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Regucalcin (RC) (Gluconolactonase) (GNL) (EC 3.1.1.17) (Senescence marker protein 30) (SMP-30)

 RGN_MOUSE               Reviewed;         299 AA.
Q64374; A2AFC8; Q3UJG3; Q60944;
01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
05-JUL-2017, entry version 126.
RecName: Full=Regucalcin;
Short=RC;
AltName: Full=Gluconolactonase;
Short=GNL;
EC=3.1.1.17;
AltName: Full=Senescence marker protein 30;
Short=SMP-30;
Name=Rgn; Synonyms=Smp30;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], AND TISSUE SPECIFICITY.
STRAIN=C57BL/6J; TISSUE=Liver;
PubMed=8765750; DOI=10.1016/0167-4781(96)00064-4;
Fujita T., Shirasawa T., Maruyama N.;
"Isolation and characterization of genomic and cDNA clones encoding
mouse senescence marker protein-30 (SMP30).";
Biochim. Biophys. Acta 1308:49-57(1996).
[2]
NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, AND INDUCTION.
TISSUE=Liver;
PubMed=9278263; DOI=10.1023/A:1006887929369;
Murata T., Yamaguchi M.;
"Molecular cloning of the cDNA coding for regucalcin and its mRNA
expression in mouse liver: the expression is stimulated by calcium
administration.";
Mol. Cell. Biochem. 173:127-133(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=C57BL/6J; TISSUE=Embryonic liver;
PubMed=16141072; DOI=10.1126/science.1112014;
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M.,
Davis M.J., Wilming L.G., Aidinis V., Allen J.E.,
Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L.,
Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M.,
Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R.,
Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G.,
di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G.,
Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M.,
Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N.,
Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T.,
Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H.,
Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K.,
Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J.,
Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L.,
Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K.,
Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P.,
Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O.,
Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G.,
Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M.,
Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B.,
Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K.,
Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A.,
Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K.,
Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C.,
Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J.,
Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y.,
Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T.,
Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N.,
Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N.,
Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S.,
Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J.,
Hayashizaki Y.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=C57BL/6J;
PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S.,
She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W.,
Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T.,
Zhou S., Teague B., Potamousis K., Churas C., Place M., Herschleb J.,
Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z.,
Lindblad-Toh K., Eichler E.E., Ponting C.P.;
"Lineage-specific biology revealed by a finished genome assembly of
the mouse.";
PLoS Biol. 7:E1000112-E1000112(2009).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=FVB/N; TISSUE=Liver;
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).
[6]
DISRUPTION PHENOTYPE.
PubMed=14975739; DOI=10.1016/j.bbrc.2004.01.091;
Ishigami A., Kondo Y., Nanba R., Ohsawa T., Handa S., Kubo S.,
Akita M., Maruyama N.;
"SMP30 deficiency in mice causes an accumulation of neutral lipids and
phospholipids in the liver and shortens the life span.";
Biochem. Biophys. Res. Commun. 315:575-580(2004).
[7]
DISRUPTION PHENOTYPE, FUNCTION, AND PATHWAY.
PubMed=16585534; DOI=10.1073/pnas.0511225103;
Kondo Y., Inai Y., Sato Y., Handa S., Kubo S., Shimokado K., Goto S.,
Nishikimi M., Maruyama N., Ishigami A.;
"Senescence marker protein 30 functions as gluconolactonase in L-
ascorbic acid biosynthesis, and its knockout mice are prone to
scurvy.";
Proc. Natl. Acad. Sci. U.S.A. 103:5723-5728(2006).
[8]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Kidney, Liver, and Pancreas;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
[9]
SUCCINYLATION [LARGE SCALE ANALYSIS] AT LYS-144; LYS-244 AND LYS-253,
AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=23806337; DOI=10.1016/j.molcel.2013.06.001;
Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z.,
Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.;
"SIRT5-mediated lysine desuccinylation impacts diverse metabolic
pathways.";
Mol. Cell 50:919-930(2013).
[10]
X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE
ANALOGS, CATALYTIC ACTIVITY, FUNCTION, PATHWAY, COFACTOR, ACTIVE SITE,
AND SUBUNIT.
PubMed=23349732; DOI=10.1371/journal.pone.0053706;
Aizawa S., Senda M., Harada A., Maruyama N., Ishida T., Aigaki T.,
Ishigami A., Senda T.;
"Structural basis of the gamma-lactone-ring formation in ascorbic acid
biosynthesis by the senescence marker protein-30/gluconolactonase.";
PLoS ONE 8:E53706-E53706(2013).
-!- FUNCTION: Gluconolactonase with low activity towards other sugar
lactones, including gulonolactone and galactonolactone. Catalyzes
a key step in ascorbic acid (vitamin C) biosynthesis. Can also
hydrolyze diisopropyl phosphorofluoridate and phenylacetate (in
vitro). Calcium-binding protein. Modulates Ca(2+) signaling, and
Ca(2+)-dependent cellular processes and enzyme activities (By
similarity). {ECO:0000250, ECO:0000269|PubMed:16585534,
ECO:0000269|PubMed:23349732}.
-!- CATALYTIC ACTIVITY: D-glucono-1,5-lactone + H(2)O = D-gluconate.
{ECO:0000269|PubMed:23349732}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000250};
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Binds 1 divalent metal cation per subunit. Most active with
Zn(2+) and Mn(2+) ions. The physiological cofactor is most likely
Ca(2+) or Mg(2+). {ECO:0000250};
-!- PATHWAY: Cofactor biosynthesis; L-ascorbate biosynthesis via UDP-
alpha-D-glucuronate pathway; L-ascorbate from UDP-alpha-D-
glucuronate: step 3/4. {ECO:0000269|PubMed:16585534,
ECO:0000269|PubMed:23349732}.
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:23349732}.
-!- SUBCELLULAR LOCATION: Cytoplasm.
-!- TISSUE SPECIFICITY: Mainly present in the liver. Weak expression
was found in the brain, lung and kidney.
{ECO:0000269|PubMed:8765750, ECO:0000269|PubMed:9278263}.
-!- DEVELOPMENTAL STAGE: Protein amounts in liver decrease
significantly with age.
-!- INDUCTION: By calcium. {ECO:0000269|PubMed:9278263}.
-!- DISRUPTION PHENOTYPE: Mice do not thrive after weaning when kept
on a vitamin C-less diet. They develop scurvy, have reduced bone
mineral density and brittle bones. Hepatocytes exhibit
accumulation of lipid droplets. Mice display increased mortality
after about 3 months, and their life span is shorter than normal.
{ECO:0000269|PubMed:14975739, ECO:0000269|PubMed:16585534}.
-!- SIMILARITY: Belongs to the SMP-30/CGR1 family. {ECO:0000305}.
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EMBL; U28937; AAC52721.1; -; mRNA.
EMBL; U32170; AAD03478.1; -; Genomic_DNA.
EMBL; D86217; BAA13046.1; -; mRNA.
EMBL; AK146465; BAE27192.1; -; mRNA.
EMBL; AL672073; CAM21274.1; -; Genomic_DNA.
EMBL; BC012710; AAH12710.1; -; mRNA.
CCDS; CCDS30043.1; -.
PIR; S72173; S72173.
RefSeq; NP_033086.1; NM_009060.2.
RefSeq; XP_006527635.1; XM_006527572.3.
UniGene; Mm.2118; -.
PDB; 4GN7; X-ray; 1.95 A; A/B=1-299.
PDB; 4GN8; X-ray; 1.70 A; A/B=1-299.
PDB; 4GN9; X-ray; 2.00 A; A/B=1-299.
PDB; 4GNA; X-ray; 1.85 A; A/B=1-299.
PDBsum; 4GN7; -.
PDBsum; 4GN8; -.
PDBsum; 4GN9; -.
PDBsum; 4GNA; -.
ProteinModelPortal; Q64374; -.
SMR; Q64374; -.
IntAct; Q64374; 3.
MINT; MINT-1854408; -.
STRING; 10090.ENSMUSP00000023832; -.
iPTMnet; Q64374; -.
PhosphoSitePlus; Q64374; -.
SwissPalm; Q64374; -.
REPRODUCTION-2DPAGE; Q64374; -.
SWISS-2DPAGE; Q64374; -.
MaxQB; Q64374; -.
PaxDb; Q64374; -.
PeptideAtlas; Q64374; -.
PRIDE; Q64374; -.
DNASU; 19733; -.
Ensembl; ENSMUST00000023832; ENSMUSP00000023832; ENSMUSG00000023070.
GeneID; 19733; -.
KEGG; mmu:19733; -.
UCSC; uc009std.1; mouse.
CTD; 9104; -.
MGI; MGI:108024; Rgn.
eggNOG; KOG4499; Eukaryota.
eggNOG; COG3386; LUCA.
GeneTree; ENSGT00390000014995; -.
HOGENOM; HOG000220627; -.
HOVERGEN; HBG004347; -.
InParanoid; Q64374; -.
KO; K01053; -.
OMA; CRWDSLT; -.
OrthoDB; EOG091G131G; -.
PhylomeDB; Q64374; -.
TreeFam; TF323663; -.
UniPathway; UPA00991; UER00938.
PRO; PR:Q64374; -.
Proteomes; UP000000589; Chromosome X.
Bgee; ENSMUSG00000023070; -.
CleanEx; MM_RGN; -.
Genevisible; Q64374; MM.
GO; GO:0005737; C:cytoplasm; IDA:MGI.
GO; GO:0005829; C:cytosol; IEA:Ensembl.
GO; GO:0005576; C:extracellular region; IBA:GO_Central.
GO; GO:0005634; C:nucleus; IDA:MGI.
GO; GO:0005509; F:calcium ion binding; ISS:UniProtKB.
GO; GO:0030234; F:enzyme regulator activity; IEA:InterPro.
GO; GO:0004341; F:gluconolactonase activity; IDA:UniProtKB.
GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
GO; GO:0007568; P:aging; IEA:Ensembl.
GO; GO:0006874; P:cellular calcium ion homeostasis; ISS:UniProtKB.
GO; GO:0001822; P:kidney development; IEA:Ensembl.
GO; GO:0019853; P:L-ascorbic acid biosynthetic process; IDA:UniProtKB.
GO; GO:0097421; P:liver regeneration; IEA:Ensembl.
GO; GO:0043066; P:negative regulation of apoptotic process; IEA:Ensembl.
GO; GO:1903011; P:negative regulation of bone development; IEA:Ensembl.
GO; GO:1903611; P:negative regulation of calcium-dependent ATPase activity; IEA:Ensembl.
GO; GO:0051344; P:negative regulation of cyclic-nucleotide phosphodiesterase activity; IEA:Ensembl.
GO; GO:2000279; P:negative regulation of DNA biosynthetic process; IEA:Ensembl.
GO; GO:1903625; P:negative regulation of DNA catabolic process; IEA:Ensembl.
GO; GO:0050680; P:negative regulation of epithelial cell proliferation; IEA:Ensembl.
GO; GO:1901318; P:negative regulation of flagellated sperm motility; IEA:Ensembl.
GO; GO:0034260; P:negative regulation of GTPase activity; IEA:Ensembl.
GO; GO:1903634; P:negative regulation of leucine-tRNA ligase activity; IEA:Ensembl.
GO; GO:0045019; P:negative regulation of nitric oxide biosynthetic process; IEA:Ensembl.
GO; GO:0032515; P:negative regulation of phosphoprotein phosphatase activity; IEA:Ensembl.
GO; GO:0006469; P:negative regulation of protein kinase activity; IEA:Ensembl.
GO; GO:1902679; P:negative regulation of RNA biosynthetic process; IEA:Ensembl.
GO; GO:0032781; P:positive regulation of ATPase activity; ISS:UniProtKB.
GO; GO:1901896; P:positive regulation of calcium-transporting ATPase activity; IEA:Ensembl.
GO; GO:1903629; P:positive regulation of dUTP diphosphatase activity; IEA:Ensembl.
GO; GO:0045723; P:positive regulation of fatty acid biosynthetic process; IEA:Ensembl.
GO; GO:0010907; P:positive regulation of glucose metabolic process; IEA:Ensembl.
GO; GO:0043547; P:positive regulation of GTPase activity; IEA:Ensembl.
GO; GO:0010922; P:positive regulation of phosphatase activity; IEA:Ensembl.
GO; GO:1903052; P:positive regulation of proteolysis involved in cellular protein catabolic process; IEA:Ensembl.
GO; GO:1901671; P:positive regulation of superoxide dismutase activity; IEA:Ensembl.
GO; GO:0010867; P:positive regulation of triglyceride biosynthetic process; IEA:Ensembl.
GO; GO:0050848; P:regulation of calcium-mediated signaling; ISS:UniProtKB.
GO; GO:0007283; P:spermatogenesis; IEA:Ensembl.
Gene3D; 2.120.10.30; -; 1.
InterPro; IPR011042; 6-blade_b-propeller_TolB-like.
InterPro; IPR008367; Regucalcin.
InterPro; IPR013658; SGL.
InterPro; IPR005511; SMP-30.
Pfam; PF08450; SGL; 1.
PRINTS; PR01791; REGUCALCIN.
PRINTS; PR01790; SMP30FAMILY.
1: Evidence at protein level;
3D-structure; Ascorbate biosynthesis; Calcium; Complete proteome;
Cytoplasm; Hydrolase; Metal-binding; Reference proteome.
CHAIN 1 299 Regucalcin.
/FTId=PRO_0000173047.
ACT_SITE 204 204 Proton donor/acceptor.
{ECO:0000305|PubMed:23349732}.
METAL 18 18 Divalent metal cation.
METAL 154 154 Divalent metal cation.
METAL 204 204 Divalent metal cation.
BINDING 101 101 Substrate.
BINDING 103 103 Substrate.
BINDING 121 121 Substrate.
MOD_RES 144 144 N6-succinyllysine.
{ECO:0000244|PubMed:23806337}.
MOD_RES 244 244 N6-succinyllysine.
{ECO:0000244|PubMed:23806337}.
MOD_RES 253 253 N6-succinyllysine.
{ECO:0000244|PubMed:23806337}.
CONFLICT 201 201 Q -> R (in Ref. 3; BAE27192).
{ECO:0000305}.
CONFLICT 236 236 Q -> P (in Ref. 3; BAE27192).
{ECO:0000305}.
STRAND 5 10 {ECO:0000244|PDB:4GN8}.
STRAND 15 23 {ECO:0000244|PDB:4GN8}.
TURN 24 27 {ECO:0000244|PDB:4GN8}.
STRAND 28 33 {ECO:0000244|PDB:4GN8}.
TURN 34 37 {ECO:0000244|PDB:4GN8}.
STRAND 38 43 {ECO:0000244|PDB:4GN8}.
TURN 44 47 {ECO:0000244|PDB:4GN8}.
STRAND 48 53 {ECO:0000244|PDB:4GN8}.
STRAND 58 64 {ECO:0000244|PDB:4GN8}.
STRAND 67 73 {ECO:0000244|PDB:4GN8}.
STRAND 76 81 {ECO:0000244|PDB:4GN8}.
TURN 82 85 {ECO:0000244|PDB:4GN8}.
STRAND 86 92 {ECO:0000244|PDB:4GN8}.
STRAND 98 107 {ECO:0000244|PDB:4GN8}.
STRAND 113 119 {ECO:0000244|PDB:4GN8}.
STRAND 132 137 {ECO:0000244|PDB:4GN8}.
STRAND 143 158 {ECO:0000244|PDB:4GN8}.
STRAND 164 169 {ECO:0000244|PDB:4GN8}.
HELIX 170 172 {ECO:0000244|PDB:4GN8}.
STRAND 174 181 {ECO:0000244|PDB:4GN8}.
TURN 182 185 {ECO:0000244|PDB:4GN8}.
STRAND 186 195 {ECO:0000244|PDB:4GN8}.
HELIX 198 200 {ECO:0000244|PDB:4GN8}.
STRAND 202 209 {ECO:0000244|PDB:4GN8}.
STRAND 214 219 {ECO:0000244|PDB:4GN8}.
TURN 220 222 {ECO:0000244|PDB:4GN8}.
STRAND 223 227 {ECO:0000244|PDB:4GN8}.
TURN 229 231 {ECO:0000244|PDB:4GN8}.
STRAND 234 239 {ECO:0000244|PDB:4GN8}.
STRAND 245 252 {ECO:0000244|PDB:4GN8}.
HELIX 253 255 {ECO:0000244|PDB:4GN8}.
STRAND 257 263 {ECO:0000244|PDB:4GN8}.
HELIX 269 274 {ECO:0000244|PDB:4GN8}.
TURN 276 279 {ECO:0000244|PDB:4GN8}.
STRAND 281 285 {ECO:0000244|PDB:4GN8}.
SEQUENCE 299 AA; 33407 MW; DAD55EF618311977 CRC64;
MSSIKVECVL RENYRCGESP VWEEASQSLL FVDIPSKIIC RWDTVSNQVQ RVAVDAPVSS
VALRQLGGYV ATIGTKFCAL NWENQSVFVL AMVDEDKKNN RFNDGKVDPA GRYFAGTMAE
ETAPAVLERH QGSLYSLFPD HSVKKYFDQV DISNGLDWSL DHKIFYYIDS LSYTVDAFDY
DLQTGQISNR RIVYKMEKDE QIPDGMCIDA EGKLWVACYN GGRVIRLDPE TGKRLQTVKL
PVDKTTSCCF GGKDYSEMYV TCARDGLNAE GLLRQPDAGN IFKITGLGVK GIAPYSYAG


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