Translation: EAW82437.1
CH471131 Genomic DNA Translation: EAW82438.1
CH471131 Genomic DNA Translation: EAW82439.1
BC015796 mRNA Translation: AAH15796.1
AF229835 mRNA Translation: AAF42870.1
CCDSiCCDS3374.1
RefSeqiNP_001139197.1, NM_001145725.1
NP_060286.1, NM_017816.2
XP_011511807.1, XM_011513505.1
XP_011511808.1, XM_011513506.2
UniGeneiHs.425427

3D structure databases

ProteinModelPortaliQ9NX58
SMRiQ9NX58
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120780, 76 interactors
CORUMiQ9NX58
IntActiQ9NX58, 50 interactors
MINTiQ9NX58
STRINGi9606.ENSP00000345917

PTM databases

iPTMnetiQ9NX58
PhosphoSitePlusiQ9NX58
SwissPalmiQ9NX58

Polymorphism and mutation databases

BioMutaiLYAR
DMDMi71153817

2D gel databases

SWISS-2DPAGEiQ9NX58

Proteomic databases

EPDiQ9NX58
MaxQBiQ9NX58
PaxDbiQ9NX58
PeptideAtlasiQ9NX58
PRIDEiQ9NX58
ProteomicsDBi83045

Protocols and materials databases

DNASUi55646
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000343470; ENSP00000345917; ENSG00000145220
ENST00000452476; ENSP00000397367; ENSG00000145220
GeneIDi55646
KEGGihsa:55646
UCSCiuc003ght.4 human

Organism-specific databases

CTDi55646
DisGeNETi55646
EuPathDBiHostDB:ENSG00000145220.13
GeneCardsiLYAR
H-InvDBiHIX0017656
HGNCiHGNC:26021 LYAR
HPAiHPA035881
MIMi617684 gene
neXtProtiNX_Q9NX58
PharmGKBiPA162394697
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2186 Eukaryota
ENOG411081U LUCA
HOGENOMiHOG000006633
HOVERGENiHBG006298
InParanoidiQ9NX58
KOiK15263
OrthoDBiEOG091G0L4Z
PhylomeDBiQ9NX58
TreeFamiTF314925

Miscellaneous databases

ChiTaRSiLYAR human
GeneWikiiLYAR
GenomeRNAii55646
PROiPR:Q9NX58
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000145220 Expressed in 197 organ(s), highest expression level in secondary oocyte
CleanExiHS_LYAR
ExpressionAtlasiQ9NX58 baseline and differential
GenevisibleiQ9NX58 HS

Family and domain databases

InterProiView protein in InterPro
IPR039999 LYAR
IPR014898 Znf_C2H2_LYAR
IPR036236 Znf_C2H2_sf
PANTHERiPTHR13100 PTHR13100, 1 hit
PfamiView protein in Pfam
PF08790 zf-LYAR, 1 hit
SUPFAMiSSF57667 SSF57667, 2 hits
PROSITEiView protein in PROSITE
PS51804 ZF_C2HC_LYAR, 2 hits
ProtoNetiSearch...

Entry informationi

Entry nameiLYAR_HUMAN
AccessioniPrimary (citable) accession number: Q9NX58
Secondary accession number(s): D3DVS4, Q6FI78, Q9NYS1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: July 19, 2005
Last modified: November 7, 2018
This is version 154 of the entry and version 2 of the sequence. See 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: 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. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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