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Krishna RG, Wold F. Post-translational modification of proteins. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 67:265-98. [PMID: 8322616 DOI: 10.1002/9780470123133.ch3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R G Krishna
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston
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2
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Rivera-Hainaj RE, Pusztai-Carey M, Venkat Reddy D, Choowongkomon K, Sönnichsen FD, Carey PR. Characterization of the carboxylate delivery module of transcarboxylase: following spontaneous decarboxylation of the 1.3S-CO2- subunit by NMR and FTIR spectroscopies. Biochemistry 2002; 41:2191-7. [PMID: 11841210 DOI: 10.1021/bi0116442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcarboxylase (TC) is a multisubunit enzyme that catalyzes the transfer of a carboxylate group from methylmalonyl-CoA (MMCoA) to pyruvate. The CO2- group is shuttled between the MMCoA and pyruvate binding sites by a biotin cofactor, covalently linked to the 1.3S subunit. Fully carboxylated 1.3S can be prepared in vitro using 1.3S, MMCoA, and catalytic amounts of the TC's MMCoA-binding subunit. The 1.3S-CO2- intermediate decarboxylates spontaneously over a period of hours, and this process was characterized by 1D and 2D NMR and FTIR spectroscopies. The NMR data yielded a first-order kinetic constant of 1.4 x 10(-3) min(-1) for the spontaneous decarboxylation. This rate was calculated from the 1D NMR spectrum by measuring the reappearance of biotin's ureido NH protons and the disappearance of peaks at 6.99 and 7.67 ppm assigned to Asn-8 and/or Asn-24 from the 1.3S's N-terminus. The latter peaks are absent in the 1D spectrum of non-carboxylated 1.3S due to exchange between two or more conformations within the N-terminus causing line broadening. It is proposed that interactions between the biotin-CO2- and the N-terminal amino acids perturb this conformational equilibrium causing some N-terminal residues to appear in the 1D NMR spectrum of the carboxylated form. Further details are apparent from a comparison of the 2D spectra of the 1.3S-CO2- and 1.3S proteins, where carboxylation causes several peaks from the C-terminal half to shift as well as the appearance of resonances due to some residues located at the N-terminal half of the protein. FTIR difference spectra were used also to follow spontaneous decarboxylation of the 1.3S-CO2-. For the carboxylated 1.3S, the difference spectra provided the vibrational signature of the CO2- on the biotin ring. A doublet was identified at 1695 and 1699 cm(-1) that increased in intensity with increasing t. This is assigned to an antisymmetric stretching vibration of the CO2- group bound to biotin on the 1.3S protein. Its position and profile provide further evidence for interactions occurring between the biotin-CO2- group and the 1.3S protein. These studies demonstrate the highly mobile, "poised" nature of the 1.3S protein engineered for its role as a CO2- translocator.
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Affiliation(s)
- Rosa E Rivera-Hainaj
- Department of Biochemistry and Department of Physiology and Biophysics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4935, USA
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3
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Reddy DV, Shenoy BC, Carey PR, Sönnichsen FD. High resolution solution structure of the 1.3S subunit of transcarboxylase from Propionibacterium shermanii. Biochemistry 2000; 39:2509-16. [PMID: 10704200 DOI: 10.1021/bi9925367] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcarboxylase (TC) from Propionibacterium shermanii, a biotin-dependent enzyme, catalyzes the transfer of a carboxyl group from methylmalonyl-CoA to pyruvate to form propionyl-CoA and oxalacetate. Within the multi-subunit enzyme complex, the 1.3S subunit functions as the carboxyl group carrier and also binds the other two subunits to assist in the overall assembly of the enzyme. The 1.3S subunit is a 123 amino acid polypeptide (12.6 kDa) to which biotin is covalently attached at Lys 89. The three-dimensional solution structure of the full-length holo-1.3S subunit of TC has been solved by multidimensional heteronuclear NMR spectroscopy. The C-terminal half of the protein (51-123) is folded into a compact all-beta-domain comprising of two four-stranded antiparallel beta-sheets connected by short loops and turns. The fold exhibits a high 2-fold internal symmetry and is similar to that of the biotin carboxyl carrier protein (BCCP) of acetyl-CoA carboxylase, but lacks an extension that has been termed "protruding thumb" in BCCP. The first 50 residues, which have been shown to be involved in intersubunit interactions in the intact enzyme, appear to be disordered in the isolated 1.3S subunit. The molecular surface of the folded domain has two distinct surfaces: one side is highly charged, while the other comprises mainly hydrophobic, highly conserved residues.
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Affiliation(s)
- D V Reddy
- Department of Physiology & Biophysics, and the Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Iwane AH, Kitamura K, Tokunaga M, Yanagida T. Myosin subfragment-1 is fully equipped with factors essential for motor function. Biochem Biophys Res Commun 1997; 230:76-80. [PMID: 9020065 DOI: 10.1006/bbrc.1996.5861] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The sliding velocity of actin filaments propelled by chicken skeletal myosin subfragment-1 (S1) was measured when the tail end of S1 was specifically bound to the glass surface. To achieve the specific binding, a regulatory light chain was replaced by a recombinant fusion protein of biotin-dependent transcarboxylase (BDTC) and chicken gizzard smooth muscle regulatory light chain (cgmRLC). The BDTC-cgmRLC of S1 was then attached to the glass surface using a biotin-avidin system. The velocity of actin filaments caused by S1 bound to the surface in this manner was 6.8 +/- 0.6 microm/sec at 29 degrees C, which was 3.5-fold greater than that (1.9 +/- 0.3 microm/sec) when bound directly to the surface as in previous studies, but similar to that caused by native chicken skeletal myosin (6.5 +/- 0.6 microm/sec). The actin-activated Mg-ATPase activity was similar to that of S1 before the RLC of S1 was exchanged for BDTC-cgmRLC. The results indicate that S1 can produce a normal fast movement of actin filaments as well as hydrolyse ATP and generate force.
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Affiliation(s)
- A H Iwane
- Faculty of Engineering Science, Osaka University, Toyonaka, Japan
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Dunn MF, Encarnación S, Araíza G, Vargas MC, Dávalos A, Peralta H, Mora Y, Mora J. Pyruvate carboxylase from Rhizobium etli: mutant characterization, nucleotide sequence, and physiological role. J Bacteriol 1996; 178:5960-70. [PMID: 8830693 PMCID: PMC178453 DOI: 10.1128/jb.178.20.5960-5970.1996] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Pyruvate carboxylase (PYC), a biotin-dependent enzyme which catalyzes the conversion of pyruvate to oxaloacetate, was hypothesized to play an important anaplerotic role in the growth of Rhizobium etli during serial subcultivation in minimal media containing succinate (S. Encarnación, M. Dunn, K. Willms, and J. Mora, J. Bacteriol. 177:3058-3066, 1995). R. etli and R. tropici pyc::Tn5-mob mutants were selected for their inability to grow in minimal medium with pyruvate as a sole carbon source. During serial subcultivation in minimal medium containing 30 mM succinate, the R. etli parent and pyc mutant strains exhibited similar decreases in growth rate with each subculture. Supplementation of the medium with biotin prevented the growth decrease of the parent but not the mutant strain, indicating that PYC was necessary for the growth of R. etli under these conditions. The R. tropici pyc mutant grew normally in subcultures regardless of biotin supplementation. The symbiotic phenotypes of the pyc mutants from both species were similar to those of the parent strains. The R. etli pyc was cloned, sequenced, and found to encode a 126-kDa protein of 1,154 amino acids. The deduced amino acid sequence is highly homologous to other PYC sequences, and the catalytic domains involved in carboxylation, pyruvate binding, and biotinylation are conserved. The sequence and biochemical data show that the R. etli PYC is a member of the alpha4, homotetrameric, acetyl coenzyme A-activated class of PYCs.
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Affiliation(s)
- M F Dunn
- Departamento de Ecología Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos.
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6
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Stolz J, Darnhofer-Demar B, Sauer N. Rapid purification of a functionally active plant sucrose carrier from transgenic yeast using a bacterial biotin acceptor domain. FEBS Lett 1995; 377:167-71. [PMID: 8543043 DOI: 10.1016/0014-5793(95)01333-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A rapid and efficient method has been used for the purification of a Plantago major sucrose carrier from Saccharomyces cerevisiae. The C-terminal fusion of a bacterial biotin acceptor domain to the carrier protein did not interfere with the targeting to the yeast plasma membrane nor with the catalytic activity of the sucrose carrier. The chimeric construct is biotinylated by yeast cells in vivo and represents the only biotinylated protein in yeast membranes. Solubilized biotinylated carrier protein binds selectively to immobilized monomeric avidin and can be eluted as pure protein with free biotin. The purified protein is functionally active and catalyzes the energy-dependent transport of sucrose into proteoliposomes.
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Affiliation(s)
- J Stolz
- Lehrstuhl für Zellbiologie und Pflanzenphysiologie, Universität Regensburg, Germany
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7
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Ha J, Daniel S, Kong IS, Park CK, Tae HJ, Kim KH. Cloning of human acetyl-CoA carboxylase cDNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 219:297-306. [PMID: 7905825 DOI: 10.1111/j.1432-1033.1994.tb19941.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Acetyl-CoA carboxylase is the rate-limiting enzyme in the biogenesis of long-chain fatty acids. In order to understand the mechanisms that regulate human acetyl-CoA carboxylase at the gene level, and the relationship between its structure and function, cDNA clones for human acetyl-CoA carboxylase have been isolated and sequenced. Human acetyl-CoA-carboxylase cDNA contains 7020 nucleotides encoding a protein of 2340 amino acids with a calculated relative molecular mass of 264575. The human enzyme shows approximately 85% identity in nucleotide sequence with previously cloned rat acetyl-CoA carboxylase, and shows 90% identity in the amino acid sequence. Two human acetyl-CoA-carboxylase mRNA species, which differ in the 5' untranslated region with the same coding sequence, have been identified. The sequence analysis reveals that type I and type II acetyl-CoA-carboxylase mRNA contain 313- and 173-base-long 5' untranslated regions, respectively. The first 240 nucleotides in the 5' untranslated region of type I acetyl-CoA-carboxylase mRNA replace the first 100 nucleotides of the (G + C)-rich region of the 5' untranslated region of the type II mRNA. These two species of mRNAs are the only species of human ACC mRNA which have been detected compared to at least five species in rat tissues, and they are expressed in a tissue-specific manner.
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MESH Headings
- Acetyl-CoA Carboxylase/biosynthesis
- Acetyl-CoA Carboxylase/genetics
- Adipose Tissue/enzymology
- Amino Acid Sequence
- Animals
- Base Sequence
- Carcinoma, Hepatocellular
- Chickens
- Cloning, Molecular
- DNA, Complementary/metabolism
- Genetic Vectors
- Humans
- Isoenzymes/biosynthesis
- Isoenzymes/genetics
- Liver Neoplasms
- Molecular Sequence Data
- Polymerase Chain Reaction
- Protein Biosynthesis
- RNA, Messenger/biosynthesis
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Rats
- Restriction Mapping
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- J Ha
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-1153
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9
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Toh H, Kondo H, Tanabe T. Molecular evolution of biotin-dependent carboxylases. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 215:687-96. [PMID: 8102604 DOI: 10.1111/j.1432-1033.1993.tb18080.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Amino-acid sequences of three functional units from various biotin-dependent carboxylases, biotin carboxylase, biotin-carboxyl-carrier protein and carboxyl transferase, were investigated by computer-assisted sequence comparison to obtain information about the structure, function, and molecular evolution of the enzymes. Biotin-dependent carboxylases, except transcarboxylase and oxaloacetate decarboxylase which lack biotin carboxylase, exert their catalytic activities through the three functional units. The three functional units correspond with functional domains or subunits of the enzymes, and the genetic information for the units is encoded in different ways from enzyme to enzyme. It is known that biotin carboxylase is homologous to carbamoyl-phosphate synthetase, and that the biotin-carboxyl-carrier protein is homologous to lipoic-acid-binding domain. The evolutionary relationships between the functional units and their homologues were described. A model for the evolutionary history of the enzymes was proposed by molecular phylogenetic analysis, which shows how a wide variety of domain and/or subunit structures for the enzymes may have been established. A repeated structure was found in biotin-carboxyl-carrier protein, and the secondary structure of the protein was predicted using the observed sequence similarity with a lipoic-acid-binding domain.
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Affiliation(s)
- H Toh
- Protein Engineering Research Institute, Osaka, Japan
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10
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Shenoy B, Kumar G, Samols D. Dissection of the biotinyl subunit of transcarboxylase into regions essential for activity and assembly. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53986-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Genbauffe FS, Cooper TG. The urea amidolyase (DUR1,2) gene of Saccharomyces cerevisiae. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1991; 2:19-32. [PMID: 1802034 DOI: 10.3109/10425179109008435] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The DNA sequence of the urea amidolyase (DUR1,2) gene from S. cerevisiae has been determined. The polypeptide structure deduced from the DNA sequence contains 1,835 amino acid residues and possesses a calculated weight of 201,665 daltons which favorably correlates with that predicted from compositional analysis of purified protein (1,881 amino acid residues and a molecular weight of 203,900). The C-terminal 57 residues of the polypeptide exhibit significant homology with similarly situated sequences found in five other biotin carboxylases whose primary structures have been determined or deduced from protein and DNA sequence data, respectively. Major S1 nuclease protection fragments derived from DUR1,2 RNA-DNA hybrids exhibit apparent termini at positions -140 and -141 upstream of the coding region. The termini of minor protection fragments also occur at eleven other positions as well.
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Affiliation(s)
- F S Genbauffe
- Department of Microbiology and Immunology, University of Tennessee, Memphis 38163
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12
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Bendrat K, Berger S, Buckel W, Etzel WA, Röhm KH. Carbon-13 labelled biotin--a new probe for the study of enzyme catalyzed carboxylation and decarboxylation reactions. FEBS Lett 1990; 277:156-8. [PMID: 2269346 DOI: 10.1016/0014-5793(90)80832-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[2'-13C]Biotin was incorporated into avidin (egg white), glutaconyl-CoA decarboxylase (EC 4.1.1.70) from Acidaminococcus fermentans and the biotin carrier of transcarboxylase from Propionibacterium freudenreichii (EC 2.1.3.1). 13C-NMR measurements showed an upfield shift of the carbonyl carbon of 3.1 and 2.0 ppm for both enzymes, whereas binding to avidin induced no significant change of the chemical shift as compared to free biotin. The data indicate that the enzymes provide an electronic environment for the covalently bound biotin which favours carboxylation. In addition it was demonstrated by NMR-measurements that glutaconyl-CoA decarboxylase, from which the hydrophobic carboxy-lyase subunit (beta) was removed, could carboxylate free biotin.
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Affiliation(s)
- K Bendrat
- Fachbereich Biologie, Universität Marburg, Germany
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13
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Browner MF, Taroni F, Sztul E, Rosenberg LE. Sequence Analysis, Biogenesis, and Mitochondrial Import of the α-Subunit of Rat Liver Propionyl-CoA Carboxylase. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)63910-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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14
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Bai DH, Moon TW, López-Casillas F, Andrews PC, Kim KH. Analysis of the biotin-binding site on acetyl-CoA carboxylase from rat. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 182:239-45. [PMID: 2567668 DOI: 10.1111/j.1432-1033.1989.tb14823.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biotin-binding site of acetyl-CoA carboxylase from rat was characterized as to its amino acid sequence and relative position in the enzyme molecule. Biotin binds to the lysyl residue in the tetrapeptide Val-Met-Lys-Met; this tetrapeptide is located in close proximity to the NH2 terminus. In all other biotin-containing enzymes, the conserved tetrapeptide Ala-Met-Lys-Met is the counterpart to that of rat acetyl-CoA carboxylase; and the lysyl residue is 35 residues from the COOH terminus. To examine the significance of these unusual features of the biotinylation site of animal acetyl-CoA carboxylase, cDNA fragments were expressed in a bacterial system and the effects of specific site-directed mutagenesis were examined. Replacement of Val by Ala in the conserved tetrapeptide abolished biotinylation of the expressed protein. However, introduction of a termination codon at residue 36, in such a way that the distance between the lysine on which biotin binds and the COOH-terminal amino acid was 35 residues and the penultimate amino acid was the hydrophobic residue leucine, increased the efficiency of biotinylation, provided a substantial portion of the NH2-terminal peptide was removed.
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Affiliation(s)
- D H Bai
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907
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16
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Thampy KG, Huang WY, Wakil SJ. A rapid purification method for rat liver pyruvate carboxylase and amino acid sequence analyses of NH2-terminal and biotin peptide. Arch Biochem Biophys 1988; 266:270-6. [PMID: 3178228 DOI: 10.1016/0003-9861(88)90258-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A rapid method for the purification of pyruvate carboxylase from rat liver has been developed. The method involves extraction of the enzyme from frozen liver powder followed by polyethylene glycol fractionation and avidin-affinity chromatography. The purified enzyme has a specific activity of 9-10 mumol/min/mg protein when assayed at 22 degrees C in the presence of acetyl-CoA. Polyacrylamide gel electrophoresis of the preparation in the presence of sodium dodecyl sulfate showed the presence of one protein band with an estimated Mr 125,000 and no significant contamination by other biotin-containing enzymes. In addition to being rapid, the method is advantageous because prior isolation of mitochondria is not necessary. Using these preparations we have determined the sequence of the first 15 amino acids from the NH2-terminal end of the molecule to be Ser-Gly-Pro-Val-Ala-Pro-Leu-Asn-Val-Leu-Leu-Leu-Glu-Tyr-Pro. The sequence of the 24 amino acid residues around the biotin site was determined to be Gly-Ala-Pro-Leu-Val-Leu-Ser-Ala-Met-biocytin-Met-Glu-Thr-Val-Val-Thr-Ser -Pro- Thr-Glu-Gly-Thr-Ile-Arg.
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Affiliation(s)
- K G Thampy
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030
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17
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Schwarz E, Oesterhelt D, Reinke H, Beyreuther K, Dimroth P. The sodium ion translocating oxalacetate decarboxylase of Klebsiella pneumoniae. Sequence of the biotin-containing alpha-subunit and relationship to other biotin-containing enzymes. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)81564-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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18
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Hanemaaijer R, Janssen A, de Kok A, Veeger C. The dihydrolipoyltransacetylase component of the pyruvate dehydrogenase complex from Azotobacter vinelandii. Molecular cloning and sequence analysis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 174:593-9. [PMID: 3292237 DOI: 10.1111/j.1432-1033.1988.tb14140.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The gene encoding the dihydrolipoyltransacetylase component (E2) of the pyruvate dehydrogenase complex from Azotobacter vinelandii has been cloned in Escherichia coli. A plasmid containing a 2.8-kbp insert of A. vinelandii chromosomal DNA was obtained and its nucleotide sequence determined. The gene comprises 1911 base pairs, 637 codons excluding the initiation codon GUG and stop codon UGA. It is preceded by the gene encoding the pyruvate dehydrogenase component (E1) of pyruvate dehydrogenase complex and by an intercistronic region of 11 base pairs containing a good ribosome binding site. The gene is followed downstream by a strong terminating sequence. The relative molecular mass (64913), amino acid composition and N-terminal sequence are in good agreement with information obtained from studies on the purified enzyme. Approximately the first half of the gene codes for the lipoyl domain. Three very homologous sequences are present, which are translated in three almost identical units, alternated with non-homologous regions which are very rich in alanyl and prolyl residues. The N-terminus of the catalytic domain is sited at residue 381. Between the lipoyl domain and the catalytic domain, a region of about 50 residues is found containing many charged amino acid residues. This region is characterized as a hinge region and is involved in the binding of the pyruvate dehydrogenase and lipoamide dehydrogenase components. The homology with the dihydrolipoyltransacetylase from E. coli is high: 50% amino acid residues are identical.
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Affiliation(s)
- R Hanemaaijer
- Department of Biochemistry, Agricultural University, Wageningen, The Netherlands
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19
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Samols D, Thornton CG, Murtif VL, Kumar GK, Haase FC, Wood HG. Evolutionary conservation among biotin enzymes. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68661-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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20
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Takai T, Yokoyama C, Wada K, Tanabe T. Primary structure of chicken liver acetyl-CoA carboxylase deduced from cDNA sequence. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)69116-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Murtif VL, Samols D. Mutagenesis affecting the carboxyl terminus of the biotinyl subunit of transcarboxylase. Effects on biotination. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)60886-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Abstract
To improve our understanding of pyruvate carboxylase (PC)(EC 6.4.1.1) structure and the evolution of the biotin-dependent carboxylases we have isolated and sequenced a yeast (Saccharomyces cerevisiae) genomic DNA fragment encoding PC. The identity of the cloned gene was confirmed by comparing the encoded protein with the sequence of a 26 amino acid biotin-containing peptide isolated from yeast PC. The yeast PC sequence is homologous (43% amino acid homology) to the rat PC sequence, although the carboxyl-terminus was found to be 44 residues from the biotinyl-lysine whereas in all biotin carboxylases sequenced to date the biotin is 35 residues from the carboxyl-terminus.
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Lamhonwah AM, Quan F, Gravel RA. Sequence homology around the biotin-binding site of human propionyl-CoA carboxylase and pyruvate carboxylase. Arch Biochem Biophys 1987; 254:631-6. [PMID: 3555348 DOI: 10.1016/0003-9861(87)90146-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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.
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Takai T, Wada K, Tanabe T. Primary structure of the biotin-binding site of chicken liver acetyl-CoA carboxylase. FEBS Lett 1987; 212:98-102. [PMID: 2879745 DOI: 10.1016/0014-5793(87)81564-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Limited proteolysis of chicken liver acetyl-CoA carboxylase by staphylococcal serine proteinase yielded a fragment of 31 kDa which contained the biotinyl active site. This polypeptide was purified by preparative polyacrylamide gel electrophoresis and characterized. The complete amino acid sequence of this polypeptide has been deduced from the nucleotide sequence of cloned DNA complementary to the chicken liver acetyl-CoA carboxylase mRNA. A highly conserved sequence of Met-Lys-Met was found in the biotin-binding site. Appreciable homology was observed among the sequences in close vicinity of the biotin sites of chicken liver acetyl-CoA carboxylase and other biotin-dependent carboxylases including biotin carboxyl carrier protein of Escherichia coli acetyl-CoA carboxylase.
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25
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Skrzypczak-Jankun E, Tulinsky A, Fillers JP, Kumar KG, Wood HG. Preliminary crystallographic data and quaternary structural implications of the central subunit of the multi-subunit complex transcarboxylase. J Mol Biol 1986; 188:495-8. [PMID: 3735431 DOI: 10.1016/0022-2836(86)90172-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The hexameric central subunit (Mr = 360,000) of the multi-subunit complex transcarboxylase has been crystallized by bulk dialysis against 250 mM-sodium acetate (pH 5.5). The crystals are cubic, a = 193.1 A, space group P4(1)32 or enantiomorph. The number of molecules per unit cell is four and was deduced from the density of the crystals (1.10 g cm-3) and the mother liquor (1.01 g cm-3) and the specific volume of the protein calculated from molecular dimensions obtained from electron microscopy studies. Four molecules per cell requires the central subunits to lie on 3-fold axes, which are perpendicular to 2-fold rotation axes, so that the molecules satisfy 32 symmetry giving one subunit as the asymmetric unit. Of the four possible models that have been considered for the quaternary structure of transcarboxylase, only that with antiparallel subunits, two sets of isologous binding sites and D3 symmetry is in agreement with the symmetry requirements of the cubic crystals.
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26
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Gravel RA, Robinson BH. Biotin-dependent carboxylase deficiencies (propionyl-CoA and pyruvate carboxylases). Ann N Y Acad Sci 1985; 447:225-34. [PMID: 3925855 DOI: 10.1111/j.1749-6632.1985.tb18441.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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KUMAR GANESHK, BEEGEN HELGA, WOOD HARLANDG. Assembly of Subunits and Structure of Transcarboxylase: Sequence Requirement and Electron Microscopy of Crystals. Ann N Y Acad Sci 1985. [DOI: 10.1111/j.1749-6632.1985.tb18460.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Wood HG, Kumar GK. Transcarboxylase: its quaternary structure and the role of the biotinyl subunit in the assembly of the enzyme and in catalysis. Ann N Y Acad Sci 1985; 447:1-22. [PMID: 3893281 DOI: 10.1111/j.1749-6632.1985.tb18422.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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29
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Abstract
There appear to be at least two underlying aetiologies for combined carboxylase deficiency; firstly, a failure of biotinylation of apocarboxylases due to a mutation of holocarboxylase synthetase (EC 6.3.4.10) which results in an enzyme with a high Km with respect to biotin and secondly, a failure of biotinylation due to a lowered availability of biotin due to biotinidase deficiency (EC 3.5.1.12). In both these disorders secondary defects of all four biotin-dependent carboxylases result which in turn causes the excretion of the metabolites characteristic of the isolated carboxylase deficiencies. In addition, both disorders respond biochemically and clinically to the administration of large amounts of biotin.
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30
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Freytag SO, Collier KJ. Molecular cloning of a cDNA for human pyruvate carboxylase. Structural relationship to other biotin-containing carboxylases and regulation of mRNA content in differentiating preadipocytes. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)90822-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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31
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Kondo H, Uno S, Komizo Y, Sunamoto J. Importance of methionine residues in the enzymatic carboxylation of biotin-containing peptides representing the local biotinyl site of E. coli acetyl-CoA carboxylase. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1984; 23:559-64. [PMID: 6147321 DOI: 10.1111/j.1399-3011.1984.tb03127.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A biotin-containing hexapeptide Ac-Glu-Ala-Met-Bct-Met-Met (1) that represents the local biotin-containing site of Escherichia coli acetyl-CoA carboxylase has been prepared by the solid phase method. Peptide 1 is carboxylated by the biotin carboxylase subunit dimer of E. coli acetyl-CoA carboxylase with the following kinetic parameters; Km 12 mM, Vmax 2.8 microM X min-1. These compare with the parameters for biotin of Km 214 mM and Vmax 28 microM X min -1. Hence, the overall reactivity (Vmax/Km) of 1 is 1.8 times greater than that of free biotin. When all methionines in 1 are replaced by alanine, the resulting peptide (2) retains a similar binding ability but with a much decreased Vmax. It was also found that peptide 3, which carries an N epsilon-benzyloxycarbonyllysine in place of biocytin in 1, decreases the Km of biotin threefold.
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32
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33
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Kondo H, Uno S, Moriuchi F, Sunamoto J, Ogushi S, Tsuru D. Synthesis and Enzymatic Carboxylation of a Biotin-containing Peptide Representing the Coenzyme Binding Site ofE. coliAcetyl–CoA Carboxylase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1983. [DOI: 10.1246/bcsj.56.1176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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34
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The amino acid sequences of the biotinyl subunit essential for the association of transcarboxylase. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33523-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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35
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Kondo H, Moriuchi F, Sunamoto J. Synthesis of Biotin-containing Peptides Representing the Biotin Binding Site ofE.coliAcetyl–CoA Carboxylase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1982. [DOI: 10.1246/bcsj.55.1579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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36
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Harmon F, Berger M, Beegen H, Wood H, Wrigley N. Transcarboxylase. An electron microscopic study of the enzyme with antibodies to biotin. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70584-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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37
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Comparison of the biotination of apotranscarboxylase and its aposubunits. Is assembly essential for biotination? J Biol Chem 1980. [DOI: 10.1016/s0021-9258(20)79717-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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