Genomes and Genes
carbon nitrogen ligases
Summary: Enzymes that catalyze the joining of two molecules by the formation of a carbon-nitrogen bond. EC 6.3.
- Thoden J, Blanchard C, Holden H, Waldrop G. Movement of the biotin carboxylase B-domain as a result of ATP binding. J Biol Chem. 2000;275:16183-90 pubmed..A comparison of this closed form of biotin carboxylase with carbamoyl-phosphate synthetase is presented. ..
- Janiyani K, Bordelon T, Waldrop G, Cronan J. Function of Escherichia coli biotin carboxylase requires catalytic activity of both subunits of the homodimer. J Biol Chem. 2001;276:29864-70 pubmed..Thus, both the in vitro and in vivo data indicate that both subunits of biotin carboxylase are required for activity and that the two subunits must be in communication during enzyme function. ..
- Sloane V, Waldrop G. Kinetic characterization of mutations found in propionic acidemia and methylcrotonylglycinuria: evidence for cooperativity in biotin carboxylase. J Biol Chem. 2004;279:15772-8 pubmed..The results of the kinetic studies have revealed the first evidence for negative cooperativity with respect to bicarbonate and suggest that Arg-338 serves to orient the carboxyphosphate intermediate for optimal carboxylation of biotin. ..
- O Callaghan C, Byford M, Wyer J, Willcox B, Jakobsen B, McMichael A, et al. BirA enzyme: production and application in the study of membrane receptor-ligand interactions by site-specific biotinylation. Anal Biochem. 1999;266:9-15 pubmed..These tetrameric proteins can be used to study protein receptor-ligand interactions at the cell surface, and site-specific biotinylation can be used to study proteins in vitro using a defined orientation. ..
- Ostrander D, O Brien D, Gorman J, Carman G. Effect of CTP synthetase regulation by CTP on phospholipid synthesis in Saccharomyces cerevisiae. J Biol Chem. 1998;273:18992-9001 pubmed..8-fold), and a decrease in diacylglycerol (1. 3-fold) when compared with control cells. These data indicated that the regulation of CTP synthetase activity by CTP plays an important role in the regulation of phospholipid synthesis. ..
- Simard D, Hewitt K, Lunn F, Iyengar A, Bearne S. Limited proteolysis of Escherichia coli cytidine 5'-triphosphate synthase. Identification of residues required for CTP formation and GTP-dependent activation of glutamine hydrolysis. Eur J Biochem. 2003;270:2195-206 pubmed..This suggests that Arg429 plays a role in both GTP-dependent activation and GTP binding. ..
- Cronan J, Reed K. Biotinylation of proteins in vivo: a useful posttranslational modification for protein analysis. Methods Enzymol. 2000;326:440-58 pubmed
- Kwon K, Streaker E, Ruparelia S, Beckett D. Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor. J Mol Biol. 2000;304:821-33 pubmed..These results suggest that multiple disordered surface loops function in the corepressor-induced dimerization required for sequence-specific DNA binding by the biotin repressor. ..
- Naganathan S, Beckett D. Nucleation of an allosteric response via ligand-induced loop folding. J Mol Biol. 2007;373:96-111 pubmed..These results indicate that the hydrophobic cluster is critical to the ligand-induced disorder-to-order transition in the ABL and that this transition is integral to the allosteric response in the biotin repressor. ..
- Streaker E, Beckett D. Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding. J Mol Biol. 2003;325:937-48 pubmed..This kinetic model is consistent with the previously proposed model for regulation of the functional switch in the repressor from enzyme to site-specific DNA-binding protein. ..
- Jitrapakdee S, Wallace J. The biotin enzyme family: conserved structural motifs and domain rearrangements. Curr Protein Pept Sci. 2003;4:217-29 pubmed..These structural homologies are so extensive as to be highly suggestive of evolutionary relationships between biotin carboxylases and these other enzymes. ..
- Abbott J, Newell J, Lightcap C, Olanich M, Loughlin D, Weller M, et al. The effects of removing the GAT domain from E. coli GMP synthetase. Protein J. 2006;25:483-91 pubmed..Kinetic characterization of the ATPP/DD domain protein provides evidence that the presence of the GAT domain can regulate the activity of the ATPP domain. ..
- Shen Y, Chou C, Chang G, Tong L. Is dimerization required for the catalytic activity of bacterial biotin carboxylase?. Mol Cell. 2006;22:807-18 pubmed..Our data suggest that dimerization is not an absolute requirement for the catalytic activity of the E. coli BC subunit, and we propose a new model for the molecular mechanism of action for BC in multisubunit and multidomain ACCs. ..
- Chapman Smith A, Cronan J. Molecular biology of biotin attachment to proteins. J Nutr. 1999;129:477S-484S pubmed publisher..Both biotin domains and biotin protein ligases are very strongly conserved throughout biology. This review concerns the protein structures and mechanisms involved in the covalent attachment of biotin to proteins. ..
- An S, Kumar R, Sheets E, Benkovic S. Reversible compartmentalization of de novo purine biosynthetic complexes in living cells. Science. 2008;320:103-6 pubmed publisher..Collectively, the data provide strong evidence for the formation of a multi-enzyme complex, the "purinosome," to carry out de novo purine biosynthesis in cells. ..
- Polyak S, Chapman Smith A, Mulhern T, Cronan J, Wallace J. Mutational analysis of protein substrate presentation in the post-translational attachment of biotin to biotin domains. J Biol Chem. 2001;276:3037-45 pubmed..Our data suggest that substitution of Thr or Val for the Met N-terminal of the biotinyl-Lys results in mutants specifically compromised in their interaction with BPL. ..
- Howarth M, Takao K, Hayashi Y, Ting A. Targeting quantum dots to surface proteins in living cells with biotin ligase. Proc Natl Acad Sci U S A. 2005;102:7583-8 pubmed..We performed time-lapse imaging of single QDs bound to AMPA receptors in neurons, and we compared the trafficking of different AMPA receptor subunits by using two-color pulse-chase labeling. ..
- Devroede N, Huysveld N, Charlier D. Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. J Bacteriol. 2006;188:3236-45 pubmed..Finally, the analysis of a P1 derivative devoid of its control region has led to a reappraisal of the effect of excess adenine on P1 and has revealed that P1 has no need for a UP element. ..
- Brodsky G, Barnes T, Bleskan J, Becker L, Cox M, Patterson D. The human GARS-AIRS-GART gene encodes two proteins which are differentially expressed during human brain development and temporally overexpressed in cerebellum of individuals with Down syndrome. Hum Mol Genet. 1997;6:2043-50 pubmed..In contrast, the GARS and GARS-AIRS-GART proteins continue to be expressed during the postnatal development of the cerebellum in individuals with Down syndrome. ..
- Endrizzi J, Kim H, Anderson P, Baldwin E. Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets. Biochemistry. 2004;43:6447-63 pubmed publisher..Overall, the E. coli structure provides a framework for homology modeling of other CTPSs and structure-based design of anti-CTPS therapeutics...
- Chapman Smith A, Cronan J. The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity. Trends Biochem Sci. 1999;24:359-63 pubmed..These, together with mutational analyses of biotinylated proteins, are beginning to elucidate the exceptional specificity of this protein modification. ..
- Kwon K, Beckett D. Function of a conserved sequence motif in biotin holoenzyme synthetases. Protein Sci. 2000;9:1530-9 pubmed..These results are of general significance for understanding structure-function relationships in biotin holoenzyme synthetases. ..
- Pappas A, Yang W, Park T, Carman G. Nucleotide-dependent tetramerization of CTP synthetase from Saccharomyces cerevisiae. J Biol Chem. 1998;273:15954-60 pubmed..Taken together, these results indicated that enzyme tetramerization was required for CTP synthetase activity and that enzyme phosphorylation played an important role in the tetramerization and regulation of the enzyme. ..
- Parrott M, Barry M. Metabolic biotinylation of secreted and cell surface proteins from mammalian cells. Biochem Biophys Res Commun. 2001;281:993-1000 pubmed..coli. This technique can be used to biotinylate secreted proteins for purification or targeting and also for biotinylating the surfaces of mammalian cells to facilitate their labeling and purification from other nontagged cells. ..
- Mukhopadhyay B, Purwantini E, Kreder C, Wolfe R. Oxaloacetate synthesis in the methanarchaeon Methanosarcina barkeri: pyruvate carboxylase genes and a putative Escherichia coli-type bifunctional biotin protein ligase gene (bpl/birA) exhibit a unique organization. J Bacteriol. 2001;183:3804-10 pubmed publisher..We found the element Tyr(Phe)ProX(5)Phe(Tyr) to be fully conserved in biotin-dependent enzymes; it might function as the hinge for their "swinging arms."..
- Higgins M, Loiselle D, Haystead T, Graves L. Human cytidine triphosphate synthetase 1 interacting proteins. Nucleosides Nucleotides Nucleic Acids. 2008;27:850-7 pubmed publisher..Thus, these studies provide novel information on the potential interacting proteins that may regulate CTPS1 function or intracellular localization. ..
- Endrizzi J, Kim H, Anderson P, Baldwin E. Mechanisms of product feedback regulation and drug resistance in cytidine triphosphate synthetases from the structure of a CTP-inhibited complex. Biochemistry. 2005;44:13491-9 pubmed..This arrangement allows for independent adaptation of UTP and CTP binding affinities while efficiently utilizing the enzyme surface. ..
- Sibler A, Kempf E, Glacet A, Orfanoudakis G, Bourel D, Weiss E. In vivo biotinylated recombinant antibodies: high efficiency of labelling and application to the cloning of active anti-human IgG1 Fab fragments. J Immunol Methods. 1999;224:129-40 pubmed..In addition, we found that these recombinant Fabs labelled with biotin in vivo are useful for the specific detection of human IgG1 by a solid-phase immunoassay. ..
- Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N. Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate. J Biol Chem. 2008;283:14739-50 pubmed publisher..The existence of formation and product stages before and after the reaction stage would be favorable to ensure both the reaction efficiency and the extreme substrate specificity of the biotinylation reaction...
- Beckett D, Kovaleva E, Schatz P. A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation. Protein Sci. 1999;8:921-9 pubmed..We conclude that the 14-mer peptide efficiently mimics the biotin acceptor function of the much larger protein domain normally recognized by BirA. ..
- Lunn F, MacLeod T, Bearne S. Mutational analysis of conserved glycine residues 142, 143 and 146 reveals Gly(142) is critical for tetramerization of CTP synthase from Escherichia coli. Biochem J. 2008;412:113-21 pubmed publisher..This 'structural sensitivity' may limit the number and/or types of mutations that could be selected for during the development of resistance to cytotoxic pyrimidine nucleotide analogues. ..
- Wood Z, Weaver L, Brown P, Beckett D, Matthews B. Co-repressor induced order and biotin repressor dimerization: a case for divergent followed by convergent evolution. J Mol Biol. 2006;357:509-23 pubmed
- Eisenstein E, Beckett D. Dimerization of the Escherichia coli biotin repressor: corepressor function in protein assembly. Biochemistry. 1999;38:13077-84 pubmed..The results suggest that one mechanism by which the adenylate promotes binding of BirA to the biotin operator is by promoting repressor dimerization. ..
- Barker D, Campbell A. Genetic and biochemical characterization of the birA gene and its product: evidence for a direct role of biotin holoenzyme synthetase in repression of the biotin operon in Escherichia coli. J Mol Biol. 1981;146:469-92 pubmed
- Ozier Kalogeropoulos O, Fasiolo F, Adeline M, Collin J, Lacroute F. Cloning, sequencing and characterization of the Saccharomyces cerevisiae URA7 gene encoding CTP synthetase. Mol Gen Genet. 1991;231:7-16 pubmed..This could involve either a divergent duplicated gene or a different route beginning with the amination of uridine mono- or diphosphate. ..
- Aimi J, Qiu H, Williams J, Zalkin H, Dixon J. De novo purine nucleotide biosynthesis: cloning of human and avian cDNAs encoding the trifunctional glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase by functional complementation. Nucleic Acids Res. 1990;18:6665-72 pubmed..Initial efforts to compare the expression of GARS-AIRS-GART between a normal fibroblast cell line and a Downs Syndrome cell line indicate that the levels of RNA are similar. ..
- Nadkarni A, McDonough V, Yang W, Stukey J, Ozier Kalogeropoulos O, Carman G. Differential biochemical regulation of the URA7- and URA8-encoded CTP synthetases from Saccharomyces cerevisiae. J Biol Chem. 1995;270:24982-8 pubmed..The URA7-encoded CTP synthetase mRNA was 2-fold more abundant when compared with URA8-encoded CTP synthetase mRNA. Both CTP synthetase isoforms were maximally expressed in the exponential phase of growth. ..
- Waldrop G, Rayment I, Holden H. Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase. Biochemistry. 1994;33:10249-56 pubmed..Those amino acid residues believed to form part of the active site pocket include His 209-Glu 211, His 236-Glu 241, Glu 276, Ile 287-Glu 296, and Arg 338.2+ represents the first X-ray model of a biotin-dependent carboxylase. ..
- Wilson K, Shewchuk L, Brennan R, Otsuka A, Matthews B. Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc Natl Acad Sci U S A. 1992;89:9257-61 pubmed..The structural details of this complex remain an open question, however. ..
- Barker D, Campbell A. The birA gene of Escherichia coli encodes a biotin holoenzyme synthetase. J Mol Biol. 1981;146:451-67 pubmed
- Margolis N, Hogan D, Tilly K, Rosa P. Plasmid location of Borrelia purine biosynthesis gene homologs. J Bacteriol. 1994;176:6427-32 pubmed..The unique plasmid location of these and perhaps other housekeeping genes may be a consequence of the segmented genomes in borreliae and reflect the need to adapt to both the arthropod and mammalian environments. ..
- Yang W, McDonough V, Ozier Kalogeropoulos O, Adeline M, Flocco M, Carman G. Purification and characterization of CTP synthetase, the product of the URA7 gene in Saccharomyces cerevisiae. Biochemistry. 1994;33:10785-93 pubmed..CTP synthetase was potently inhibited by the product CTP which also increased the positive cooperativity of the enzyme toward UTP.(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Ozier Kalogeropoulos O, Adeline M, Yang W, Carman G, Lacroute F. Use of synthetic lethal mutants to clone and characterize a novel CTP synthetase gene in Saccharomyces cerevisiae. Mol Gen Genet. 1994;242:431-9 pubmed..Nevertheless, URA8 alone also allows yeast growth, at least under standard laboratory conditions. ..
- Kaikkonen M, Viholainen J, Närvänen A, Yla Herttuala S, Airenne K. Targeting and purification of metabolically biotinylated baculovirus. Hum Gene Ther. 2008;19:589-600 pubmed publisher..These results demonstrate the utility of metabolically biotinylated baculovirus for vector targeting and viral purification applications. ..
- Heinis C, Huber A, Demartis S, Bertschinger J, Melkko S, Lozzi L, et al. Selection of catalytically active biotin ligase and trypsin mutants by phage display. Protein Eng. 2001;14:1043-52 pubmed..The results obtained provide evidence that catalytic activities can be recovered using phage display technology, but stress the importance of both library design and stringent biopanning conditions for the recovery of novel enzymes. ..
- Piyathilake C, Azrad M, Macaluso M, Johanning G, Cornwell P, Partridge E, et al. Protective association of MTHFR polymorphism on cervical intraepithelial neoplasia is modified by riboflavin status. Nutrition. 2007;23:229-35 pubmed..The practical implications of this complex gene-nutrient-disease interaction will require further investigation. ..
- Choi M, Carman G. Phosphorylation of human CTP synthetase 1 by protein kinase A: identification of Thr455 as a major site of phosphorylation. J Biol Chem. 2007;282:5367-77 pubmed..cerevisiae cells, and this was accompanied by a 2.5-fold increase in the cellular concentration of CTP and a 1.5-fold increase in the choline-dependent synthesis of phosphatidylcholine. ..
- J ger W, Peters Wendisch P, Kalinowski J, P hler A. A Corynebacterium glutamicum gene encoding a two-domain protein similar to biotin carboxylases and biotin-carboxyl-carrier proteins. Arch Microbiol. 1996;166:76-82 pubmed..Since it was not possible to inactivate the C. glutamicum gene, the gene most likely encodes a subunit of the essential acetyl-CoA carboxylase, which catalyzes the committed step in fatty acid synthesis...
- Blanchard C, Chapman Smith A, Wallace J, Waldrop G. The biotin domain peptide from the biotin carboxyl carrier protein of Escherichia coli acetyl-CoA carboxylase causes a marked increase in the catalytic efficiency of biotin carboxylase and carboxyltransferase relative to free biotin. J Biol Chem. 1999;274:31767-9 pubmed..The K(m) for holoBCCP87 was 0.45 +/- 0.07 mM while the V(max) was 2031.8 +/- 231.0 min(-1). The V/K or catalytic efficiency of carboxyltransferase with holoBCCP87 as substrate is 2000-fold greater than with biotin as substrate. ..
- Samanani N, Facchini P. Purification and characterization of norcoclaurine synthase. The first committed enzyme in benzylisoquinoline alkaloid biosynthesis in plants. J Biol Chem. 2002;277:33878-83 pubmed..NCS activity was highest in soluble protein extracts from roots followed by stems, leaves, and flower buds...