ID   IMPA3_HUMAN             Reviewed;         359 AA.
AC   Q9NX62; Q6NVY7;
DT   29-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   27-MAR-2024, entry version 175.
DE   RecName: Full=Golgi-resident adenosine 3',5'-bisphosphate 3'-phosphatase {ECO:0000250|UniProtKB:Q80V26};
DE            Short=Golgi-resident PAP phosphatase {ECO:0000250|UniProtKB:Q80V26};
DE            Short=gPAPP {ECO:0000250|UniProtKB:Q80V26};
DE            EC=3.1.3.7 {ECO:0000250|UniProtKB:Q80V26};
DE   AltName: Full=3'(2'), 5'-bisphosphate nucleotidase 2 {ECO:0000312|HGNC:HGNC:26019};
DE   AltName: Full=Inositol monophosphatase domain-containing protein 1 {ECO:0000250|UniProtKB:Q80V26};
DE   AltName: Full=Myo-inositol monophosphatase A3 {ECO:0000303|Ref.1};
DE   AltName: Full=Phosphoadenosine phosphate 3'-nucleotidase {ECO:0000250|UniProtKB:Q80V26};
GN   Name=BPNT2 {ECO:0000312|HGNC:HGNC:26019}; Synonyms=IMPA3, IMPAD1;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RA   Parthasarathy L., Parthasarathy R.;
RT   "Molecular cloning and expression of human myo-inositol monophosphatase A3
RT   cDNA (IMPA3).";
RL   Submitted (APR-2001) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=14702039; DOI=10.1038/ng1285;
RA   Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA   Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA   Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA   Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA   Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA   Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA   Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA   Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA   Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA   Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA   Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA   Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA   Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA   Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA   Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA   Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA   Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA   Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA   Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA   Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA   Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA   Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA   Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA   Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA   Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA   Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA   Isogai T., Sugano S.;
RT   "Complete sequencing and characterization of 21,243 full-length human
RT   cDNAs.";
RL   Nat. Genet. 36:40-45(2004).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Skin, and Testis;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [4]
RP   SUBCELLULAR LOCATION, AND GLYCOSYLATION.
RX   PubMed=18695242; DOI=10.1073/pnas.0801182105;
RA   Frederick J.P., Tafari A.T., Wu S.M., Megosh L.C., Chiou S.T., Irving R.P.,
RA   York J.D.;
RT   "A role for a lithium-inhibited Golgi nucleotidase in skeletal development
RT   and sulfation.";
RL   Proc. Natl. Acad. Sci. U.S.A. 105:11605-11612(2008).
RN   [5]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA   Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA   Bennett K.L., Superti-Furga G., Colinge J.;
RT   "Initial characterization of the human central proteome.";
RL   BMC Syst. Biol. 5:17-17(2011).
RN   [6]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA   Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA   Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA   Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT   "N-terminal acetylome analyses and functional insights of the N-terminal
RT   acetyltransferase NatB.";
RL   Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN   [7]
RP   ACETYLATION AT MET-1.
RX   PubMed=25732826; DOI=10.1016/j.celrep.2015.01.053;
RA   Aksnes H., Van Damme P., Goris M., Starheim K.K., Marie M., Stoeve S.I.,
RA   Hoel C., Kalvik T.V., Hole K., Glomnes N., Furnes C., Ljostveit S.,
RA   Ziegler M., Niere M., Gevaert K., Arnesen T.;
RT   "An organellar nalpha-acetyltransferase, naa60, acetylates cytosolic N
RT   termini of transmembrane proteins and maintains Golgi integrity.";
RL   Cell Rep. 10:1362-1374(2015).
RN   [8]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=25944712; DOI=10.1002/pmic.201400617;
RA   Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA   Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT   "N-terminome analysis of the human mitochondrial proteome.";
RL   Proteomics 15:2519-2524(2015).
RN   [9]
RP   VARIANTS CDP-GPAPP ASN-177 AND PRO-183.
RX   PubMed=21549340; DOI=10.1016/j.ajhg.2011.04.002;
RA   Vissers L.E., Lausch E., Unger S., Campos-Xavier A.B., Gilissen C.,
RA   Rossi A., Del Rosario M., Venselaar H., Knoll U., Nampoothiri S., Nair M.,
RA   Spranger J., Brunner H.G., Bonafe L., Veltman J.A., Zabel B.,
RA   Superti-Furga A.;
RT   "Chondrodysplasia and abnormal joint development associated with mutations
RT   in IMPAD1, encoding the Golgi-resident nucleotide phosphatase, gPAPP.";
RL   Am. J. Hum. Genet. 88:608-615(2011).
CC   -!- FUNCTION: Exhibits 3'-nucleotidase activity toward adenosine 3',5'-
CC       bisphosphate (PAP), namely hydrolyzes adenosine 3',5'-bisphosphate into
CC       adenosine 5'-monophosphate (AMP) and a phosphate. May play a role in
CC       the formation of skeletal elements derived through endochondral
CC       ossification, possibly by clearing adenosine 3',5'-bisphosphate
CC       produced by Golgi sulfotransferases during glycosaminoglycan sulfation.
CC       Has no activity toward 3'-phosphoadenosine 5'-phosphosulfate (PAPS) or
CC       inositol phosphate (IP) substrates including I(1)P, I(1,4)P2,
CC       I(1,3,4)P3, I(1,4,5)P3 and I(1,3,4,5)P4.
CC       {ECO:0000250|UniProtKB:Q80V26}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=adenosine 3',5'-bisphosphate + H2O = AMP + phosphate;
CC         Xref=Rhea:RHEA:10040, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:58343, ChEBI:CHEBI:456215; EC=3.1.3.7;
CC         Evidence={ECO:0000250|UniProtKB:Q80V26};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC   -!- ACTIVITY REGULATION: Strongly inhibited by lithium.
CC       {ECO:0000250|UniProtKB:Q80V26}.
CC   -!- PATHWAY: Sulfur metabolism. {ECO:0000250|UniProtKB:Q80V26}.
CC   -!- SUBCELLULAR LOCATION: Golgi apparatus {ECO:0000269|PubMed:18695242}.
CC       Golgi apparatus, trans-Golgi network membrane
CC       {ECO:0000269|PubMed:18695242}; Single-pass type II membrane protein
CC       {ECO:0000255, ECO:0000269|PubMed:18695242}. Note=The catalytic core is
CC       predicted to reside within the Golgi lumen.
CC       {ECO:0000269|PubMed:18695242}.
CC   -!- PTM: Contains N-linked glycan resistant to endoglycosydase H.
CC       {ECO:0000269|PubMed:18695242}.
CC   -!- DISEASE: Chondrodysplasia with joint dislocations, GPAPP type (CDP-
CC       GPAPP) [MIM:614078]: A condition consisting of congenital joint
CC       dislocations, chondrodysplasia with short stature, micrognathia and
CC       cleft palate, and a distinctive face. {ECO:0000269|PubMed:21549340}.
CC       Note=The disease is caused by variants affecting the gene represented
CC       in this entry.
CC   -!- SIMILARITY: Belongs to the inositol monophosphatase superfamily.
CC       {ECO:0000305}.
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DR   EMBL; AK000428; BAA91158.1; -; mRNA.
DR   EMBL; AY032885; AAK52336.1; -; mRNA.
DR   EMBL; BC017797; AAH17797.1; -; mRNA.
DR   EMBL; BC067814; AAH67814.1; -; mRNA.
DR   CCDS; CCDS6169.1; -.
DR   RefSeq; NP_060283.3; NM_017813.4.
DR   AlphaFoldDB; Q9NX62; -.
DR   SMR; Q9NX62; -.
DR   BioGRID; 120268; 50.
DR   IntAct; Q9NX62; 20.
DR   MINT; Q9NX62; -.
DR   STRING; 9606.ENSP00000262644; -.
DR   DEPOD; IMPAD1; -.
DR   GlyConnect; 1400; 14 N-Linked glycans (1 site).
DR   GlyCosmos; Q9NX62; 2 sites, 14 glycans.
DR   GlyGen; Q9NX62; 4 sites, 13 N-linked glycans (1 site), 2 O-linked glycans (3 sites).
DR   iPTMnet; Q9NX62; -.
DR   MetOSite; Q9NX62; -.
DR   PhosphoSitePlus; Q9NX62; -.
DR   SwissPalm; Q9NX62; -.
DR   BioMuta; IMPAD1; -.
DR   DMDM; 74734687; -.
DR   EPD; Q9NX62; -.
DR   jPOST; Q9NX62; -.
DR   MassIVE; Q9NX62; -.
DR   MaxQB; Q9NX62; -.
DR   PaxDb; 9606-ENSP00000262644; -.
DR   PeptideAtlas; Q9NX62; -.
DR   ProteomicsDB; 83047; -.
DR   Pumba; Q9NX62; -.
DR   Antibodypedia; 2290; 114 antibodies from 23 providers.
DR   DNASU; 54928; -.
DR   Ensembl; ENST00000262644.9; ENSP00000262644.4; ENSG00000104331.9.
DR   GeneID; 54928; -.
DR   KEGG; hsa:54928; -.
DR   MANE-Select; ENST00000262644.9; ENSP00000262644.4; NM_017813.5; NP_060283.3.
DR   UCSC; uc003xte.5; human.
DR   AGR; HGNC:26019; -.
DR   CTD; 54928; -.
DR   DisGeNET; 54928; -.
DR   GeneCards; BPNT2; -.
DR   HGNC; HGNC:26019; BPNT2.
DR   HPA; ENSG00000104331; Low tissue specificity.
DR   MalaCards; BPNT2; -.
DR   MIM; 614010; gene.
DR   MIM; 614078; phenotype.
DR   neXtProt; NX_Q9NX62; -.
DR   OpenTargets; ENSG00000104331; -.
DR   Orphanet; 280586; Chondrodysplasia with joint dislocations, gPAPP type.
DR   VEuPathDB; HostDB:ENSG00000104331; -.
DR   eggNOG; KOG3853; Eukaryota.
DR   GeneTree; ENSGT00940000160216; -.
DR   HOGENOM; CLU_034742_0_0_1; -.
DR   InParanoid; Q9NX62; -.
DR   OMA; MKSHEAI; -.
DR   OrthoDB; 3665671at2759; -.
DR   PhylomeDB; Q9NX62; -.
DR   TreeFam; TF314300; -.
DR   BioCyc; MetaCyc:HS02567-MONOMER; -.
DR   PathwayCommons; Q9NX62; -.
DR   Reactome; R-HSA-156584; Cytosolic sulfonation of small molecules.
DR   SignaLink; Q9NX62; -.
DR   BioGRID-ORCS; 54928; 23 hits in 1153 CRISPR screens.
DR   ChiTaRS; IMPAD1; human.
DR   GenomeRNAi; 54928; -.
DR   Pharos; Q9NX62; Tbio.
DR   PRO; PR:Q9NX62; -.
DR   Proteomes; UP000005640; Chromosome 8.
DR   RNAct; Q9NX62; Protein.
DR   Bgee; ENSG00000104331; Expressed in medial globus pallidus and 204 other cell types or tissues.
DR   ExpressionAtlas; Q9NX62; baseline and differential.
DR   GO; GO:0005829; C:cytosol; IDA:HPA.
DR   GO; GO:0012505; C:endomembrane system; IBA:GO_Central.
DR   GO; GO:0005794; C:Golgi apparatus; IDA:MGI.
DR   GO; GO:0005796; C:Golgi lumen; TAS:Reactome.
DR   GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR   GO; GO:0016604; C:nuclear body; IDA:HPA.
DR   GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR   GO; GO:0032588; C:trans-Golgi network membrane; ISS:UniProtKB.
DR   GO; GO:0008441; F:3'(2'),5'-bisphosphate nucleotidase activity; IEA:UniProtKB-EC.
DR   GO; GO:0097657; F:3',5'-nucleotide bisphosphate phosphatase activity; ISS:UniProtKB.
DR   GO; GO:0008254; F:3'-nucleotidase activity; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0002063; P:chondrocyte development; IEA:Ensembl.
DR   GO; GO:0030204; P:chondroitin sulfate metabolic process; IEA:Ensembl.
DR   GO; GO:0042733; P:embryonic digit morphogenesis; IEA:Ensembl.
DR   GO; GO:0001958; P:endochondral ossification; IEA:Ensembl.
DR   GO; GO:0046854; P:phosphatidylinositol phosphate biosynthetic process; IEA:InterPro.
DR   GO; GO:0009791; P:post-embryonic development; IEA:Ensembl.
DR   GO; GO:0001501; P:skeletal system development; IBA:GO_Central.
DR   CDD; cd01640; IPPase; 1.
DR   Gene3D; 3.40.190.80; -; 1.
DR   Gene3D; 3.30.540.10; Fructose-1,6-Bisphosphatase, subunit A, domain 1; 1.
DR   InterPro; IPR000760; Inositol_monophosphatase-like.
DR   InterPro; IPR020550; Inositol_monophosphatase_CS.
DR   PANTHER; PTHR43028; 3'(2'),5'-BISPHOSPHATE NUCLEOTIDASE 1; 1.
DR   PANTHER; PTHR43028:SF6; GOLGI-RESIDENT ADENOSINE 3',5'-BISPHOSPHATE 3'-PHOSPHATASE; 1.
DR   Pfam; PF00459; Inositol_P; 1.
DR   SUPFAM; SSF56655; Carbohydrate phosphatase; 1.
DR   PROSITE; PS00630; IMP_2; 1.
DR   Genevisible; Q9NX62; HS.
PE   1: Evidence at protein level;
KW   Acetylation; Disease variant; Glycoprotein; Golgi apparatus; Hydrolase;
KW   Magnesium; Membrane; Metal-binding; Reference proteome; Signal-anchor;
KW   Transmembrane; Transmembrane helix.
FT   CHAIN           1..359
FT                   /note="Golgi-resident adenosine 3',5'-bisphosphate 3'-
FT                   phosphatase"
FT                   /id="PRO_0000289041"
FT   TOPO_DOM        1..12
FT                   /note="Cytoplasmic"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        13..33
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TOPO_DOM        34..359
FT                   /note="Lumenal"
FT                   /evidence="ECO:0000255"
FT   REGION          86..106
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        110
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   ACT_SITE        179
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         133
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         133
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         174
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         174
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         176
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         177
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         242
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         245
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         268
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         272
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   BINDING         300
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:Q9Z1N4"
FT   MOD_RES         1
FT                   /note="N-acetylmethionine"
FT                   /evidence="ECO:0000269|PubMed:25732826"
FT   CARBOHYD        259
FT                   /note="N-linked (GlcNAc...) asparagine"
FT                   /evidence="ECO:0000305|PubMed:18695242"
FT   VARIANT         177
FT                   /note="D -> N (in CDP-GPAPP; dbSNP:rs387907101)"
FT                   /evidence="ECO:0000269|PubMed:21549340"
FT                   /id="VAR_065847"
FT   VARIANT         183
FT                   /note="T -> P (in CDP-GPAPP; dbSNP:rs387907102)"
FT                   /evidence="ECO:0000269|PubMed:21549340"
FT                   /id="VAR_065848"
FT   CONFLICT        51
FT                   /note="G -> E (in Ref. 3; AAH67814)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        123
FT                   /note="T -> A (in Ref. 3; AAH67814)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        156
FT                   /note="K -> E (in Ref. 3; AAH67814)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   359 AA;  38681 MW;  4818E989A9684847 CRC64;
     MAPMGIRLSP LGVAVFCLLG LGVLYHLYSG FLAGRFSLFG LGGEPGGGAA GPAAAADGGT
     VDLREMLAVS VLAAVRGGDE VRRVRESNVL HEKSKGKTRE GAEDKMTSGD VLSNRKMFYL
     LKTAFPSVQI NTEEHVDAAD QEVILWDHKI PEDILKEVTT PKEVPAESVT VWIDPLDATQ
     EYTEDLRKYV TTMVCVAVNG KPMLGVIHKP FSEYTAWAMV DGGSNVKARS SYNEKTPRIV
     VSRSHSGMVK QVALQTFGNQ TTIIPAGGAG YKVLALLDVP DKSQEKADLY IHVTYIKKWD
     ICAGNAILKA LGGHMTTLSG EEISYTGSDG IEGGLLASIR MNHQALVRKL PDLEKTGHK
//