G2Cdb::Gene report

Gene id
G00002196
Gene symbol
PC (HGNC)
Species
Homo sapiens
Description
pyruvate carboxylase
Orthologue
G00000947 (Mus musculus)

Databases (7)

Gene
ENSG00000173599 (Ensembl human gene)
5091 (Entrez Gene)
834 (G2Cdb plasticity & disease)
PC (GeneCards)
Literature
608786 (OMIM)
Marker Symbol
HGNC:8636 (HGNC)
Protein Sequence
P11498 (UniProt)

Synonyms (1)

  • PCB

Literature (26)

Pubmed - other

  • Decreased levels of metabolic enzymes in pancreatic islets of patients with type 2 diabetes.

    MacDonald MJ, Longacre MJ, Langberg EC, Tibell A, Kendrick MA, Fukao T and Ostenson CG

    Children's Diabetes Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA. mjmacdon@wisc.edu

    Glucose-stimulated insulin secretion is defective in patients with type 2 diabetes. We sought to acquire new information about enzymes of glucose metabolism, with an emphasis on mitochondrial enzymes, by comparing pancreatic islets of type 2 diabetes patients with those of non-diabetic controls.

    Methods: Expression of genes encoding 13 metabolic enzymes was estimated with microarrays and activities of up to nine metabolic enzymes were measured.

    Results: The activities of the mitochondrial enzymes, glycerol phosphate dehydrogenase, pyruvate carboxylase (PC) and succinyl-CoA:3-ketoacid-CoA transferase (SCOT) were decreased by 73%, 65% and 92%, respectively, in the diabetic compared with the non-diabetic islets. ATP citrate lyase, a cytosolic enzyme of the mitochondrial citrate pyruvate shuttle, was decreased 57%. Activities of propionyl-CoA carboxylase, NADP-isocitrate dehydrogenase, cytosolic malic enzyme, aspartate aminotransferase and malate dehydrogenase were not significantly different from those of the control. The low activities of PC and SCOT were confirmed with western blots, which showed that their protein levels were low. The correlation of relative mRNA signals with enzyme activities was good in four instances, moderate in four instances and poor in one instance. In diabetic islets, the mRNA signal of the islet cell-enriched transcription factor musculoaponeurotic fibrosarcoma oncogene homologue A, which regulates expression of islet genes, including the PC gene, was decreased to 54% of the control level. PC activity and protein levels in the non-diabetic islets were significantly lower than in islets from non-diabetic rodents.

    Low levels of certain islet metabolic enzymes, especially mitochondrial enzymes, are associated with human type 2 diabetes.

    Funded by: NIDDK NIH HHS: DK28348, R01 DK028348, R01 DK028348-16, R01 DK028348-17, R01 DK028348-18, R01 DK028348-19, R01 DK028348-20, R01 DK028348-21, R01 DK028348-22, R01 DK028348-23, R01 DK028348-24, R01 DK028348-25, R01 DK028348-26, R01 DK028348-27

    Diabetologia 2009;52;6;1087-91

  • Structural insights on pathogenic effects of novel mutations causing pyruvate carboxylase deficiency.

    Monnot S, Serre V, Chadefaux-Vekemans B, Aupetit J, Romano S, De Lonlay P, Rival JM, Munnich A, Steffann J and Bonnefont JP

    INSERM unit U781, Université Paris Descartes, Hôpital Necker-Enfants Malades, Paris, France. monnot.sophie@free.fr

    Pyruvate carboxylase (PC), a key enzyme for gluconeogenesis and anaplerotic pathways, consists of four domains, namely, biotin carboxylase (BC), carboxyltransferase (CT), pyruvate carboxylase tetramerization (PT), and biotin carboxyl carrier protein (BCCP). PC deficiency is a rare metabolic disorder inherited in an autosomal recessive way. The most severe form (form B) is characterized by neonatal lethal lactic acidosis, whereas patients with form A suffer chronic lactic acidosis with psychomotor retardation. Diagnosis of PC deficiency relies on enzymatic assay and identification of the PC gene mutations. To date, six mutations of the PC gene have been identified. We report nine novel mutations of the PC gene, in five unrelated patients: three being affected with form B, and the others with form A. Three of them were frameshift mutations predicted to introduce a premature termination codon, the remaining ones being five nucleotide substitutions and one in frame deletion. Impact of these mutations on mRNA was assessed by RT-PCR. Evidence for a deleterious effect of the missense mutations was achieved using protein alignments and three-dimensional structural prediction, thanks to our modeling of the human PC structure. Altogether, our data and those previously reported indicate that form B is consistently associated with at least one truncating mutation, mostly lying in CT (C-terminal part) or BCCP domains, whereas form A always results from association of two missense mutations located in BC or CT (N-terminal part) domains. Finally, although most PC mutations are suggested to interfere with biotin metabolism, none of the PC-deficient patients was biotin-responsive.

    Human mutation 2009;30;5;734-40

  • The molecular basis of pyruvate carboxylase deficiency: mosaicism correlates with prolonged survival.

    Wang D, Yang H, De Braganca KC, Lu J, Yu Shih L, Briones P, Lang T and De Vivo DC

    Colleen Giblin Laboratories for Pediatric Neurology Research, Department of Neurology, Columbia University, New York, NY 10032, USA.

    Pyruvate carboxylase (PC) deficiency (OMIM, 266150) is a rare autosomal recessive disease. The revised PC gene structure described in this report consists of 20 coding exons and four non-coding exons at the 5'-untranslated region (5'-UTR). The gene codes for three transcripts due to alternative splicing: variant 1 (NM_000920.3), variant 2 (NM_022172.2) and variant 3 (BC011617.2). PC deficiency is manifested by three clinical phenotypes-an infantile form (Type A), a neonatal form (Type B), and a benign form (Type C). We report the molecular basis for eight cases (one Type A, five Type B and two Type C) of PC deficiency. Eight novel complex mutations were identified representing different combinations of missense mutations, deletions, a splice site substitution and a nonsense mutation. The classical phenotypes (A, B and C) correlated poorly with clinical outcomes. Mosaicism was found in five cases (one Type A, three Type B and one Type C) and four of these cases had prolonged survival. Death in the fifth case resulted from unrelated medical complications. The discrepancy between the current findings and the existing classification system should be addressed to accommodate these new observations.

    Funded by: NCRR NIH HHS: 1 UL1 RR024156-01, UL1 RR024156; NINDS NIH HHS: K12 NS001698, K12 NS001698-05S4, K12-NS01698, NS37949, R01 NS037949, R01 NS037949-10

    Molecular genetics and metabolism 2008;95;1-2;31-8

  • Thrombophilia and unexplained pregnancy loss in Indian patients.

    Vora S, Shetty S, Salvi V, Satoskar P and Ghosh K

    National Institute of Immunohaematology (ICMR), K.E.M. Hospital, Parel, Mumbai 400012, Maharashtra, India.

    Background: The role of acquired and congenital thrombophilias in the aetiology of unexplained pregnancy loss in the Indian population has not been studied in detail. We studied the association of acquired and inherited markers of thrombophilia in a large group of patients with unexplained pregnancy loss.

    Methods: A total of 602 women with pregnancy loss were referred to us for evaluation of thrombophilia between April 2000 and June 2005. After investigations to rule out cytogenetic, hormonal, anatomical and microbiological causes, no cause was ascertained in 430 women for the pregnancy loss. Of these, 49 women, who had a history of only one pregnancy loss, were excluded. The remaining 381 women comprised the study group. These patients and 100 age-matched women who did not have any obstetric complication and had at least one normal healthy child (controls) underwent detailed investigations for the presence of thrombophilia markers. These included screening coagulations tests, tests for lupus anticoagulant (LA), IgG and IgM antibodies to anticardiolipin antibodies (ACA), beta2 glycoprotein 1 (beta2GP1) and annexin V. The genetic markers studied included protein C (PC), protein 5 (PS), antithrombin III (AT III), factor V Leiden (FVL), PT gene G20210A, MTHFR C677T, EPCR 23 bp insertion and PAI 4G/5G polymorphisms.

    Results: Of the 381 women with pregnancy loss, 183 had 2 and 198 had > or = 3 pregnancy losses. Early pregnancy loss occurred in 136 patients, late pregnancy loss in 119, and both early and late pregnancy losses in 126. The strongest association was observed with ACA (OR 32.5, 95% CI: 8.6-21.8, p < 0.001) followed by annexin V (OR 17.1, 95% CI: 2.9-99.4, p < 0.001), LA (OR 8.2, 95% CI: 1.4-47.7, p = 0.01) and anti-beta2GP1 (OR 5.8, 95% CI: 1.6-22.1, p = 0.007). No association of antiphospholipid antibodies with the time of pregnancy loss was found except LA which was significantly associated with early pregnancy loss compared with late pregnancy loss (p < 0.05). The risk of pregnancy loss with PS deficiency (OR 17.8, 95% CI: 3.1-102.9, p < 0.001) was the highest observed for any heritable thrombophilia followed by PC deficiency (OR 5.8, 95% CI: 1-34, p = 0.06). There were no statistically significant differences in the frequency of any of the genetic thrombophilias studied between women with early and late pregnancy loss. A combination of > or = 2 genetic factors was observed in 41 (10.8%) while that of genetic and acquired risk factors were observed in 79 (20.7%) patients. No more than one risk factor was observed in any of the controls. In all, 176 (46.2%) patients had at least one acquired thrombophilia while 143 (37.5%) had at least one genetic thrombophilia marker. Overall, 288 patients (75.6%) had either an acquired, genetic or both markers of thrombophilia.

    Conclusion: Thrombophilia is an important factor in both early and late pregnancy losses. Women with unexplained pregnancy loss should be screened for the presence of thrombophilias.

    The National medical journal of India 2008;21;3;116-9

  • Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.

    Xiang S and Tong L

    Department of Biological Sciences, 212 Amsterdam Avenue, Columbia University, New York, New York 10027, USA.

    Pyruvate carboxylase (PC) catalyzes the biotin-dependent production of oxaloacetate and has important roles in gluconeogenesis, lipogenesis, insulin secretion and other cellular processes. PC contains the biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) domains. We report here the crystal structures at 2.8-A resolution of full-length PC from Staphylococcus aureus and the C-terminal region (missing only the BC domain) of human PC. A conserved tetrameric association is observed for both enzymes, and our structural and mutagenesis studies reveal a previously uncharacterized domain, the PC tetramerization (PT) domain, which is important for oligomerization. A BCCP domain is located in the active site of the CT domain, providing the first molecular insights into how biotin participates in the carboxyltransfer reaction. There are dramatic differences in domain positions in the monomer and the organization of the tetramer between these enzymes and the PC from Rhizobium etli.

    Funded by: NIDDK NIH HHS: DK67238

    Nature structural & molecular biology 2008;15;3;295-302

  • Novel localization of OCTN1, an organic cation/carnitine transporter, to mammalian mitochondria.

    Lamhonwah AM and Tein I

    Division of Neurology, Department of Pediatrics, University of Toronto, Ont., Canada.

    Carnitine is a zwitterion essential for the beta-oxidation of fatty acids. We report novel localization of the organic cation/carnitine transporter, OCTN1, to mitochondria. We made GFP- and RFP-human OCTN1 cDNA constructs and showed expression of hOCTN1 in several transfected mammalian cell lines. Immunostaining of GFP-hOCTN1 transfected cells with different intracellular markers and confocal fluorescent microscopy demonstrated mitochondrial expression of OCTN1. There was striking co-localization of an RFP-hOCTN1 fusion protein and a mitochondrial-GFP marker construct in transfected MEF-3T3 and no co-localization of GFP-hOCTN1 in transfected human skin fibroblasts with other intracellular markers. L-[(3)H]Carnitine uptake in freshly isolated mitochondria of GFP-hOCTN1 transfected HepG2 demonstrated a K(m) of 422 microM and Western blot with an anti-GFP antibody identified the expected GFP-hOCTN1 fusion protein (90 kDa). We showed endogenous expression of native OCTN1 in HepG2 mitochondria with anti-GST-hOCTN1 antibody. Further, we definitively confirmed intact L-[(3)H]carnitine uptake (K(m) 1324 microM), solely attributable to OCTN1, in isolated mitochondria of mutant human skin fibroblasts having <1% of carnitine acylcarnitine translocase activity (alternate mitochondrial carnitine transporter). This mitochondrial localization was confirmed by TEM of murine heart incubated with highly specific rabbit anti-GST-hOCTN1 antibody and immunogold labeled goat anti-rabbit antibody. This suggests an important yet different role for OCTN1 from other OCTN family members in intracellular carnitine homeostasis.

    Biochemical and biophysical research communications 2006;345;4;1315-25

  • A case of pyruvate carboxylase deficiency with atypical clinical and neuroradiological presentation.

    Schiff M, Levrat V, Acquaviva C, Vianey-Saban C, Rolland MO and Guffon N

    Département de Pédiatrie, Pavillon S, Hôpital Edouard Herriot, Place d'Arsonval, 69437 Lyon Cedex 03, France. manuel.schiff@chu-lyon.fr

    Pyruvate carboxylase (PC) is a key enzyme for gluconeogenesis and anaplerotic pathways in brain. PC deficiency is a rare autosomal recessive neurometabolic disorder with three described characteristic presentations. We report a patient with atypical clinical and neuroradiological aspects. He survived from neonatal lactic acidemia and is alive at 9 years of age with a mild developmental delay. A brain MRI performed by the age of 18 months disclosed an unusual subcortical leucodystrophic process.

    Molecular genetics and metabolism 2006;87;2;175-7

  • Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.

    Kimura K, Wakamatsu A, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, Ishii S, Sugiyama T, Saito K, Isono Y, Irie R, Kushida N, Yoneyama T 5a8 , Otsuka R, Kanda K, Yokoi T, Kondo H, Wagatsuma M, Murakawa K, Ishida S, Ishibashi T, Takahashi-Fujii A, Tanase T, Nagai K, Kikuchi H, Nakai K, Isogai T and Sugano S

    Life Science Research Laboratory, Central Research Laboratory, Hitachi, Ltd., Kokubunji, Tokyo, 185-8601, Japan.

    By analyzing 1,780,295 5'-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by more than 500 bp and thus are very likely to constitute mutually distinct alternative promoters. To our surprise, at least 7674 (52%) human RefSeq genes were subject to regulation by putative alternative promoters (PAPs). On average, there were 3.1 PAPs per gene, with the composition of one CpG-island-containing promoter per 2.6 CpG-less promoters. In 17% of the PAP-containing loci, tissue-specific use of the PAPs was observed. The richest tissue sources of the tissue-specific PAPs were testis and brain. It was also intriguing that the PAP-containing promoters were enriched in the genes encoding signal transduction-related proteins and were rarer in the genes encoding extracellular proteins, possibly reflecting the varied functional requirement for and the restricted expression of those categories of genes, respectively. The patterns of the first exons were highly diverse as well. On average, there were 7.7 different splicing types of first exons per locus partly produced by the PAPs, suggesting that a wide variety of transcripts can be achieved by this mechanism. Our findings suggest that use of alternate promoters and consequent alternative use of first exons should play a pivotal role in generating the complexity required for the highly elaborated molecular systems in humans.

    Genome research 2006;16;1;55-65

  • The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

    Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J and MGC Project Team

    The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.

    Funded by: PHS HHS: N01-C0-12400

    Genome research 2004;14;10B;2121-7

  • Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation.

    Brandenberger R, Wei H, Zhang S, Lei S, Murage J, Fisk GJ, Li Y, Xu C, Fang R, Guegler K, Rao MS, Mandalam R, Lebkowski J and Stanton LW

    Geron Corporation, Menlo Park, California 94025, USA. rbrandenberger@geron.com

    Human embryonic stem (hES) cells hold promise for generating an unlimited supply of cells for replacement therapies. To characterize hES cells at the molecular level, we obtained 148,453 expressed sequence tags (ESTs) from undifferentiated hES cells and three differentiated derivative subpopulations. Over 32,000 different transcripts expressed in hES cells were identified, of which more than 16,000 do not match closely any gene in the UniGene public database. Queries to this EST database revealed 532 significantly upregulated and 140 significantly downregulated genes in undifferentiated hES cells. These data highlight changes in the transcriptional network that occur when hES cells differentiate. Among the differentially regulated genes are several components of signaling pathways and transcriptional regulators that likely play key roles in hES cell growth and differentiation. The genomic data presented here may facilitate the derivation of clinically useful cell types from hES cells.

    Nature biotechnology 2004;22;6;707-16

  • Expression and characterization of a human pyruvate carboxylase variant by retroviral gene transfer.

    Carbone MA and Robinson BH

    Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8.

    Type A pyruvate carboxylase (PC) deficiency presents mainly in the Amerindian population, specifically the Ojibwa, Cree and Micmac tribes of the Algonquin-speaking peoples. The gene for PC contains a homozygous founder mutation (G1828-->A) that results in an Ala610-->Thr amino acid substitution in Ojibwa with Type A PC deficiency. The mutation is located in the highly conserved pyruvate-binding domain of PC. The present paper describes a retroviral expression system for human PC used to analyse the effects of this mutation. We show, through immunoblot analysis, PC enzyme activity assays, reverse-transcription PCR and mitochondrial-import experiments, that this mutation is disease-causing in the Ojibwa population owing to its decreased catalytic activity, decreased steady-state levels of expression and inefficient import into the mitochondria. Our data suggest that this mutation may affect the stability of the protein, resulting in decreased steady-state levels of expression, and that it may also affect the secondary structure of the protein during the import process, thereby inhibiting proper translocation into the mitochondria, where PC is active.

    The Biochemical journal 2003;370;Pt 1;275-82

  • Immunohistochemical localization of pyruvate carboxylase and carbamyl-phosphate synthetase I in normal and neoplastic human pancreatic tissues.

    Sato T, Kashima K, Gamachi A, Daa T, Nakayama I and Yokoyama S

    Department of Pathology, Oita Medical University, Oita, Japan. satot@oita-med.ac.jp

    Introduction: It has been suggested that pyruvate carboxylase (PC) and carbamyl-phosphate synthetase I (CPS I) might be colocalized with carbonic anhydrase V (CA V), which is generally considered to provide HCO3- ions for PC and CPS I.

    Aim: To examine the immunohistochemical staining of endogenous biotin; of three mitochondrial biotin-binding enzymes (namely, PC, CPS I, and propionyl CoA-carboxylase); and of cytosolic acetyl CoA-carboxylase in pancreatic tissues.

    Methodology: Immunohistochemical analysis was performed on 23 samples of normal pancreas and 63 samples of neoplastic pancreatic tissues.

    Results: It was found that the distribution of PC, CPS I, and endogenous biotin was not related to that of CA V but was similar to that of CA II in normal centroacinar cells, intercalated duct cells, and intralobular duct cells. In addition, PC was detected unexpectedly in delta-cells of islets.

    Conclusion: It seems likely that CA II plays a major role in the secretion of NaHCO3 into the pancreatic juice. Hence, it is possible that PC and CPS I in the centroacinar cells, intercalated duct cells, and intralobular duct cells are strongly activated and might use HCO3- ions provided by CA II and not by CA V. Among the pancreatic neoplasms examined, ductal adenocarcinomas exhibited significantly elevated immunoreactivity specific for the four biotin-binding enzymes.

    Pancreas 2002;25;2;130-5

  • Intron retention and frameshift mutations result in severe pyruvate carboxylase deficiency in two male siblings.

    Carbone MA, Applegarth DA and Robinson BH

    Research Institute, Hospital for Sick Children and the Department of Biochemistry at the University of Toronto, Toronto, Ontario, Canada.

    This paper describes the molecular characterization of two male siblings displaying the complex (Type B) form of pyruvate carboxylase (PC) deficiency in which severe neonatal lactic acidosis and redox abnormalities results in death within the first few weeks of life. The two male siblings were found to be compound heterozygous for a TAGG deletion at the exon15/intron15 splice site (IVS15+2-5delTAGG) and a dinucleotide deletion in exon 16 (2491-2492delGT) of the PC gene. We also demonstrate through RT-PCR and sequencing of aberrant transcripts that the IVS15+2-5delTAGG results in the retention of intron 15 during pre-mRNA splicing. In addition, both deletions are predicted to result in a frameshift to generate a premature termination codon such that the encoded mRNA could be subject to nonsense mediated decay.

    Human mutation 2002;20;1;48-56

  • Structure, function and regulation of pyruvate carboxylase.

    Jitrapakdee S and Wallace JC

    Department of Biochemistry, University of Adelaide, Adelaide, South Australia 5005, Australia.

    Pyruvate carboxylase (PC; EC 6.4.1.1), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate. PC has been found in a wide variety of prokaryotes and eukaryotes. In mammals, PC plays a crucial role in gluconeogenesis and lipogenesis, in the biosynthesis of neurotransmitter substances, and in glucose-induced insulin secretion by pancreatic islets. The reaction catalysed by PC and the physical properties of the enzyme have been studied extensively. Although no high-resolution three-dimensional structure has yet been determined by X-ray crystallography, structural studies of PC have been conducted by electron microscopy, by limited proteolysis, and by cloning and sequencing of genes and cDNA encoding the enzyme. Most well characterized forms of active PC consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain. Different physiological conditions, including diabetes, hyperthyroidism, genetic obesity and postnatal development, increase the level of PC expression through transcriptional and translational mechanisms, whereas insulin inhibits PC expression. Glucocorticoids, glucagon and catecholamines cause an increase in PC activity or in the rate of pyruvate carboxylation in the short term. Molecular defects of PC in humans have recently been associated with four point mutations within the structural region of the PC gene, namely Val145-->Ala, Arg451-->Cys, Ala610-->Thr and Met743-->Thr.

    The Biochemical journal 1999;340 ( Pt 1);1-16

  • Amerindian pyruvate carboxylase deficiency is associated with two distinct missense mutations.

    Carbone MA, MacKay N, Ling M, Cole DE, Douglas C, Rigat B, Feigenbaum A, Clarke JT, Haworth JC, Greenberg CR, Seargeant L and Robinson BH

    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.

    We characterized the pyruvate carboxylase (PC) gene by PCR amplification, subcloning, and sequencing. The coding region has 19 exons and 18 introns spanning approximately 16 kb of genomic DNA. Screening both the cDNA and the gene of individuals with the simple A form of PC deficiency revealed an 1828G-->A missense mutation in 11 Ojibwa and 2 Cree patients and a 2229G-->T transversion mutation in 2 brothers of Micmac origin. Carrier frequency may be as high as 1/10 in some groupings. The two point mutations are located in a region of homology conserved among yeast, rat, and human PC, in the vicinity of the carboxylation domain of the enzyme. These data provide the first characterization of the human PC gene structure, the identification of common pathogenic mutations, and the demonstration of a founder effect in the Ojibwa and Cree patients.

    American journal of human genetics 1998;62;6;1312-9

  • Molecular characterization of pyruvate carboxylase deficiency in two consanguineous families.

    Wexler ID, Kerr DS, Du Y, Kaung MM, Stephenson W, Lusk MM, Wappner RS and Higgins JJ

    Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44118, USA.

    Pyruvate carboxylase (PC) is a biotinylated mitochondrial enzyme that catalyzes the conversion of pyruvate to oxaloacetate. Children with inborn errors of PC metabolism have lactic acidosis, hypoglycemia, and mental retardation. The variable severity of the clinical phenotype is dependent on both genetic and environmental factors. Two consanguineous families with moderate forms of PC deficiency were characterized at the biochemical and molecular levels. In both families, the probands were found to have low PC activity (range, 2-25% of control) in blood lymphocytes and skin fibroblasts associated with either diminished or normal protein levels. In the first case, sequencing of patient-specific PC cDNA demonstrated a T to C substitution at nucleotide 434, which causes a valine to alanine change at amino acid residue 145. Direct sequencing of the parents showed that they are heterozygous for this mutation. In the second family, a brother and sister had mental retardation and episodes of severe lactic/ketoacidosis in early childhood. In these cases, a C to T substitution at nucleotide 1351 results in a cysteine for arginine substitution at amino acid residue 451; the parents were also found to be heterozygous for this mutation. In both families, no other mutations were found, and both substitutions occurred in relatively conserved amino acid residues. These mutations, located in the biotin carboxylase domain, provide a unique opportunity to analyze how natural occurring mutations affect PC function.

    Funded by: NICHD NIH HHS: HD-32434; NIDDK NIH HHS: DK20478

    Pediatric research 1998;43;5;579-84

  • Pyruvate carboxylase.

    Wallace JC, Jitrapakdee S and Chapman-Smith A

    Department of Biochemistry, University of Adelaide, Australia. jwallace@biochem.adelaide.edu.au

    Pyruvate carboxylase [EC 6.4.1.1] is a member of the family of biotin-dependent carboxylases and is found widely among eukaryotic tissues and in many prokaryotic species. It catalyses the ATP-dependent carboxylation of pyruvate to form oxaloacetate which may be utilised in the synthesis of glucose, fat, some amino acids or their derivatives and several neurotransmitters. Diabetes and hyperthyroidism increase the level of expression of pyruvate carboxylase in the long term, while its activity in the short term is controlled by the intramitochondrial concentrations of acetyl-CoA and pyruvate. Many details of this enzyme's regulation are yet to be described in molecular terms. However, progress towards this goal and towards understanding the relationship of pyruvate carboxylase structure to its catalytic reaction mechanism, has been enormously enhanced recently by the cloning and sequencing of genes and cDNAs encoding the approximately 130 kDa subunit of this homotetramer. Defects in the expression or biotinylation of pyruvate carboxylase in humans almost invariably results in early death or at best a severely debilitating psychomotor retardation, clearly reflecting the vital role it plays in intermediary metabolism in many tissues including the brain.

    The international journal of biochemistry & cell biology 1998;30;1;1-5

  • Assignment of the human pyruvate carboxylase gene (PC) to 11q13.4 by fluorescence in situ hybridisation.

    Walker ME, Baker E, Wallace JC and Sutherland GR

    Department of Biochemistry, University of Adelaide, Australia.

    The gene for pyruvate carboxylase (PC) has been localised by fluorescence in situ hybridisation to normal and FRA11A human chromosomes. PC maps to 11q13 and distal to FRA11A, localising PC to 11q13.4-->q13.5.

    Cytogenetics and cell genetics 1995;69;3-4;187-9

  • Primary amino acid sequence and structure of human pyruvate carboxylase.

    Wexler ID, Du Y, Lisgaris MV, Mandal SK, Freytag SO, Yang BS, Liu TC, Kwon M, Patel MS and Kerr DS

    Department of Biochemistry, Case Western Reserve University School of Medicine, Rainbow Babies and Childrens Hospital, Cleveland, OH 44106.

    Pyruvate carboxylase (PC) (pyruvate:carbon dioxide ligase (ADP-forming), EC 6.4.1.1.), a nuclear-encoded mitochondrial enzyme, catalyzes the conversion of pyruvate to oxaloacetate. We have isolated and characterized cDNAs spanning the entire coding region of human PC. The sequence of human PC has an open reading frame of 3537 nucleotides which encodes for a polypeptide with a length of 1178 amino acids. The identity of the cDNA as PC is confirmed by comparison to PC cDNAs of other species and sequenced peptide fragments of mammalian PC. The M(r) of the full length precursor protein is 129,576 and that of the mature apoprotein is 127,370. RNA blot analysis from a variety of human tissues demonstrates that the highest level of PC mRNA is found in liver corresponding to this tissue's high level of PC activity. Based on homology with other biotin-containing proteins, the ATP, pyruvate, and biotin-binding sites can be identified. One of two patients with documented PC deficiency was found to be missing PC mRNA, further confirming the identity of this cDNA.

    Funded by: NICHD NIH HHS: HD 00878; NIDDK NIH HHS: DK 20478

    Biochimica et biophysica acta 1994;1227;1-2;46-52

  • MRI, clinical, and biochemical features of partial pyruvate carboxylase deficiency.

    Higgins JJ, Glasgow AM, Lusk M and Kerr DS

    Clinical Neurogenetics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892.

    We report a boy with a partial deficiency of pyruvate carboxylase as documented in enzyme assays of skin fibroblasts, lymphocytes, and hepatic tissue. Magnetic resonance imaging at age 20 months demonstrated a leukodystrophic process involving the brain stem and subcortical white matter, which, except for the brain stem, improved after biotin treatment. The lymphocyte pyruvate carboxylase activity of both heterozygous parents slightly increased after receiving oral biotin for 1 month, but a definitive enzymatic response to biotin was not confirmed in our patient. At age 6 years, he is dysarthric with a spastic quadriparesis despite improvements in development and myelination. This is the first demonstration of magnetic resonance imaging changes in this disease.

    Funded by: NIDDK NIH HHS: DK-20478

    Journal of child neurology 1994;9;4;436-9

  • cDNA cloning of human kidney pyruvate carboxylase.

    MacKay N, Rigat B, Douglas C, Chen HS and Robinson BH

    Department of Biochemistry, University of Toronto, Ontario, Canada.

    cDNA clones covering a total of 4017 bp were isolated corresponding to the full length of the message for human pyruvate carboxylase. The coding sequence consisted of a stretch of 3534 bp flanked by a 5' untranslated sequence of 82 bp and a 3' untranslated region of 389 bp excluding the poly-A tail. The translated amino acid sequence of 1178 residues contained consensus sequences for the covalent attachment for biotin, the binding of ATP and the binding of the substrate, pyruvate.

    Biochemical and biophysical research communications 1994;202;2;1009-14

  • Interactions between pyruvate carboxylase and other mitochondrial enzymes.

    Fahien LA, Davis JW and Laboy J

    Department of Pharmacology, University of Wisconsin Medical School, Madison 53706.

    Although pyruvate carboxylase associated with both mitochondrial aspartate aminotransferase and malate dehydrogenase, it had a higher affinity for the amino-transferase. Furthermore, the aminotransferase enhanced dissociation of malate dehydrogenase from pyruvate carboxylase. Glutamate dehydrogenase did not associate with pyruvate carboxylase alone, but it apparently associated with the pyruvate carboxylase-aminotransferase complex, and malate dehydrogenase associated with the resulting ternary complex. Citrate synthase and other proteins tested did not associate with pyruvate carboxylase. However, citrate synthase associated with the pyruvate carboxylase-malate dehydrogenase complex. Apparently as a consequence of these heteroenzyme interactions, the rate of the pyruvate carboxylase reaction was slightly greater when coupled with malate dehydrogenase or both malate dehydrogenase and citrate synthase than when coupled with citrate synthase alone. In addition, in the presence of both coupling enzymes, the rate of conversion of pyruvate to citrate was higher than predicted on the basis of the Michaelis-Menten relationship of the two coupling enzymes. Therefore, binding of malate dehydrogenase to pyruvate carboxylase enhances pyruvate carboxylase activity. Association of citrate synthase with the malate dehydrogenase-pyruvate carboxylase binary complex does not alter activation of pyruvate carboxylase but results in citrate synthase being more reactive than free citrate synthase with oxalacetate.

    Funded by: NCI NIH HHS: CA40445

    The Journal of biological chemistry 1993;268;24;17935-42

  • Utilization of glutamine and of TCA cycle constituents as precursors for transmitter glutamate and GABA.

    Peng L, Hertz L, Huang R, Sonnewald U, Petersen SB, Westergaard N, Larsson O and Schousboe A

    Department of Pharmacology, University of Saskatchewan, Saskatoon, Canada.

    In the present review evidence is presented that (1) glutamine synthesis in astrocytes is essential for synthesis of GABA in neurons; (2) alpha-ketoglutarate in the presence of alanine (as an amino group donor) can replace glutamine as a precursor for synthesis of transmitter glutamate, but maybe not as a precursor for transmitter GABA; (3) differences exist in the intraneuronal metabolic pathways for utilization of alpha-ketoglutarate plus alanine and of glutamine, and (4) alanine also functions as a substrate for oxidative metabolism in glutamatergic neurons. It should be emphasized that the supply of precursors for transmitter glutamate and GABA in glutamatergic and GABAergic neurons depends on metabolic processes in astrocytes regardless whether glutamine or alpha-ketoglutarate plus L-alanine function as the transmitter precursors. The key reason that an interaction with astrocytes is essential is that both pyruvate carboxylase, the major enzyme in the brain for net synthesis of tricarboxylic acid cycle intermediates, and glutamine synthetase, the enzyme forming glutamine from glutamate, are specifically located in astrocytes, but not in neurons.

    Developmental neuroscience 1993;15;3-5;367-77

  • Sequence homology around the biotin-binding site of human propionyl-CoA carboxylase and pyruvate carboxylase.

    Lamhonwah AM, Quan F and Gravel RA

    Biotin-dependent carboxylases require covalently bound biotin for enzymatic activity. The biotin is attached through a lysine residue, which in a number of bacterial, avian, and mammalian carboxylases, is found within the conserved sequence Ala-Met-Lys-Met. We have determined the partial nucleotide sequence of cDNA clones for human propionyl-CoA carboxylase and pyruvate carboxylase. The predicted amino acid sequence of both these proteins contains the conserved tetrapeptide 35 residues from the carboxy terminus. In addition, both proteins contain the tripeptide, Pro-Met-Pro, 26 residues toward the amino terminus from the biotin attachment site. The overall amino acid homology through this region is 43%. Similar findings have been made for the biotin-containing polypeptides of transcarboxylase of Propionibacterium shermanii and acetyl-CoA carboxylase of Escherichia coli (W. L. Maloy, B. U. Bowien, G. K. Zwolinski, K. G. Kumar, and H. G. Wood (1979) J. Biol. Chem. 254, 11615-11622). The implications of this sequence conservation with regard to the function and evolution of biotin-dependent carboxylases is discussed. We propose that the 60 amino acids surrounding the biotin site are bounded by a proline "hinge" and the carboxy terminus has remained conserved as a result of constraints imposed by biotinylation of the enzyme.

    Archives of biochemistry and biophysics 1987;254;2;631-6

  • Molecular cloning of a cDNA for human pyruvate carboxylase. Structural relationship to other biotin-containing carboxylases and regulation of mRNA content in differentiating preadipocytes.

    Freytag SO and Collier KJ

    An oligonucleotide probe specific for the amino acid sequence at the biotin site in pyruvate carboxylase was used to screen a human liver cDNA library. Nine cDNA clones were isolated and three proved to be pyruvate carboxylase clones based on nucleotide sequencing and Northern blotting. The biotin site amino acid sequence of human pyruvate carboxylase agreed perfectly with that of the sheep enzyme in 14 consecutive positions. The highly conserved amino acid sequence, Ala-Met-Lys-Met, found at the biotin site in most biotin-containing carboxylases was also present in human pyruvate carboxylase. The termination codon was located 35 residues 3' to the lysine residue at which the biotin is attached. Therefore, the biotin cofactor is covalently linked near the carboxyl-terminal end of the carboxylase protein. These data are consistent with that observed for other biotin-containing carboxylases and strongly suggests that the genes encoding the biotin-containing carboxylases may have evolved from a common ancestral gene. Northern blotting of mRNA isolated from human, baboon, and rat liver demonstrated that the pyruvate carboxylase mRNA was 4.2 kilobase pairs in length in all species examined. Southern blot analysis of genomic DNA isolated from human-Chinese hamster somatic cell hybrids localized the pyruvate carboxylase gene on the long arm of human chromosome 11. The human cDNA was also used to quantitate pyruvate carboxylase mRNA levels in a differentiating mouse preadipocyte cell line. These data demonstrated that pyruvate carboxylase mRNA content increased 23-fold in 7 days after the onset of differentiation.

    Funded by: NIADDK NIH HHS: AM06852

    The Journal of biological chemistry 1984;259;20;12831-7

Gene lists (4)

Gene List Source Species Name Description Gene count
L00000009 G2C Homo sapiens Human PSD Human orthologues of mouse PSD adapted from Collins et al (2006) 1080
L00000010 G2C Homo sapiens Human mitochondria Human orthologues of mouse mitochondria adapted from Collins et al (2006) 91
L00000016 G2C Homo sapiens Human PSP Human orthologues of mouse PSP adapted from Collins et al (2006) 1121
L00000069 G2C Homo sapiens BAYES-COLLINS-HUMAN-PSD-FULL Human cortex biopsy PSD full list 1461
© G2C 2014. The Genes to Cognition Programme received funding from The Wellcome Trust and the EU FP7 Framework Programmes:
EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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