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GATOR complex protein NPRL3 (-14 gene protein) (Alpha-globin regulatory element-containing gene protein) (Nitrogen permease regulator 3-like protein) (Protein CGTHBA)

 NPRL3_HUMAN             Reviewed;         569 AA.
Q12980; D3DU40; Q1W6H0; Q4TT56; Q92469;
26-SEP-2001, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
10-OCT-2018, entry version 125.
RecName: Full=GATOR complex protein NPRL3 {ECO:0000305};
AltName: Full=-14 gene protein {ECO:0000303|PubMed:8575760};
AltName: Full=Alpha-globin regulatory element-containing gene protein {ECO:0000303|PubMed:8575760};
AltName: Full=Nitrogen permease regulator 3-like protein {ECO:0000312|HGNC:HGNC:14124};
AltName: Full=Protein CGTHBA;
Name=NPRL3 {ECO:0000312|HGNC:HGNC:14124};
Synonyms=C16orf35 {ECO:0000312|HGNC:HGNC:14124}, CGTHBA,
MARE {ECO:0000305|PubMed:8575760};
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=8575760; DOI=10.1006/geno.1995.9951;
Vyas P., Vickers M.A., Picketts D.J., Higgs D.;
"Conservation of position and sequence of a novel, widely expressed
gene containing the major human alpha-globin regulatory element.";
Genomics 29:679-689(1995).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=16728641; DOI=10.1126/science.1126431;
De Gobbi M., Viprakasit V., Hughes J.R., Fisher C., Buckle V.J.,
Ayyub H., Gibbons R.J., Vernimmen D., Yoshinaga Y., de Jong P.,
Cheng J.-F., Rubin E.M., Wood W.G., Bowden D., Higgs D.R.;
"A regulatory SNP causes a human genetic disease by creating a new
transcriptional promoter.";
Science 312:1215-1217(2006).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15616553; DOI=10.1038/nature03187;
Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X.,
Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A.,
Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J.,
Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L.,
Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A.,
Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D.,
Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J.,
Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M.,
Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I.,
Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W.,
Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A.,
Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S.,
Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J.,
Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D.,
Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L.,
Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A.,
Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L.,
Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N.,
Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M.,
Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L.,
Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D.,
Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P.,
Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M.,
Rubin E.M., Pennacchio L.A.;
"The sequence and analysis of duplication-rich human chromosome 16.";
Nature 432:988-994(2004).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
Venter J.C.;
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
[5]
INTERACTION WITH NPRL2.
PubMed=19521502; DOI=10.1371/journal.pgen.1000515;
Neklesa T.K., Davis R.W.;
"A genome-wide screen for regulators of TORC1 in response to amino
acid starvation reveals a conserved Npr2/3 complex.";
PLoS Genet. 5:E1000515-E1000515(2009).
[6]
FUNCTION, IDENTIFICATION IN GATOR COMPLEX, AND INTERACTION WITH RRAG
PROTEINS.
PubMed=23723238; DOI=10.1126/science.1232044;
Bar-Peled L., Chantranupong L., Cherniack A.D., Chen W.W.,
Ottina K.A., Grabiner B.C., Spear E.D., Carter S.L., Meyerson M.,
Sabatini D.M.;
"A Tumor suppressor complex with GAP activity for the Rag GTPases that
signal amino acid sufficiency to mTORC1.";
Science 340:1100-1106(2013).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-476, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
[8]
SUBCELLULAR LOCATION.
PubMed=28199306; DOI=10.1038/nature21423;
Wolfson R.L., Chantranupong L., Wyant G.A., Gu X., Orozco J.M.,
Shen K., Condon K.J., Petri S., Kedir J., Scaria S.M.,
Abu-Remaileh M., Frankel W.N., Sabatini D.M.;
"KICSTOR recruits GATOR1 to the lysosome and is necessary for
nutrients to regulate mTORC1.";
Nature 543:438-442(2017).
[9]
INVOLVEMENT IN FFEVF3, VARIANTS FFEVF3 GLN-92 AND LYS-249, AND TISSUE
SPECIFICITY.
PubMed=26505888; DOI=10.1002/ana.24547;
Epilepsy Electroclinical Study Group;
Ricos M.G., Hodgson B.L., Pippucci T., Saidin A., Ong Y.S.,
Heron S.E., Licchetta L., Bisulli F., Bayly M.A., Hughes J.,
Baldassari S., Palombo F., Santucci M., Meletti S., Berkovic S.F.,
Rubboli G., Thomas P.Q., Scheffer I.E., Tinuper P., Geoghegan J.,
Schreiber A.W., Dibbens L.M.;
"Mutations in the mammalian target of rapamycin pathway regulators
NPRL2 and NPRL3 cause focal epilepsy.";
Ann. Neurol. 79:120-131(2016).
[10]
INVOLVEMENT IN FFEVF3, AND VARIANT FFEVF3 GLN-92.
PubMed=26285051; DOI=10.1002/ana.24502;
Sim J.C., Scerri T., Fanjul-Fernandez M., Riseley J.R., Gillies G.,
Pope K., van Roozendaal H., Heng J.I., Mandelstam S.A.,
McGillivray G., MacGregor D., Kannan L., Maixner W., Harvey A.S.,
Amor D.J., Delatycki M.B., Crino P.B., Bahlo M., Lockhart P.J.,
Leventer R.J.;
"Familial cortical dysplasia caused by mutation in the mammalian
target of rapamycin regulator NPRL3.";
Ann. Neurol. 79:132-137(2016).
[11]
INVOLVEMENT IN FFEVF3, VARIANT FFEVF3 LYS-249, AND TISSUE SPECIFICITY.
PubMed=27173016; DOI=10.1111/epi.13391;
Weckhuysen S., Marsan E., Lambrecq V., Marchal C., Morin-Brureau M.,
An-Gourfinkel I., Baulac M., Fohlen M., Kallay Zetchi C., Seeck M.,
de la Grange P., Dermaut B., Meurs A., Thomas P., Chassoux F.,
Leguern E., Picard F., Baulac S.;
"Involvement of GATOR complex genes in familial focal epilepsies and
focal cortical dysplasia.";
Epilepsia 57:994-1003(2016).
-!- FUNCTION: As a component of the GATOR1 complex functions as an
inhibitor of the amino acid-sensing branch of the TORC1 pathway.
The GATOR1 complex strongly increases GTP hydrolysis by RRAGA and
RRAGB within RRAGC-containing heterodimers, thereby deactivating
RRAGs, releasing mTORC1 from lysosomal surface and inhibiting
mTORC1 signaling. The GATOR1 complex is negatively regulated by
GATOR2 the other GATOR subcomplex in this amino acid-sensing
branch of the TORC1 pathway. {ECO:0000269|PubMed:23723238}.
-!- SUBUNIT: Forms a heterodimer with NPRL2. Within the GATOR complex,
component of the GATOR1 subcomplex, made of DEPDC5, NPRL2 and
NPRL3. GATOR1 mediates the strong interaction of the GATOR complex
with RRAGA/RRAGC and RRAGB/RRAGC heterodimers.
{ECO:0000269|PubMed:23723238}.
-!- INTERACTION:
Q8WTW4:NPRL2; NbExp=5; IntAct=EBI-2650314, EBI-1043552;
Q5T011:SZT2; NbExp=5; IntAct=EBI-2650314, EBI-10749411;
-!- SUBCELLULAR LOCATION: Lysosome membrane
{ECO:0000269|PubMed:28199306}. Note=Localization to lysosomes is
amino acid-independent. {ECO:0000269|PubMed:28199306}.
-!- TISSUE SPECIFICITY: Widely expressed. Expressed in the frontal
lobe cortex as well as in the temporal, parietal, and occipital
lobes (PubMed:27173016, PubMed:26505888).
{ECO:0000269|PubMed:26505888, ECO:0000269|PubMed:27173016}.
-!- DISEASE: Note=Inactivating mutations and truncating deletions in
the genes encoding GATOR1 proteins are detected in glioblastoma
and ovarian tumors and are associated with loss of heterozygosity
events. Inactivation of GATOR1 proteins promotes constitutive
localization of mTORC1 to the lysosomal membrane and blocks mTORC1
inactivation following amino acid withdrawal (PubMed:23723238).
{ECO:0000269|PubMed:23723238}.
-!- DISEASE: Epilepsy, familial focal, with variable foci 3 (FFEVF3)
[MIM:617118]: An autosomal dominant form of epilepsy characterized
by focal seizures arising from different cortical regions,
including the temporal, frontal, parietal, and occipital lobes.
Seizure types commonly include temporal lobe epilepsy, frontal
lobe epilepsy, and nocturnal frontal lobe epilepsy. Some patients
may have intellectual disability or autism spectrum disorders.
Seizure onset usually occurs in the first or second decades,
although later onset has been reported, and there is phenotypic
variability within families. A subset of patients have structural
brain abnormalities. Penetrance of the disorder is incomplete.
{ECO:0000269|PubMed:26285051, ECO:0000269|PubMed:26505888,
ECO:0000269|PubMed:27173016}. Note=The disease is caused by
mutations affecting the gene represented in this entry.
-!- SIMILARITY: Belongs to the NPR3 family. {ECO:0000305}.
-!- CAUTION: Ser-489 is missing in the human genome assembly but is
present in all available mRNAs and ESTs. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X90857; CAA62368.1; -; mRNA.
EMBL; DQ431198; ABD95907.1; -; Genomic_DNA.
EMBL; Z69666; CAI94885.1; -; Genomic_DNA.
EMBL; Z69720; CAI94885.1; JOINED; Genomic_DNA.
EMBL; Z84722; CAI94885.1; JOINED; Genomic_DNA.
EMBL; Z69720; CAI95611.1; -; Genomic_DNA.
EMBL; Z69666; CAI95611.1; JOINED; Genomic_DNA.
EMBL; Z84722; CAI95611.1; JOINED; Genomic_DNA.
EMBL; CH471112; EAW85865.1; -; Genomic_DNA.
EMBL; CH471112; EAW85867.1; -; Genomic_DNA.
CCDS; CCDS73795.1; -.
RefSeq; NP_001070818.1; NM_001077350.2.
UniGene; Hs.19699; -.
PDB; 6CES; EM; 4.00 A; M=1-569.
PDB; 6CET; EM; 4.40 A; M=1-569.
PDBsum; 6CES; -.
PDBsum; 6CET; -.
ProteinModelPortal; Q12980; -.
SMR; Q12980; -.
BioGrid; 113796; 22.
CORUM; Q12980; -.
DIP; DIP-62051N; -.
IntAct; Q12980; 9.
STRING; 9606.ENSP00000382834; -.
iPTMnet; Q12980; -.
PhosphoSitePlus; Q12980; -.
BioMuta; NPRL3; -.
DMDM; 18202492; -.
EPD; Q12980; -.
MaxQB; Q12980; -.
PaxDb; Q12980; -.
PeptideAtlas; Q12980; -.
PRIDE; Q12980; -.
ProteomicsDB; 59074; -.
DNASU; 8131; -.
Ensembl; ENST00000611875; ENSP00000478273; ENSG00000103148.
Ensembl; ENST00000620134; ENSP00000483814; ENSG00000103148.
GeneID; 8131; -.
KEGG; hsa:8131; -.
UCSC; uc032dmr.2; human.
CTD; 8131; -.
DisGeNET; 8131; -.
EuPathDB; HostDB:ENSG00000103148.15; -.
GeneCards; NPRL3; -.
HGNC; HGNC:14124; NPRL3.
HPA; HPA011741; -.
MalaCards; NPRL3; -.
MIM; 600928; gene.
MIM; 617118; phenotype.
neXtProt; NX_Q12980; -.
OpenTargets; ENSG00000103148; -.
PharmGKB; PA25550; -.
eggNOG; KOG3830; Eukaryota.
eggNOG; ENOG410XP4E; LUCA.
GeneTree; ENSGT00390000015916; -.
HOGENOM; HOG000004787; -.
HOVERGEN; HBG019399; -.
InParanoid; Q12980; -.
KO; K20406; -.
OMA; AHLVYWG; -.
OrthoDB; EOG091G03SH; -.
PhylomeDB; Q12980; -.
TreeFam; TF105965; -.
SIGNOR; Q12980; -.
ChiTaRS; NPRL3; human.
GenomeRNAi; 8131; -.
PRO; PR:Q12980; -.
Proteomes; UP000005640; Chromosome 16.
Bgee; ENSG00000103148; Expressed in 215 organ(s), highest expression level in blood.
CleanEx; HS_C16orf35; -.
ExpressionAtlas; Q12980; baseline and differential.
Genevisible; Q12980; HS.
GO; GO:1990130; C:GATOR1 complex; IDA:SGD.
GO; GO:0005765; C:lysosomal membrane; IDA:UniProtKB.
GO; GO:0005096; F:GTPase activator activity; IEA:UniProtKB-KW.
GO; GO:0035909; P:aorta morphogenesis; IEA:Ensembl.
GO; GO:0048738; P:cardiac muscle tissue development; IEA:Ensembl.
GO; GO:0034198; P:cellular response to amino acid starvation; IMP:UniProtKB.
GO; GO:0032007; P:negative regulation of TOR signaling; IMP:SGD.
GO; GO:2000785; P:regulation of autophagosome assembly; IBA:GO_Central.
GO; GO:0060021; P:roof of mouth development; IEA:Ensembl.
GO; GO:0038202; P:TORC1 signaling; IBA:GO_Central.
GO; GO:0003281; P:ventricular septum development; IEA:Ensembl.
InterPro; IPR005365; NPR3.
PANTHER; PTHR13153; PTHR13153; 1.
Pfam; PF03666; NPR3; 2.
1: Evidence at protein level;
3D-structure; Complete proteome; Disease mutation; Epilepsy;
GTPase activation; Lysosome; Membrane; Phosphoprotein;
Reference proteome.
CHAIN 1 569 GATOR complex protein NPRL3.
/FTId=PRO_0000220638.
MOD_RES 476 476 Phosphoserine.
{ECO:0000244|PubMed:24275569}.
VARIANT 92 92 R -> Q (in FFEVF3; unknown pathological
significance; dbSNP:rs367729589).
{ECO:0000269|PubMed:26285051,
ECO:0000269|PubMed:26505888}.
/FTId=VAR_077126.
VARIANT 249 249 E -> K (in FFEVF3; unknown pathological
significance; dbSNP:rs200041907).
{ECO:0000269|PubMed:26505888,
ECO:0000269|PubMed:27173016}.
/FTId=VAR_077127.
CONFLICT 489 489 Missing (in Ref. 2; CAI94885/CAI95611).
{ECO:0000305}.
SEQUENCE 569 AA; 63605 MW; 44BEF42AA7F2841D CRC64;
MRDNTSPISV ILVSSGSRGN KLLFRYPFQR SQEHPASQTS KPRSRYAASN TGDHADEQDG
DSRFSDVILA TILATKSEMC GQKFELKIDN VRFVGHPTLL QHALGQISKT DPSPKREAPT
MILFNVVFAL RANADPSVIN CLHNLSRRIA TVLQHEERRC QYLTREAKLI LALQDEVSAM
ADGNEGPQSP FHHILPKCKL ARDLKEAYDS LCTSGVVRLH INSWLEVSFC LPHKIHYAAS
SLIPPEAIER SLKAIRPYHA LLLLSDEKSL LGELPIDCSP ALVRVIKTTS AVKNLQQLAQ
DADLALLQVF QLAAHLVYWG KAIIIYPLCE NNVYMLSPNA SVCLYSPLAE QFSHQFPSHD
LPSVLAKFSL PVSLSEFRNP LAPAVQETQL IQMVVWMLQR RLLIQLHTYV CLMASPSEEE
PRPREDDVPF TARVGGRSLS TPNALSFGSP TSSDDMTLTS PSMDNSSAEL LPSGDSPLNQ
RMTENLLASL SEHERAAILS VPAAQNPEDL RMFARLLHYF RGRHHLEEIM YNENTRRSQL
LMLFDKFRSV LVVTTHEDPV IAVFQALLP


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