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GATOR complex protein NPRL2 (Gene 21 protein) (G21 protein) (Nitrogen permease regulator 2-like protein) (NPR2-like protein) (Tumor suppressor candidate 4)

 NPRL2_HUMAN             Reviewed;         380 AA.
Q8WTW4; A8K831; Q6FGS2; Q9Y249; Q9Y497;
10-MAY-2004, integrated into UniProtKB/Swiss-Prot.
10-MAY-2004, sequence version 2.
12-SEP-2018, entry version 131.
RecName: Full=GATOR complex protein NPRL2 {ECO:0000305};
AltName: Full=Gene 21 protein {ECO:0000303|Ref.1};
Short=G21 protein {ECO:0000303|Ref.1};
AltName: Full=Nitrogen permease regulator 2-like protein {ECO:0000303|PubMed:11085536};
Short=NPR2-like protein {ECO:0000303|PubMed:11085536};
AltName: Full=Tumor suppressor candidate 4 {ECO:0000303|PubMed:18616680};
Name=NPRL2 {ECO:0000312|HGNC:HGNC:24969};
Synonyms=TUSC4 {ECO:0000303|PubMed:18616680};
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
Kondo M., Sekido Y., Latif F., Cundiff S., Duh F.-M., Wei M.-H.,
Lerman M.I., Minna J.D.;
"Gene 21, a new candidate human tumor suppressor gene located in the
3p21.3 small cell lung cancer homozygous deletion region homologous to
the yeast nitrogen permease regulator NPR2.";
Submitted (OCT-1998) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Colon;
PubMed=14702039; DOI=10.1038/ng1285;
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.,
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.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.;
"Cloning of human full open reading frames in Gateway(TM) system entry
vector (pDONR201).";
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16641997; DOI=10.1038/nature04728;
Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R.,
Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R.,
Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V.,
Hume J., Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R.,
Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B.,
Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S.,
Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q.,
Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z.,
Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C.,
Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G.,
Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B.,
Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R.,
Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J.,
Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A.,
Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B.,
Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H.,
Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J.,
Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J.,
Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H.,
Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G.,
Gibbs R.A.;
"The DNA sequence, annotation and analysis of human chromosome 3.";
Nature 440:1194-1198(2006).
[5]
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 (JUL-2005) to the EMBL/GenBank/DDBJ databases.
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Kidney, and Skin;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[7]
DISCUSSION OF SEQUENCE.
PubMed=11085536;
The international lung cancer chromosome 3p21.3 tumor suppressor gene consortium;
Lerman M.I., Minna J.D.;
"The 630-kb lung cancer homozygous deletion region on human chromosome
3p21.3: identification and evaluation of the resident candidate tumor
suppressor genes.";
Cancer Res. 60:6116-6133(2000).
[8]
DISCUSSION OF SEQUENCE.
PubMed=11980673;
Ji L., Nishizaki M., Gao B., Burbee D., Kondo M., Kamibayashi C.,
Xu K., Yen N., Atkinson E.N., Fang B., Lerman M.I., Roth J.A.,
Minna J.D.;
"Expression of several genes in the human chromosome 3p21.3 homozygous
deletion region by an adenovirus vector results in tumor suppressor
activities in vitro and in vivo.";
Cancer Res. 62:2715-2720(2002).
[9]
FUNCTION, AND INTERACTION WITH PDPK1.
PubMed=18616680; DOI=10.1111/j.1349-7006.2008.00874.x;
Kurata A., Katayama R., Watanabe T., Tsuruo T., Fujita N.;
"TUSC4/NPRL2, a novel PDK1-interacting protein, inhibits PDK1 tyrosine
phosphorylation and its downstream signaling.";
Cancer Sci. 99:1827-1834(2008).
[10]
INTERACTION WITH NPRL3.
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).
[11]
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).
[12]
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).
[13]
INVOLVEMENT IN FFEVF2, VARIANTS FFEVF2 PRO-105; SER-110 AND HIS-214,
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).
[14]
INVOLVEMENT IN FFEVF2, VARIANT FFEVF2 HIS-198, 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}.
-!- FUNCTION: Suppresses Src-dependent tyrosine phosphorylation and
activation of PDPK1 and its downstream signaling. Down-regulates
PDPK1 kinase activity by interfering with tyrosine phosphorylation
at 'Tyr-9', 'Tyr-373' and 'Tyr-376' residues. May act as a tumor
suppressor. Suppresses cell growth and enhances sensitivity to
various anticancer drugs. {ECO:0000269|PubMed:18616680}.
-!- SUBUNIT: Forms a heterodimer with NPRL3. Interacts with PDPK1.
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:18616680,
ECO:0000269|PubMed:19521502, ECO:0000269|PubMed:23723238}.
-!- SUBCELLULAR LOCATION: Lysosome membrane
{ECO:0000269|PubMed:28199306}. Note=Localization to lysosomes is
amino acid-independent. {ECO:0000269|PubMed:28199306}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8WTW4-1; Sequence=Displayed;
Name=2;
IsoId=Q8WTW4-2; Sequence=VSP_010329, VSP_010330, VSP_010331;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Most abundant in skeletal muscle, followed by
brain, liver and pancreas, with lower amounts in lung, kidney,
placenta and heart. Expressed in the frontal lobe cortex as well
as in the temporal, parietal, and occipital lobes
(PubMed:27173016, PubMed:26505888). Expressed in most lung cancer
cell lines tested. {ECO:0000269|PubMed:26505888,
ECO:0000269|PubMed:27173016}.
-!- DISEASE: Note=Inactivating mutations and truncating deletions in
the genes encoding GATOR1 proteins, including NPRL2, 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 2 (FFEVF2)
[MIM:617116]: 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:26505888, ECO:0000269|PubMed:27173016}.
Note=The disease is caused by mutations affecting the gene
represented in this entry.
-!- SIMILARITY: Belongs to the NPR2 family. {ECO:0000305}.
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EMBL; AF040707; AAC62535.1; -; mRNA.
EMBL; AF040708; AAC62536.1; -; mRNA.
EMBL; AK292196; BAF84885.1; -; mRNA.
EMBL; CR542035; CAG46832.1; -; mRNA.
EMBL; AC002481; AAB67310.1; -; Genomic_DNA.
EMBL; CH471055; EAW65106.1; -; Genomic_DNA.
EMBL; CH471055; EAW65107.1; -; Genomic_DNA.
EMBL; BC021984; AAH21984.1; -; mRNA.
EMBL; BC056861; AAH56861.1; -; mRNA.
CCDS; CCDS2826.1; -. [Q8WTW4-1]
RefSeq; NP_006536.3; NM_006545.4. [Q8WTW4-1]
UniGene; Hs.437083; -.
PDB; 6CES; EM; 4.00 A; N=1-380.
PDB; 6CET; EM; 4.40 A; N=1-380.
PDBsum; 6CES; -.
PDBsum; 6CET; -.
ProteinModelPortal; Q8WTW4; -.
SMR; Q8WTW4; -.
BioGrid; 115885; 19.
CORUM; Q8WTW4; -.
DIP; DIP-50746N; -.
IntAct; Q8WTW4; 5.
MINT; Q8WTW4; -.
STRING; 9606.ENSP00000232501; -.
iPTMnet; Q8WTW4; -.
PhosphoSitePlus; Q8WTW4; -.
BioMuta; NPRL2; -.
DMDM; 47117604; -.
EPD; Q8WTW4; -.
MaxQB; Q8WTW4; -.
PaxDb; Q8WTW4; -.
PeptideAtlas; Q8WTW4; -.
PRIDE; Q8WTW4; -.
ProteomicsDB; 74610; -.
ProteomicsDB; 74611; -. [Q8WTW4-2]
DNASU; 10641; -.
Ensembl; ENST00000232501; ENSP00000232501; ENSG00000114388. [Q8WTW4-1]
GeneID; 10641; -.
KEGG; hsa:10641; -.
UCSC; uc003daj.2; human. [Q8WTW4-1]
CTD; 10641; -.
DisGeNET; 10641; -.
EuPathDB; HostDB:ENSG00000114388.12; -.
GeneCards; NPRL2; -.
HGNC; HGNC:24969; NPRL2.
HPA; HPA038196; -.
HPA; HPA038197; -.
MalaCards; NPRL2; -.
MIM; 607072; gene.
MIM; 617116; phenotype.
neXtProt; NX_Q8WTW4; -.
OpenTargets; ENSG00000114388; -.
PharmGKB; PA165697981; -.
eggNOG; KOG3789; Eukaryota.
eggNOG; ENOG410XP7B; LUCA.
GeneTree; ENSGT00390000001414; -.
HOGENOM; HOG000007022; -.
HOVERGEN; HBG055255; -.
InParanoid; Q8WTW4; -.
KO; K20405; -.
OMA; YASMTHG; -.
OrthoDB; EOG091G0759; -.
PhylomeDB; Q8WTW4; -.
TreeFam; TF106159; -.
SIGNOR; Q8WTW4; -.
ChiTaRS; NPRL2; human.
GeneWiki; TUSC4; -.
GenomeRNAi; 10641; -.
PRO; PR:Q8WTW4; -.
Proteomes; UP000005640; Chromosome 3.
Bgee; ENSG00000114388; Expressed in 112 organ(s), highest expression level in cerebellar hemisphere.
CleanEx; HS_TUSC4; -.
ExpressionAtlas; Q8WTW4; baseline and differential.
Genevisible; Q8WTW4; 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:0004672; F:protein kinase activity; IDA:UniProtKB.
GO; GO:0034198; P:cellular response to amino acid starvation; IMP:UniProtKB.
GO; GO:0006995; P:cellular response to nitrogen starvation; IBA:GO_Central.
GO; GO:0033673; P:negative regulation of kinase activity; IDA:UniProtKB.
GO; GO:0032007; P:negative regulation of TOR signaling; IMP:SGD.
GO; GO:0010508; P:positive regulation of autophagy; IBA:GO_Central.
GO; GO:2000785; P:regulation of autophagosome assembly; IBA:GO_Central.
InterPro; IPR009348; NPR2.
PANTHER; PTHR12991; PTHR12991; 2.
Pfam; PF06218; NPR2; 2.
1: Evidence at protein level;
3D-structure; Alternative splicing; Complete proteome;
Disease mutation; Epilepsy; GTPase activation; Lysosome; Membrane;
Reference proteome; Tumor suppressor.
CHAIN 1 380 GATOR complex protein NPRL2.
/FTId=PRO_0000213319.
REGION 1 133 Interaction with PDPK1.
{ECO:0000269|PubMed:18616680}.
VAR_SEQ 1 120 Missing (in isoform 2).
{ECO:0000303|Ref.1, ECO:0000303|Ref.3}.
/FTId=VSP_010329.
VAR_SEQ 312 323 KLIQFGLMKNLI -> SEENLLGHLGVT (in isoform
2). {ECO:0000303|Ref.1,
ECO:0000303|Ref.3}.
/FTId=VSP_010330.
VAR_SEQ 324 380 Missing (in isoform 2).
{ECO:0000303|Ref.1, ECO:0000303|Ref.3}.
/FTId=VSP_010331.
VARIANT 105 105 L -> P (in FFEVF2; dbSNP:rs886037965).
{ECO:0000269|PubMed:26505888}.
/FTId=VAR_077122.
VARIANT 110 110 T -> S (in FFEVF2; unknown pathological
significance).
{ECO:0000269|PubMed:26505888}.
/FTId=VAR_077123.
VARIANT 198 198 P -> H (in FFEVF2; unknown pathological
significance; dbSNP:rs745518585).
{ECO:0000269|PubMed:27173016}.
/FTId=VAR_077124.
VARIANT 214 214 D -> H (in FFEVF2; unknown pathological
significance; dbSNP:rs149128231).
{ECO:0000269|PubMed:26505888}.
/FTId=VAR_077125.
CONFLICT 17 17 P -> L (in Ref. 6; AAH21984).
{ECO:0000305}.
SEQUENCE 380 AA; 43658 MW; 5ECA201CE073F964 CRC64;
MGSGCRIECI FFSEFHPTLG PKITYQVPED FISRELFDTV QVYIITKPEL QNKLITVTAM
EKKLIGCPVC IEHKKYSRNA LLFNLGFVCD AQAKTCALEP IVKKLAGYLT TLELESSFVS
MEESKQKLVP IMTILLEELN ASGRCTLPID ESNTIHLKVI EQRPDPPVAQ EYDVPVFTKD
KEDFFNSQWD LTTQQILPYI DGFRHIQKIS AEADVELNLV RIAIQNLLYY GVVTLVSILQ
YSNVYCPTPK VQDLVDDKSL QEACLSYVTK QGHKRASLRD VFQLYCSLSP GTTVRDLIGR
HPQQLQHVDE RKLIQFGLMK NLIRRLQKYP VRVTREEQSH PARLYTGCHS YDEICCKTGM
SYHELDERLE NDPNIIICWK


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GENTAUR France SARL
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Tel 01 43 25 01 50

Fax 01 43 25 01 60
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BNP PARIBAS PARIS PL MAUBERT BIC BNPAFRPPPRG

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GENTAUR GmbH
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Support Karolina Elandt
Tel: 0035929830070
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San Jose, CA 95123
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Tel (408) 780-0908,
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Genprice Inc, Invoices and accounting
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GENTAUR Poland Sp. z o.o.


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