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Hydroxymethylglutaryl-CoA lyase, mitochondrial (HL) (HMG-CoA lyase) (EC 4.1.3.4) (3-hydroxy-3-methylglutarate-CoA lyase)

 HMGCL_HUMAN             Reviewed;         325 AA.
P35914; B4DUP4; B7UCC6; D3Y5K7; Q6IBC0; Q96FP8;
01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
25-OCT-2002, sequence version 2.
28-FEB-2018, entry version 176.
RecName: Full=Hydroxymethylglutaryl-CoA lyase, mitochondrial;
Short=HL;
Short=HMG-CoA lyase;
EC=4.1.3.4;
AltName: Full=3-hydroxy-3-methylglutarate-CoA lyase;
Flags: Precursor;
Name=HMGCL;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
TISSUE=Liver;
PubMed=8440722;
Mitchell G.A., Robert M.-F., Hruz P.W., Wang S., Fontaine G.,
Behnke C.E., Mende-Mueller L.M., Schappert K., Lee C., Gibson K.M.,
Miziorko H.M.;
"3-hydroxy-3-methylglutaryl coenzyme A lyase (HL). Cloning of human
and chicken liver HL cDNAs and characterization of a mutation causing
human HL deficiency.";
J. Biol. Chem. 268:4376-4381(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
Phelan M., Farmer A.;
"Cloning of human full-length CDSs in BD Creator(TM) system donor
vector.";
Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
TISSUE=Skeletal muscle, and Testis;
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).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16710414; DOI=10.1038/nature04727;
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D.,
Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A.,
Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F.,
McDonald L., Evans R., Phillips K., Atkinson A., Cooper R., Jones C.,
Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P.,
Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K.,
Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G.,
Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D.,
Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G.,
Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J.,
Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R.,
Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D.,
Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G.,
Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M.,
Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J.,
Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M.,
Loveland J., Lovell J., Lush M.J., Lyne R., Martin S.,
Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S.,
Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C.,
Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z.,
Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E.,
Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A.,
Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R.,
Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V.,
Beck S., Rogers J., Bentley D.R.;
"The DNA sequence and biological annotation of human chromosome 1.";
Nature 441:315-321(2006).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton 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.
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Brain;
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).
[8]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 21-325 (ISOFORM 1).
PubMed=8617516; DOI=10.1006/geno.1996.0164;
Wang S.P., Robert M.-F., Gibson K.M., Wanders R.J.A., Mitchell G.A.;
"3-hydroxy-3-methylglutaryl CoA lyase (HL): mouse and human HL gene
(HMGCL) cloning and detection of large gene deletions in two unrelated
HL-deficient patients.";
Genomics 33:99-104(1996).
[9]
NUCLEOTIDE SEQUENCE [MRNA] OF 60-277 (ISOFORMS 2 AND 3), ALTERNATIVE
SPLICING, AND TISSUE SPECIFICITY.
TISSUE=Skeletal muscle;
PubMed=21952825; DOI=10.1007/s11033-011-1270-8;
Puisac B., Ramos M., Arnedo M., Menao S., Gil-Rodriguez M.C.,
Teresa-Rodrigo M.E., Pie A., de Karam J.C., Wesselink J.J.,
Gimenez I., Ramos F.J., Casals N., Gomez-Puertas P., Hegardt F.G.,
Pie J.;
"Characterization of splice variants of the genes encoding human
mitochondrial HMG-CoA lyase and HMG-CoA synthase, the main enzymes of
the ketogenesis pathway.";
Mol. Biol. Rep. 39:4777-4785(2012).
[10]
SUBCELLULAR LOCATION.
PubMed=7527399;
Ashmarina L.I., Rusnak N., Miziorko H.M., Mitchell G.A.;
"3-Hydroxy-3-methylglutaryl-CoA lyase is present in mouse and human
liver peroxisomes.";
J. Biol. Chem. 269:31929-31932(1994).
[11]
FUNCTION.
PubMed=8566388; DOI=10.1042/bst023489s;
Holmes H.C., Burns S.P., Chalmers R.A., Bain M.S., Iles R.A.;
"Ketogenic flux from lipids and leucine, assessment in 3-hydroxy-3-
methylglutaryl CoA lyase deficiency.";
Biochem. Soc. Trans. 23:489S-489S(1995).
[12]
SUBUNIT, SUBCELLULAR LOCATION, DISULFIDE BOND, AND MUTAGENESIS OF
CYS-323.
PubMed=12464283; DOI=10.1016/S0003-9861(02)00584-2;
Tuinstra R.L., Burgner J.W. II, Miziorko H.M.;
"Investigation of the oligomeric status of the peroxisomal isoform of
human 3-hydroxy-3-methylglutaryl-CoA lyase.";
Arch. Biochem. Biophys. 408:286-294(2002).
[13]
MUTAGENESIS OF GLU-37; ASP-42; GLU-72; ASP-204; HIS-233; GLU-279 AND
ASP-280, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND ENZYME
REGULATION.
PubMed=12874287; DOI=10.1074/jbc.M304472200;
Tuinstra R.L., Miziorko H.M.;
"Investigation of conserved acidic residues in 3-hydroxy-3-
methylglutaryl-CoA lyase: implications for human disease and for
functional roles in a family of related proteins.";
J. Biol. Chem. 278:37092-37098(2003).
[14]
MUTAGENESIS OF ARG-41; ASP-42 AND HIS-233, AND BIOPHYSICOCHEMICAL
PROPERTIES.
PubMed=15122894; DOI=10.1021/bi0499765;
Tuinstra R.L., Wang C.-Z., Mitchell G.A., Miziorko H.M.;
"Evaluation of 3-hydroxy-3-methylglutaryl-coenzyme A lyase arginine-41
as a catalytic residue: use of acetyldithio-coenzyme A to monitor
product enolization.";
Biochemistry 43:5287-5295(2004).
[15]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-48, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19608861; DOI=10.1126/science.1175371;
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M.,
Walther T.C., Olsen J.V., Mann M.;
"Lysine acetylation targets protein complexes and co-regulates major
cellular functions.";
Science 325:834-840(2009).
[16]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[17]
FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF CYS-323.
PubMed=22865860; DOI=10.1074/jbc.M112.393231;
Montgomery C., Pei Z., Watkins P.A., Miziorko H.M.;
"Identification and characterization of an extramitochondrial human 3-
Hydroxy-3-methylglutaryl-CoA lyase.";
J. Biol. Chem. 287:33227-33236(2012).
[18]
FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=22847177; DOI=10.1194/jlr.M025700;
Arnedo M., Menao S., Puisac B., Teresa-Rodrigo M.E.,
Gil-Rodriguez M.C., Lopez-Vinas E., Gomez-Puertas P., Casals N.,
Casale C.H., Hegardt F.G., Pie J.;
"Characterization of a novel HMG-CoA Lyase enzyme with a dual location
in endoplasmic reticulum and cytosol.";
J. Lipid Res. 53:2046-2056(2012).
[19]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[20]
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).
[21]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25944712; DOI=10.1002/pmic.201400617;
Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M.,
Ayoub D., Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
"N-terminome analysis of the human mitochondrial proteome.";
Proteomics 15:2519-2524(2015).
[22]
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 28-325 IN COMPLEX WITH
MAGNESIUM AND SUBSTRATE ANALOG, AND HOMODIMERIZATION.
PubMed=16330550; DOI=10.1074/jbc.M506880200;
Fu Z., Runquist J.A., Forouhar F., Hussain M., Hunt J.F.,
Miziorko H.M., Kim J.J.;
"Crystal structure of human 3-hydroxy-3-methylglutaryl-CoA Lyase:
insights into catalysis and the molecular basis for
hydroxymethylglutaric aciduria.";
J. Biol. Chem. 281:7526-7532(2006).
[23]
VARIANT HMGCLD ARG-233.
PubMed=8798725; DOI=10.1074/jbc.271.40.24604;
Roberts J., Mitchell G.A., Miziorko H.M.;
"Modeling of a mutation responsible for human 3-hydroxy-3-
methylglutaryl-CoA lyase deficiency implicates histidine-233 as an
active site residue.";
J. Biol. Chem. 271:24604-24609(1996).
[24]
VARIANTS HMGCLD GLN-41; GLU-42; GLY-42 AND HIS-42.
PubMed=9463337; DOI=10.1086/301730;
Mitchell G.A., Ozand P.T., Robert M.-F., Ashmarina L., Roberts J.,
Gibson K.M., Wanders R.J., Wang S., Chevalier I., Ploechl E.,
Miziorko H.;
"HMG CoA lyase deficiency: identification of five causal point
mutations in codons 41 and 42, including a frequent Saudi Arabian
mutation, R41Q.";
Am. J. Hum. Genet. 62:295-300(1998).
[25]
VARIANTS HMGCLD ARG-233 AND PRO-263.
PubMed=9784232; DOI=10.1006/abbi.1998.0788;
Zapater N., Pie J., Lloberas J., Rolland M.O., Leroux B.,
Vidailhet M., Divry P., Hegardt F.G., Casals N.;
"Two missense point mutations in different alleles in the 3-hydroxy-3-
methylglutaryl coenzyme A lyase gene produce 3-hydroxy-3-
methylglutaric aciduria in a French patient.";
Arch. Biochem. Biophys. 358:197-203(1998).
[26]
VARIANT HMGCLD LYS-279.
PubMed=11129331; DOI=10.1007/s004390000363;
Muroi J., Yorifuji T., Uematsu A., Shigematsu Y., Onigata K.,
Maruyama H., Nobutoki T., Kitamura A., Nakahata T.;
"Molecular and clinical analysis of Japanese patients with 3-hydroxy-
3-methylglutaryl CoA lyase (HL) deficiency.";
Hum. Genet. 107:320-326(2000).
[27]
VARIANTS HMGCLD ARG-75; TYR-201 AND ASN-204.
PubMed=12746442; DOI=10.1074/jbc.M304276200;
Casals N., Gomez-Puertas P., Pie J., Mir C., Roca R., Puisac B.,
Aledo R., Clotet J., Menao S., Serra D., Asins G., Till J.,
Elias-Jones A.C., Cresto J.C., Chamoles N.A., Abdenur J.E.,
Mayatepek E., Besley G., Valencia A., Hegardt F.G.;
"Structural (betaalpha)8 TIM barrel model of 3-hydroxy-3-
methylglutaryl-coenzyme A lyase.";
J. Biol. Chem. 278:29016-29023(2003).
[28]
VARIANT HMGCLD GLN-41.
PubMed=17173698; DOI=10.1186/1471-2350-7-86;
Al-Sayed M., Imtiaz F., Alsmadi O.A., Rashed M.S., Meyer B.F.;
"Mutations underlying 3-hydroxy-3-methylglutaryl CoA lyase deficiency
in the Saudi population.";
BMC Med. Genet. 7:86-86(2006).
[29]
VARIANT HMGCLD GLU-203, AND CHARACTERIZATION OF VARIANT HMGCLD
GLU-203.
PubMed=16601870; DOI=10.1007/s10545-006-0138-x;
Mir C., Lopez-Vinas E., Aledo R., Puisac B., Rizzo C.,
Dionisi-Vici C., Deodato F., Pie J., Gomez-Puertas P., Hegardt F.G.,
Casals N.;
"A single-residue mutation, G203E, causes 3-hydroxy-3-methylglutaric
aciduria by occluding the substrate channel in the 3D structural model
of HMG-CoA lyase.";
J. Inherit. Metab. Dis. 29:64-70(2006).
[30]
VARIANT HMGCLD ASN-48, AND CHARACTERIZATION OF VARIANT HMGCLD ASN-48.
PubMed=17459752; DOI=10.1016/j.ymgme.2007.03.007;
Carrasco P., Menao S., Lopez-Vinas E., Santpere G., Clotet J.,
Sierra A.Y., Gratacos E., Puisac B., Gomez-Puertas P., Hegardt F.G.,
Pie J., Casals N.;
"C-terminal end and aminoacid Lys48 in HMG-CoA lyase are involved in
substrate binding and enzyme activity.";
Mol. Genet. Metab. 91:120-127(2007).
[31]
VARIANT HMGCLD GLN-165.
PubMed=19036343; DOI=10.1016/j.cca.2008.11.004;
Lin W.D., Wang C.H., Lai C.C., Tsai Y., Wu J.Y., Chen C.P., Tsai F.J.;
"Molecular analysis of Taiwanese patients with 3-hydroxy-3-
methylglutaryl CoA lyase deficiency.";
Clin. Chim. Acta 401:33-36(2009).
[32]
VARIANTS HMGCLD LYS-37; GLY-42; PHE-142; TYR-174; SER-192; PHE-200 AND
ARG-233, AND CHARACTERIZATION OF VARIANTS HMGCLD LYS-37; PHE-142;
TYR-174; SER-192 AND PHE-200.
PubMed=19177531; DOI=10.1002/humu.20966;
Menao S., Lopez-Vinas E., Mir C., Puisac B., Gratacos E., Arnedo M.,
Carrasco P., Moreno S., Ramos M., Gil M.C., Pie A., Ribes A.,
Perez-Cerda C., Ugarte M., Clayton P.T., Korman S.H., Serra D.,
Asins G., Ramos F.J., Gomez-Puertas P., Hegardt F.G., Casals N.,
Pie J.;
"Ten novel HMGCL mutations in 24 patients of different origin with 3-
hydroxy-3-methyl-glutaric aciduria.";
Hum. Mutat. 30:E520-E529(2009).
-!- FUNCTION: Key enzyme in ketogenesis (ketone body formation).
Terminal step in leucine catabolism. Ketone bodies (beta-
hydroxybutyrate, acetoacetate and acetone) are essential as an
alternative source of energy to glucose, as lipid precursors and
as regulators of metabolism. {ECO:0000269|PubMed:22847177,
ECO:0000269|PubMed:22865860, ECO:0000269|PubMed:8566388}.
-!- CATALYTIC ACTIVITY: (S)-3-hydroxy-3-methylglutaryl-CoA = acetyl-
CoA + acetoacetate. {ECO:0000255|PROSITE-ProRule:PRU10115,
ECO:0000269|PubMed:22847177, ECO:0000269|PubMed:22865860}.
-!- COFACTOR:
Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
Evidence={ECO:0000269|PubMed:12874287};
-!- ENZYME REGULATION: Stimulated by reducing agents such as
dithiothreitol (DTT). {ECO:0000269|PubMed:12874287}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=200 uM for magnesium ion {ECO:0000269|PubMed:12874287,
ECO:0000269|PubMed:15122894};
KM=48 uM for HMG-CoA {ECO:0000269|PubMed:12874287,
ECO:0000269|PubMed:15122894};
Vmax=191 umol/min/mg enzyme {ECO:0000269|PubMed:12874287,
ECO:0000269|PubMed:15122894};
-!- PATHWAY: Metabolic intermediate metabolism; (S)-3-hydroxy-3-
methylglutaryl-CoA degradation; acetoacetate from (S)-3-hydroxy-3-
methylglutaryl-CoA: step 1/1.
-!- SUBUNIT: Homodimer; disulfide-linked. Can also form homotetramers.
{ECO:0000269|PubMed:12464283, ECO:0000269|PubMed:16330550}.
-!- SUBCELLULAR LOCATION: Mitochondrion matrix. Peroxisome.
Note=Unprocessed form is peroxisomal.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Name=1;
IsoId=P35914-1; Sequence=Displayed;
Name=2; Synonyms=HMGCS2delta5,6;
IsoId=P35914-2; Sequence=VSP_047444;
Note=The transcript is not translated, but would result in a
catalytically impaired product if it was.;
Name=3; Synonyms=HMGCS2delta5,6,7;
IsoId=P35914-3; Sequence=VSP_047444, VSP_043788;
Note=Very low expression. The transcript is not translated, but
would result in a catalytically inactive product if it was.;
-!- TISSUE SPECIFICITY: Highest expression in liver. Expressed in
pancreas, kidney, intestine, testis, fibroblasts and lymphoblasts.
Very low expression in brain and skeletal muscle. The relative
expression of isoform 2 (at mRNA level) is highest in heart (30%),
skeletal muscle (22%), and brain (14%).
{ECO:0000269|PubMed:21952825}.
-!- DISEASE: 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD)
[MIM:246450]: An autosomal recessive disease affecting ketogenesis
and L-leucine catabolism. The disease usually appears in the first
year of life after a fasting period and its clinical acute
symptoms include vomiting, seizures, metabolic acidosis,
hypoketotic hypoglycemia and lethargy. These symptoms sometimes
progress to coma, with fatal outcome in some cases.
{ECO:0000269|PubMed:11129331, ECO:0000269|PubMed:12746442,
ECO:0000269|PubMed:16601870, ECO:0000269|PubMed:17173698,
ECO:0000269|PubMed:17459752, ECO:0000269|PubMed:19036343,
ECO:0000269|PubMed:19177531, ECO:0000269|PubMed:8798725,
ECO:0000269|PubMed:9463337, ECO:0000269|PubMed:9784232}. Note=The
disease is caused by mutations affecting the gene represented in
this entry.
-!- SIMILARITY: Belongs to the HMG-CoA lyase family. {ECO:0000305}.
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EMBL; L07033; AAA92733.1; -; mRNA.
EMBL; AK300733; BAG62406.1; -; mRNA.
EMBL; AK313869; BAG36597.1; -; mRNA.
EMBL; BT009792; AAP88794.1; -; mRNA.
EMBL; CR456884; CAG33165.1; -; mRNA.
EMBL; AL031295; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AL590728; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; CH471134; EAW95094.1; -; Genomic_DNA.
EMBL; BC010570; AAH10570.1; -; mRNA.
EMBL; AH003700; AAB19099.1; -; Genomic_DNA.
EMBL; FJ472654; ACK58684.1; -; mRNA.
EMBL; GU433941; ADD21697.1; -; mRNA.
CCDS; CCDS243.1; -. [P35914-1]
CCDS; CCDS53279.1; -. [P35914-2]
PIR; A45470; A45470.
RefSeq; NP_000182.2; NM_000191.2. [P35914-1]
RefSeq; NP_001159531.1; NM_001166059.1. [P35914-2]
UniGene; Hs.533444; -.
PDB; 2CW6; X-ray; 2.10 A; A/B/C/D/E/F=28-325.
PDB; 3MP3; X-ray; 2.40 A; A/B/C/D/E/F=28-325.
PDB; 3MP4; X-ray; 2.20 A; A/B/C/D/E/F=28-325.
PDB; 3MP5; X-ray; 2.25 A; A/B/C/D/E/F=28-325.
PDBsum; 2CW6; -.
PDBsum; 3MP3; -.
PDBsum; 3MP4; -.
PDBsum; 3MP5; -.
ProteinModelPortal; P35914; -.
SMR; P35914; -.
BioGrid; 109398; 24.
IntAct; P35914; 10.
MINT; P35914; -.
STRING; 9606.ENSP00000363614; -.
DrugBank; DB04594; 3-hydroxyglutaric acid.
SwissLipids; SLP:000001292; -. [P35914-1]
iPTMnet; P35914; -.
PhosphoSitePlus; P35914; -.
BioMuta; HMGCL; -.
DMDM; 24418852; -.
EPD; P35914; -.
PaxDb; P35914; -.
PeptideAtlas; P35914; -.
PRIDE; P35914; -.
DNASU; 3155; -.
Ensembl; ENST00000374490; ENSP00000363614; ENSG00000117305. [P35914-1]
Ensembl; ENST00000436439; ENSP00000389281; ENSG00000117305. [P35914-2]
GeneID; 3155; -.
KEGG; hsa:3155; -.
UCSC; uc001bib.4; human. [P35914-1]
CTD; 3155; -.
DisGeNET; 3155; -.
EuPathDB; HostDB:ENSG00000117305.14; -.
GeneCards; HMGCL; -.
HGNC; HGNC:5005; HMGCL.
HPA; HPA004727; -.
MalaCards; HMGCL; -.
MIM; 246450; phenotype.
MIM; 613898; gene.
neXtProt; NX_P35914; -.
OpenTargets; ENSG00000117305; -.
Orphanet; 20; 3-hydroxy-3-methylglutaric aciduria.
PharmGKB; PA29336; -.
eggNOG; KOG2368; Eukaryota.
eggNOG; COG0119; LUCA.
GeneTree; ENSGT00390000017690; -.
HOGENOM; HOG000219757; -.
HOVERGEN; HBG064656; -.
InParanoid; P35914; -.
KO; K01640; -.
OMA; FGGCPMA; -.
OrthoDB; EOG091G0DA9; -.
PhylomeDB; P35914; -.
TreeFam; TF105363; -.
BioCyc; MetaCyc:HS04116-MONOMER; -.
BRENDA; 4.1.3.4; 2681.
Reactome; R-HSA-77111; Synthesis of Ketone Bodies.
SABIO-RK; P35914; -.
UniPathway; UPA00896; UER00863.
ChiTaRS; HMGCL; human.
EvolutionaryTrace; P35914; -.
GenomeRNAi; 3155; -.
PRO; PR:P35914; -.
Proteomes; UP000005640; Chromosome 1.
Bgee; ENSG00000117305; -.
CleanEx; HS_HMGCL; -.
ExpressionAtlas; P35914; baseline and differential.
Genevisible; P35914; HS.
GO; GO:0005743; C:mitochondrial inner membrane; IEA:Ensembl.
GO; GO:0005759; C:mitochondrial matrix; TAS:Reactome.
GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
GO; GO:0005777; C:peroxisome; IDA:UniProtKB.
GO; GO:0031406; F:carboxylic acid binding; IEA:Ensembl.
GO; GO:0000062; F:fatty-acyl-CoA binding; IEA:Ensembl.
GO; GO:0004419; F:hydroxymethylglutaryl-CoA lyase activity; IDA:UniProtKB.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IDA:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0005102; F:receptor binding; IPI:UniProtKB.
GO; GO:0006637; P:acyl-CoA metabolic process; IEA:Ensembl.
GO; GO:0046951; P:ketone body biosynthetic process; IDA:UniProtKB.
GO; GO:0006552; P:leucine catabolic process; TAS:BHF-UCL.
GO; GO:0006629; P:lipid metabolic process; IDA:BHF-UCL.
GO; GO:0001889; P:liver development; IEA:Ensembl.
GO; GO:0007005; P:mitochondrion organization; IEA:Ensembl.
GO; GO:0051262; P:protein tetramerization; IDA:UniProtKB.
GO; GO:0070542; P:response to fatty acid; IEA:Ensembl.
GO; GO:0007584; P:response to nutrient; IEA:Ensembl.
GO; GO:0042594; P:response to starvation; IEA:Ensembl.
Gene3D; 3.20.20.70; -; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR000138; HMG_CoA_lyase_AS.
InterPro; IPR000891; PYR_CT.
Pfam; PF00682; HMGL-like; 1.
PROSITE; PS01062; HMG_COA_LYASE; 1.
PROSITE; PS50991; PYR_CT; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Alternative splicing; Complete proteome;
Disease mutation; Disulfide bond; Lyase; Metal-binding; Mitochondrion;
Peroxisome; Reference proteome; Transit peptide.
TRANSIT 1 27 Mitochondrion.
CHAIN 28 325 Hydroxymethylglutaryl-CoA lyase,
mitochondrial.
/FTId=PRO_0000013478.
DOMAIN 33 300 Pyruvate carboxyltransferase.
{ECO:0000255|PROSITE-ProRule:PRU01151}.
MOTIF 323 325 Microbody targeting signal.
{ECO:0000255}.
ACT_SITE 266 266 {ECO:0000255|PROSITE-ProRule:PRU10115}.
METAL 42 42 Divalent metal cation.
METAL 233 233 Divalent metal cation.
METAL 235 235 Divalent metal cation.
METAL 275 275 Divalent metal cation.
BINDING 41 41 Substrate.
MOD_RES 48 48 N6-acetyllysine; alternate.
{ECO:0000244|PubMed:19608861}.
MOD_RES 48 48 N6-succinyllysine; alternate.
{ECO:0000250|UniProtKB:P38060}.
MOD_RES 111 111 N6-acetyllysine.
{ECO:0000250|UniProtKB:P38060}.
MOD_RES 137 137 N6-acetyllysine; alternate.
{ECO:0000250|UniProtKB:P38060}.
MOD_RES 137 137 N6-succinyllysine; alternate.
{ECO:0000250|UniProtKB:P38060}.
MOD_RES 179 179 N6-acetyllysine; alternate.
{ECO:0000250|UniProtKB:P38060}.
MOD_RES 179 179 N6-succinyllysine; alternate.
{ECO:0000250|UniProtKB:P38060}.
MOD_RES 324 324 N6-acetyllysine.
{ECO:0000250|UniProtKB:P38060}.
DISULFID 323 323 Interchain.
{ECO:0000269|PubMed:12464283}.
VAR_SEQ 117 187 Missing (in isoform 2 and isoform 3).
{ECO:0000303|PubMed:14702039,
ECO:0000303|PubMed:21952825}.
/FTId=VSP_047444.
VAR_SEQ 188 250 Missing (in isoform 3).
{ECO:0000303|PubMed:21952825}.
/FTId=VSP_043788.
VARIANT 37 37 E -> K (in HMGCLD; activity lower than 5%
respect to the wild-type).
{ECO:0000269|PubMed:19177531}.
/FTId=VAR_058440.
VARIANT 41 41 R -> Q (in HMGCLD; loss of activity and
of proton exchange; dbSNP:rs121964997).
{ECO:0000269|PubMed:17173698,
ECO:0000269|PubMed:9463337}.
/FTId=VAR_003744.
VARIANT 42 42 D -> E (in HMGCLD; reduced activity).
{ECO:0000269|PubMed:9463337}.
/FTId=VAR_003745.
VARIANT 42 42 D -> G (in HMGCLD; loss of activity).
{ECO:0000269|PubMed:19177531,
ECO:0000269|PubMed:9463337}.
/FTId=VAR_003746.
VARIANT 42 42 D -> H (in HMGCLD; loss of activity).
{ECO:0000269|PubMed:9463337}.
/FTId=VAR_003747.
VARIANT 48 48 K -> N (in HMGCLD; abolishes almost all
enzymatic activity).
{ECO:0000269|PubMed:17459752}.
/FTId=VAR_058441.
VARIANT 70 70 V -> L (in HMGCLD; dbSNP:rs121964996).
/FTId=VAR_003748.
VARIANT 75 75 S -> R (in HMGCLD).
{ECO:0000269|PubMed:12746442}.
/FTId=VAR_058442.
VARIANT 142 142 S -> F (in HMGCLD; activity lower than 5%
respect to the wild-type).
{ECO:0000269|PubMed:19177531}.
/FTId=VAR_058443.
VARIANT 165 165 R -> Q (in HMGCLD; dbSNP:rs199587895).
{ECO:0000269|PubMed:19036343}.
/FTId=VAR_065453.
VARIANT 174 174 C -> Y (in HMGCLD; activity lower than 5%
respect to the wild-type;
dbSNP:rs765475941).
{ECO:0000269|PubMed:19177531}.
/FTId=VAR_058444.
VARIANT 192 192 F -> S (in HMGCLD; activity lower than 5%
respect to the wild-type).
{ECO:0000269|PubMed:19177531}.
/FTId=VAR_058445.
VARIANT 200 200 I -> F (in HMGCLD; activity lower than 5%
respect to the wild-type).
{ECO:0000269|PubMed:19177531}.
/FTId=VAR_058446.
VARIANT 201 201 S -> Y (in HMGCLD; dbSNP:rs760106433).
{ECO:0000269|PubMed:12746442}.
/FTId=VAR_058447.
VARIANT 203 203 G -> E (in HMGCLD; complete loss of
activity). {ECO:0000269|PubMed:16601870}.
/FTId=VAR_058448.
VARIANT 204 204 D -> N (in HMGCLD).
{ECO:0000269|PubMed:12746442}.
/FTId=VAR_058449.
VARIANT 233 233 H -> R (in HMGCLD; loss of activity;
dbSNP:rs727503963).
{ECO:0000269|PubMed:19177531,
ECO:0000269|PubMed:8798725,
ECO:0000269|PubMed:9784232}.
/FTId=VAR_003749.
VARIANT 263 263 L -> P (in HMGCLD).
{ECO:0000269|PubMed:9784232}.
/FTId=VAR_058450.
VARIANT 279 279 E -> K (in HMGCLD; dbSNP:rs121964998).
{ECO:0000269|PubMed:11129331}.
/FTId=VAR_014202.
MUTAGEN 37 37 E->D: Normal activity.
{ECO:0000269|PubMed:12874287}.
MUTAGEN 41 41 R->M: Reduced activity, and loss of
proton exchange.
{ECO:0000269|PubMed:15122894}.
MUTAGEN 42 42 D->A,N: Loss of activity, and reduced
proton exchange rate.
{ECO:0000269|PubMed:12874287,
ECO:0000269|PubMed:15122894}.
MUTAGEN 72 72 E->A: Loss of activity, and reduced
affinity for metal cofactor and
substrate. {ECO:0000269|PubMed:12874287}.
MUTAGEN 204 204 D->A: Reduced activity, and reduced
affinity for metal cofactor and
substrate. {ECO:0000269|PubMed:12874287}.
MUTAGEN 233 233 H->A: Loss of activity, and reduced
proton exchange rate.
{ECO:0000269|PubMed:12874287,
ECO:0000269|PubMed:15122894}.
MUTAGEN 266 266 C->A: Loss of activity.
MUTAGEN 279 279 E->A: Reduced thermal stability, but
normal activity.
{ECO:0000269|PubMed:12874287}.
MUTAGEN 280 280 D->A: Normal activity.
{ECO:0000269|PubMed:12874287}.
MUTAGEN 323 323 C->S: Abolishes interchain
homodimerization. Exhibits no DTT
stimulated activity.
{ECO:0000269|PubMed:12464283,
ECO:0000269|PubMed:22865860}.
CONFLICT 243 243 A -> T (in Ref. 1; AAA92733).
{ECO:0000305}.
STRAND 34 37 {ECO:0000244|PDB:2CW6}.
TURN 39 41 {ECO:0000244|PDB:2CW6}.
HELIX 42 45 {ECO:0000244|PDB:2CW6}.
HELIX 53 65 {ECO:0000244|PDB:2CW6}.
STRAND 69 71 {ECO:0000244|PDB:2CW6}.
TURN 79 81 {ECO:0000244|PDB:2CW6}.
HELIX 83 85 {ECO:0000244|PDB:2CW6}.
HELIX 88 94 {ECO:0000244|PDB:2CW6}.
HELIX 110 118 {ECO:0000244|PDB:2CW6}.
STRAND 122 130 {ECO:0000244|PDB:2CW6}.
HELIX 132 139 {ECO:0000244|PDB:2CW6}.
HELIX 143 159 {ECO:0000244|PDB:2CW6}.
STRAND 163 169 {ECO:0000244|PDB:2CW6}.
TURN 170 172 {ECO:0000244|PDB:2CW6}.
TURN 175 177 {ECO:0000244|PDB:2CW6}.
HELIX 182 194 {ECO:0000244|PDB:2CW6}.
STRAND 198 204 {ECO:0000244|PDB:2CW6}.
HELIX 211 224 {ECO:0000244|PDB:2CW6}.
HELIX 227 229 {ECO:0000244|PDB:2CW6}.
STRAND 230 235 {ECO:0000244|PDB:2CW6}.
HELIX 241 250 {ECO:0000244|PDB:2CW6}.
STRAND 255 259 {ECO:0000244|PDB:2CW6}.
HELIX 278 288 {ECO:0000244|PDB:2CW6}.
HELIX 296 309 {ECO:0000244|PDB:2CW6}.
HELIX 317 322 {ECO:0000244|PDB:2CW6}.
SEQUENCE 325 AA; 34360 MW; B82B2488A10D6980 CRC64;
MAAMRKALPR RLVGLASLRA VSTSSMGTLP KRVKIVEVGP RDGLQNEKNI VSTPVKIKLI
DMLSEAGLSV IETTSFVSPK WVPQMGDHTE VLKGIQKFPG INYPVLTPNL KGFEAAVAAG
AKEVVIFGAA SELFTKKNIN CSIEESFQRF DAILKAAQSA NISVRGYVSC ALGCPYEGKI
SPAKVAEVTK KFYSMGCYEI SLGDTIGVGT PGIMKDMLSA VMQEVPLAAL AVHCHDTYGQ
ALANTLMALQ MGVSVVDSSV AGLGGCPYAQ GASGNLATED LVYMLEGLGI HTGVNLQKLL
EAGNFICQAL NRKTSSKVAQ ATCKL


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