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1.
Biosci Biotechnol Biochem ; 85(9): 2026-2029, 2021 Aug 25.
Article in English | MEDLINE | ID: mdl-34190979

ABSTRACT

Quinohemoprotein amine dehydrogenase (QHNDH) containing a peptidyl quinone cofactor, cysteine tryptophylquinone, is produced in the periplasm of Gram-negative bacteria through an intricate process of post-translational modification that requires at least 8 genes including those encoding 3 nonidentical subunits and 3 modifying enzymes. Our heterologous expression study has revealed that the 8 genes are necessary and sufficient for the QHNDH biogenesis.


Subject(s)
Oxidoreductases Acting on CH-NH Group Donors/biosynthesis , Electrophoresis, Polyacrylamide Gel , Oxidoreductases Acting on CH-NH Group Donors/chemistry , Oxidoreductases Acting on CH-NH Group Donors/genetics , Protein Conformation , Protein Processing, Post-Translational
2.
Nat Commun ; 12(1): 933, 2021 02 10.
Article in English | MEDLINE | ID: mdl-33568660

ABSTRACT

Bioconversion of peptidyl amino acids into enzyme cofactors is an important post-translational modification. Here, we report a flavoprotein, essential for biosynthesis of a protein-derived quinone cofactor, cysteine tryptophylquinone, contained in a widely distributed bacterial enzyme, quinohemoprotein amine dehydrogenase. The purified flavoprotein catalyzes the single-turnover dihydroxylation of the tryptophylquinone-precursor, tryptophan, in the protein substrate containing triple intra-peptidyl crosslinks that are pre-formed by a radical S-adenosylmethionine enzyme within the ternary complex of these proteins. Crystal structure of the peptidyl tryptophan dihydroxylase reveals a large pocket that may dock the protein substrate with the bound flavin adenine dinucleotide situated close to the precursor tryptophan. Based on the enzyme-protein substrate docking model, we propose a chemical reaction mechanism of peptidyl tryptophan dihydroxylation catalyzed by the flavoprotein monooxygenase. The diversity of the tryptophylquinone-generating systems suggests convergent evolution of the peptidyl tryptophan-derived cofactors in different proteins.


Subject(s)
Bacterial Proteins/metabolism , Coenzymes/metabolism , Dipeptides/metabolism , Flavoproteins/metabolism , Indolequinones/metabolism , Mixed Function Oxygenases/metabolism , Paracoccus denitrificans/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Catalysis , Coenzymes/chemistry , Dipeptides/chemistry , Flavin-Adenine Dinucleotide/chemistry , Flavin-Adenine Dinucleotide/metabolism , Flavoproteins/chemistry , Indolequinones/chemistry , Mixed Function Oxygenases/chemistry , Paracoccus denitrificans/chemistry , Paracoccus denitrificans/genetics , Paracoccus denitrificans/metabolism , Tryptophan/chemistry , Tryptophan/metabolism
3.
Virology ; 497: 23-32, 2016 10.
Article in English | MEDLINE | ID: mdl-27420796

ABSTRACT

Sodium taurocholate cotransporting polypeptide (NTCP) was recently discovered as a hepatitis B virus (HBV) receptor, however, the detailed mechanism of HBV entry is not yet fully understood. We investigated the cellular entry pathway of HBV using recombinant HBV surface antigen L protein particles (bio-nanocapsules, BNCs). After the modification of L protein in BNCs with myristoyl group, myristoylated BNCs (Myr-BNCs) were found to bind to NTCP in vitro, and inhibit in vitro HBV infection competitively, suggesting that Myr-BNCs share NTCP-dependent infection machinery with HBV. Nevertheless, the cellular entry rates of Myr-BNCs and plasma-derived HBV surface antigen (HBsAg) particles were the same as those of BNCs in NTCP-overexpressing HepG2 cells. Moreover, the cellular entry of these particles was mainly driven by heparan sulfate proteoglycan-mediated endocytosis regardless of NTCP expression. Taken together, cell-surface NTCP may not be involved in the cellular uptake of HBV, while presumably intracellular NTCP plays a critical role.


Subject(s)
Heparan Sulfate Proteoglycans/metabolism , Hepatitis B virus/physiology , Hepatitis B/metabolism , Hepatitis B/virology , Organic Anion Transporters, Sodium-Dependent/metabolism , Symporters/metabolism , Viral Envelope Proteins/metabolism , Amino Acid Sequence , Animals , Cells, Cultured , Endocytosis , Humans , Nanoparticles/chemistry , Organic Anion Transporters, Sodium-Dependent/chemistry , Protein Binding , Protein Interaction Domains and Motifs , Symporters/chemistry , Viral Envelope Proteins/chemistry , Virus Internalization , Virus Uncoating
4.
Biochem Biophys Res Commun ; 474(2): 406-412, 2016 05 27.
Article in English | MEDLINE | ID: mdl-27120459

ABSTRACT

A hollow nanoparticle known as a bio-nanocapsule (BNC) consisting of hepatitis B virus (HBV) envelope L protein and liposome (LP) can encapsulate drugs and genes and thereby deliver them in vitro and in vivo to human hepatic tissues, specifically by utilizing the HBV-derived infection machinery. Recently, we identified a low pH-dependent fusogenic domain at the N-terminal part of the pre-S1 region of the HBV L protein (amino acid residues 9 to 24; NPLGFFPDHQLDPAFG), which shows membrane destabilizing activity (i.e., membrane fusion, membrane disruption, and payload release) upon interaction with target LPs. In this study, instead of BNC and HBV, we generated LPs displaying a mutated form of the pre-S1 (9-24) peptide, and performed a membrane disruption assay using target LPs containing pyranine (fluorophore) and p-xylene-bis (N-pyridinium bromide) (DPX) as a quencher. The membrane disruption activity was found to correlate with the hydrophobicity of the whole structure, while the peptide retained a random-coil structure even under low pH condition. One large hydrophobic cluster (I) and one small hydrophobic cluster (II) residing in the peptide would be connected by the protonation of residues D16 and D20, and thereby exhibit strong membrane disruption activity in a low pH-dependent manner. Furthermore, the introduction of a positively charged residue enhanced the activity significantly, suggesting that a sole positively charged residue (H17) may be important for the interaction with target LPs by electrostatic interaction. Collectively, these results suggest that the pre-S1 (9-24) peptide may be involved in the endosomal escape of the BNC's payloads, as well as in the HBV uncoating process.


Subject(s)
Cell Membrane/chemistry , DNA Mutational Analysis/methods , Hepatitis B Surface Antigens/chemistry , Hepatitis B Surface Antigens/genetics , Hepatitis B virus/genetics , Mutation/genetics , Protein Precursors/chemistry , Protein Precursors/genetics , Base Sequence , Hydrogen-Ion Concentration , Hydrophobic and Hydrophilic Interactions , Molecular Sequence Data , Polymorphism, Single Nucleotide/genetics , Protein Domains/genetics
5.
Acta Biomater ; 35: 238-47, 2016 Apr 15.
Article in English | MEDLINE | ID: mdl-26876802

ABSTRACT

The bio-nanocapsule (BNC) is an approximately 30-nm particle comprising the hepatitis B virus (HBV) envelope L protein and a lipid bilayer. The L protein harbors the HBV-derived infection machinery; therefore, BNC can encapsulate payloads such as drugs, nucleic acids, and proteins and deliver them into human hepatocytes specifically in vitro and in vivo. To diversify the possible functions of BNC, we generated ZZ-BNC by replacing the domain indispensable for the human hepatotrophic property of BNC (N-terminal region of L protein) with the tandem form of the IgG Fc-binding Z domain of Staphylococcus aureus protein A. Thus, the ZZ-BNC is an active targeting-based drug delivery system (DDS) nanocarrier that depends on the specificity of the IgGs displayed. However, the Z domain limits the animal species and subtypes of IgGs that can be displayed on ZZ-BNC. In this study, we introduced into BNC an Ig κ light chain-binding B1 domain of Finegoldia magna protein L (protein-L B1 domain) and an Ig Fc-binding C2 domain of Streptococcus species protein G (protein-G C2 domain) to produce LG-BNC. The LL-BNC was constructed in a similar way using a tandem form of the protein-L B1 domain. Both LG-BNC and LL-BNC could display rat IgGs, mouse IgG1, human IgG3, and human IgM, all of which not binding to ZZ-BNC, and accumulate in target cells in an antibody specificity-dependent manner. Thus, these BNCs could display a broad spectrum of Igs, significantly improving the prospects for BNCs as active targeting-based DDS nanocarriers. STATEMENT OF SIGNIFICANCE: We previously reported that ZZ-BNC, bio-nanocapsule deploying the IgG-binding Z domain of protein A, could display cell-specific antibody in an oriented immobilization manner, and act as an active targeting-based DDS nanocarrier. Since the Z domain can only bind to limited types of Igs, we generated BNCs deploying other Ig-binding domains: LL-BNC harboring the tandem form of Ig-binding domain of protein L, and LG-BNC harboring the Ig binding domains of protein L and protein G sequentially. Both BNCs could display a broader spectrum of Igs than does the ZZ-BNC. When these BNCs displayed anti-CD11c IgG or anti-EGFR IgG, both of which cannot bind to Z domain, they could bind to and then enter their respective target cells.


Subject(s)
Biocompatible Materials/chemistry , Drug Delivery Systems/methods , Immunoglobulins/metabolism , Nanocapsules/chemistry , Animals , Antibodies/metabolism , Endocytosis , Glycoside Hydrolases/metabolism , Humans , Immunoglobulin G/metabolism , Kinetics , Mice , Nanocapsules/ultrastructure , Protein Domains , Rats , Saccharomyces cerevisiae/metabolism
6.
Biotechnol Bioeng ; 113(8): 1796-804, 2016 08.
Article in English | MEDLINE | ID: mdl-26853220

ABSTRACT

Protein phosphorylation is an important post-translational modification for intracellular signaling molecules, mostly found in serine and threonine residues. Tyrosine phosphorylations are very few events (less than 0.1% to phosphorylated serine/threonine residues), but capable of governing cell fate decisions involved in proliferation, differentiation, apoptosis, and oncogenic transformation. Hence, it is important for drug discovery and system biology to measure the intracellular level of phosphotyrosine. Although mammalian cells have been conventionally utilized for this purpose, accurate determination of phosphotyrosine level often suffers from high background due to the unexpected crosstalk among endogenous signaling molecules. This situation led us firstly to establish the ligand-induced activation of homomeric receptor tyrosine kinase (i.e., epidermal growth factor receptor) in Saccharomyces cerevisiae, a lower eukaryote possessing organelles similar to higher eukaryote but not showing substantial level of tyrosine kinase activity. In this study, we expressed heteromeric receptor tyrosine kinase (i.e., a complex of interleukin-5 receptor (IL5R) α chain, common ß chain, and JAK2 tyrosine kinase) in yeast. When coexpressed with a cell wall-anchored form of IL5, the yeast exerted the autophosphorylation of JAK2, followed by the phosphorylation of transcription factor STAT5a and subsequent nuclear accumulation of phosphorylated STAT5a. Taken together, yeast could be an ideal host for sensitive detection of phosphotyrosine generated by a wide variety of tyrosine kinases. Biotechnol. Bioeng. 2016;113: 1796-1804. © 2016 Wiley Periodicals, Inc.


Subject(s)
Cytokines/metabolism , Janus Kinases/metabolism , STAT Transcription Factors/metabolism , Saccharomyces cerevisiae/metabolism , Cell Surface Display Techniques , Phosphorylation , Phosphotyrosine/metabolism , Protein-Tyrosine Kinases/metabolism , Signal Transduction
8.
J Biol Chem ; 290(38): 23094-109, 2015 Sep 18.
Article in English | MEDLINE | ID: mdl-26269595

ABSTRACT

The catalytic reaction of copper amine oxidase proceeds through a ping-pong mechanism comprising two half-reactions. In the initial half-reaction, the substrate amine reduces the Tyr-derived cofactor, topa quinone (TPQ), to an aminoresorcinol form (TPQamr) that is in equilibrium with a semiquinone radical (TPQsq) via an intramolecular electron transfer to the active-site copper. We have analyzed this reductive half-reaction in crystals of the copper amine oxidase from Arthrobacter globiformis. Anerobic soaking of the crystals with an amine substrate shifted the equilibrium toward TPQsq in an "on-copper" conformation, in which the 4-OH group ligated axially to the copper center, which was probably reduced to Cu(I). When the crystals were soaked with substrate in the presence of halide ions, which act as uncompetitive and noncompetitive inhibitors with respect to the amine substrate and dioxygen, respectively, the equilibrium in the crystals shifted toward the "off-copper" conformation of TPQamr. The halide ion was bound to the axial position of the copper center, thereby preventing TPQamr from adopting the on-copper conformation. Furthermore, transient kinetic analyses in the presence of viscogen (glycerol) revealed that only the rate constant in the step of TPQamr/TPQsq interconversion is markedly affected by the viscogen, which probably perturbs the conformational change. These findings unequivocally demonstrate that TPQ undergoes large conformational changes during the reductive half-reaction.


Subject(s)
Amine Oxidase (Copper-Containing)/chemistry , Arthrobacter/enzymology , Bacterial Proteins/chemistry , Copper/chemistry , Crystallography, X-Ray , Protein Structure, Tertiary
9.
J Biol Chem ; 290(17): 11144-66, 2015 Apr 24.
Article in English | MEDLINE | ID: mdl-25778402

ABSTRACT

The bacterial enzyme designated QhpD belongs to the radical S-adenosyl-L-methionine (SAM) superfamily of enzymes and participates in the post-translational processing of quinohemoprotein amine dehydrogenase. QhpD is essential for the formation of intra-protein thioether bonds within the small subunit (maturated QhpC) of quinohemoprotein amine dehydrogenase. We overproduced QhpD from Paracoccus denitrificans as a stable complex with its substrate QhpC, carrying the 28-residue leader peptide that is essential for the complex formation. Absorption and electron paramagnetic resonance spectra together with the analyses of iron and sulfur contents suggested the presence of multiple (likely three) [4Fe-4S] clusters in the purified and reconstituted QhpD. In the presence of a reducing agent (sodium dithionite), QhpD catalyzed the multiple-turnover reaction of reductive cleavage of SAM into methionine and 5'-deoxyadenosine and also the single-turnover reaction of intra-protein sulfur-to-methylene carbon thioether bond formation in QhpC bound to QhpD, producing a multiknotted structure of the polypeptide chain. Homology modeling and mutagenic analysis revealed several conserved residues indispensable for both in vivo and in vitro activities of QhpD. Our findings uncover another challenging reaction catalyzed by a radical SAM enzyme acting on a ribosomally translated protein substrate.


Subject(s)
Bacterial Proteins/chemistry , Iron-Sulfur Proteins/chemistry , Oxidoreductases/chemistry , Paracoccus denitrificans/enzymology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Electron Spin Resonance Spectroscopy , Iron-Sulfur Proteins/genetics , Iron-Sulfur Proteins/metabolism , Oxidoreductases/genetics , Oxidoreductases/metabolism , Paracoccus denitrificans/genetics
10.
Biochemistry ; 53(5): 895-907, 2014 Feb 11.
Article in English | MEDLINE | ID: mdl-24437536

ABSTRACT

The structural genes encoding quinohemoprotein amine dehydrogenase (QHNDH) in Gram-negative bacteria constitute a polycistronic operon together with several nearby genes, which are collectively termed "qhp". We previously showed that the qhpD gene, which lies between qhpA and qhpC (encoding the α and γ subunits of QHNDH, respectively), and the qhpE gene, which follows qhpB (encoding the ß subunit), both encode enzymes specifically involved in the posttranslational modification of the γ subunit and are hence essential for QHNDH biogenesis in Paracoccus denitrificans [Ono, K., et al. (2006) J. Biol. Chem. 281, 13672-13684; Nakai, T., et al. (2012) J. Biol. Chem. 287, 6530-6538]. Here we further demonstrate that the qhpF gene, which follows qhpE, and the qhpG and qhpR genes, peripherally located in the complementary strand, are also indispensable for QHNDH biogenesis. The qhpF gene encodes an efflux ABC transporter, which probably translocates the γ subunit into the periplasm in a process coupled with hydrolysis of ATP. The qhpG gene encodes a putative FAD-dependent monooxygenase, which is required for the generation of the quinone cofactor in the γ subunit. Finally, the qhpR gene encodes an AraC family transcriptional regulator, which activates expression of the qhp operon in response to the addition of n-butylamine to the culture medium. Database analysis of the qhp genes reveals that they are very widely distributed, not only in many Gram-negative species but also in a few Gram-positive bacteria.


Subject(s)
Bacterial Proteins/genetics , Genes, Bacterial , Oxidoreductases Acting on CH-NH Group Donors/genetics , Bacterial Proteins/metabolism , Base Sequence , Butylamines/pharmacology , Databases, Genetic , Gram-Negative Bacteria/enzymology , Gram-Negative Bacteria/genetics , Molecular Sequence Data , Mutation , Operon , Oxidoreductases Acting on CH-NH Group Donors/metabolism , Periplasm/metabolism , Promoter Regions, Genetic , Protein Subunits/genetics , Protein Subunits/metabolism , Protein Transport , Transcriptional Activation
11.
J Biol Chem ; 287(9): 6530-8, 2012 Feb 24.
Article in English | MEDLINE | ID: mdl-22235135

ABSTRACT

Quinohemoprotein amine dehydrogenase (QHNDH), an αßγ heterotrimer present in the periplasm of several Gram-negative bacteria, catalyzes the oxidative deamination of various aliphatic amines such as n-butylamine for assimilation as carbon and energy sources. The γ subunit of mature QHNDH contains a protein-derived quinone cofactor, cysteine tryptophylquinone, and three intrapeptidyl thioether cross-links between Cys and Asp or Glu residues. In its cytoplasmic nascent form, the γ subunit has a 28-residue N-terminal leader peptide that is necessary for the production of active QHNDH but must be removed in the following maturation process. Here, we describe the role of a subtilisin-like serine protease encoded in the fifth ORF of the n-butylamine-utilizing operon of Paracoccus denitrificans (termed ORF5) in QHNDH biogenesis. ORF5 disruption caused bacterial cell growth inhibition in n-butylamine-containing medium and production of inactive QHNDH, in which the γ subunit retained the leader peptide. Supply of plasmid-encoded ORF5 restored the cell growth and production of active QHNDH, containing the correctly processed γ subunit. ORF5 expressed in Escherichia coli but not its catalytic triad mutant cleaved synthetic peptides surrogating for the γ subunit leader peptide, although extremely slowly. The cleaved leader peptide remained unstably bound to ORF5, most likely as an acyl enzyme intermediate attached to the active-site Ser residue. These results demonstrate that ORF5 is essential for QHNDH biogenesis, serving as a processing protease to cleave the γ subunit leader peptide nearly in a disposable manner.


Subject(s)
Oxidoreductases Acting on CH-NH Group Donors/genetics , Paracoccus denitrificans/enzymology , Paracoccus denitrificans/genetics , Serine Proteases/genetics , Serine Proteases/metabolism , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Escherichia coli/genetics , Molecular Sequence Data , Mutagenesis/physiology , Open Reading Frames/genetics , Oxidoreductases Acting on CH-NH Group Donors/chemistry , Paracoccus denitrificans/growth & development , Plasmids/genetics , Protein Processing, Post-Translational/physiology , Protein Structure, Tertiary , Subtilisin/genetics , Subtilisin/metabolism
13.
J Biol Chem ; 285(8): 5282-95, 2010 Feb 19.
Article in English | MEDLINE | ID: mdl-20018860

ABSTRACT

Mitochondrial mRNA editing in trypanosomatid parasites involves several multiprotein assemblies, including three very similar complexes that contain the key enzymatic editing activities and sediment at ~20S on glycerol gradients. These ~20S editosomes have a common set of 12 proteins, including enzymes for uridylyl (U) removal and addition, 2 RNA ligases, 2 proteins with RNase III-like domains, and 6 proteins with predicted oligonucleotide binding (OB) folds. In addition, each of the 3 distinct ~20S editosomes contains a different RNase III-type endonuclease, 1 of 3 related proteins and, in one case, an additional exonuclease. Here we present a protein-protein interaction map that was obtained through a combination of yeast two-hybrid analysis and subcomplex reconstitution with recombinant protein. This map interlinks ten of the proteins and in several cases localizes the protein region mediating the interaction, which often includes the predicted OB-fold domain. The results indicate that the OB-fold proteins form an extensive protein-protein interaction network that connects the two trimeric subcomplexes that catalyze U removal or addition and RNA ligation. One of these proteins, KREPA6, interacts with the OB-fold zinc finger protein in each subcomplex that interconnects their two catalytic proteins. Another OB-fold protein, KREPA3, appears to link to the putative endonuclease subcomplex. These results reveal a physical organization that underlies the coordination of the various catalytic and substrate binding activities within the ~20S editosomes during the editing process.


Subject(s)
Multienzyme Complexes/metabolism , Peptide Mapping , Protozoan Proteins/metabolism , RNA Editing/physiology , Ribonuclease III/metabolism , Ribonucleoproteins/metabolism , Trypanosoma brucei brucei/enzymology , Multienzyme Complexes/genetics , Protozoan Proteins/genetics , RNA/biosynthesis , RNA/genetics , RNA, Messenger/biosynthesis , RNA, Messenger/genetics , RNA, Mitochondrial , RNA, Protozoan/biosynthesis , RNA, Protozoan/genetics , Ribonuclease III/genetics , Ribonucleoproteins/genetics , Trypanosoma brucei brucei/genetics
14.
J Biochem ; 143(6): 747-58, 2008 Jun.
Article in English | MEDLINE | ID: mdl-18316329

ABSTRACT

Pyruvate dehydrogenase (PDH), branched-chain 2-oxo acid dehydrogenase (BCDH) and 2-oxoglutarate dehydrogenase (OGDH) are multienzyme complexes that play crucial roles in several common metabolic pathways. These enzymes belong to a family of 2-oxo acid dehydrogenase complexes that contain multiple copies of three different components (E1, E2 and E3). For the Thermus thermophilus enzymes, depending on its substrate specificity (pyruvate, branched-chain 2-oxo acid or 2-oxoglutarate), each complex has distinctive E1 (E1p, E1b or E1o) and E2 (E2p, E2b or E2o) components and one of the two possible E3 components (E3b and E3o). (The suffixes, p, b and o identify their respective enzymes, PDH, BCDH and OGDH.) Our biochemical characterization demonstrates that only three specific E3*E2 complexes can form (E3b*E2p, E3b*E2b and E3o*E2o). X-ray analyses of complexes formed between the E3 components and the peripheral subunit-binding domains (PSBDs), derived from the corresponding E2-binding partners, reveal that E3b interacts with E2p and E2b in essentially the same manner as observed for Geobacillus stearothermophilus E3*E2p, whereas E3o interacts with E2o in a novel fashion. The buried intermolecular surfaces of the E3b*PSBDp/b and E3o*PSBDo complexes differ in size, shape and charge distribution and thus, these differences presumably confer the binding specificities for the complexes.


Subject(s)
3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)/chemistry , 3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)/metabolism , NAD/metabolism , Thermus thermophilus/enzymology , Amino Acid Sequence , Binding Sites , Crystallization , Crystallography, X-Ray , Kinetics , Magnetic Resonance Spectroscopy , Molecular Sequence Data , Protein Conformation , Sequence Homology, Amino Acid , Static Electricity
15.
EMBO J ; 24(8): 1523-36, 2005 Apr 20.
Article in English | MEDLINE | ID: mdl-15791207

ABSTRACT

The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.


Subject(s)
Amino Acid Oxidoreductases/chemistry , Bacterial Proteins/chemistry , Hyperglycinemia, Nonketotic/metabolism , Protein Structure, Quaternary , Thioctic Acid/analogs & derivatives , Amino Acid Oxidoreductases/genetics , Amino Acid Oxidoreductases/metabolism , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Crystallography, X-Ray , Dimerization , Glycine Decarboxylase Complex H-Protein , Glycine Dehydrogenase (Decarboxylating) , Humans , Models, Molecular , Molecular Sequence Data , Protein Binding , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/metabolism , Sequence Alignment , Thermus thermophilus/chemistry , Thermus thermophilus/metabolism , Thioctic Acid/metabolism
16.
J Mol Biol ; 337(4): 1011-33, 2004 Apr 02.
Article in English | MEDLINE | ID: mdl-15033367

ABSTRACT

The alpha(2)beta(2) tetrameric E1 component of the branched-chain 2-oxo acid (BCOA) dehydrogenase multienzyme complex is a thiamin diphosphate (ThDP)-dependent enzyme. E1 catalyzes the decarboxylation of a BCOA concomitant with the formation of the alpha-carbanion/enamine intermediate, 2-(1-hydroxyalkyl)-ThDP, followed by transfer of the 1-hydroxyalkyl group to the distal sulfur atom on the lipoamide of the E2 component. In order to elucidate the catalytic mechanism of E1, the alpha- and beta-subunits of E1 from Thermus thermophilus HB8 have been co-expressed in Escherichia coli, purified and crystallized as a stable complex, and the following crystal structures have been analyzed: the apoenzyme (E1(apo)), the holoenzyme (E1(holo)), E1(holo) in complex with the substrate analogue 4-methylpentanoate (MPA) as an ES complex model, and E1(holo) in complex with 4-methyl-2-oxopentanoate (MOPA) as the alpha-carbanion/enamine intermediate (E1(ceim)). Binding of cofactors to E1(apo) induces a disorder-order transition in two loops adjacent to the active site. Furthermore, upon binding of MPA to E1(holo), the loop comprised of Gly121beta-Gln131beta moves close to the active site and interacts with MPA. The carboxylate group of MPA is recognized mainly by Tyr86beta and N4' of ThDP. The hydrophobic moiety of MPA is recognized by Phe66alpha, Tyr95alpha, Met128alpha and His131alpha. As an intermediate, MOPA is decarboxylated and covalently linked to ThDP, and the conformation of the protein loop is almost the same as in the substrate-free (holoenzyme) form. These results suggest that E1 undergoes an open-closed conformational change upon formation of the ES complex with a BCOA, and the mobile region participates in the recognition of the carboxylate group of the BCOA. ES complex models of E1(holo).MOPA and of E1(ceim).lipoamide built from the above structures suggest that His273alpha and His129beta' are potential proton donors to the carbonyl group of a BCOA and to the proximal sulfur atom on the lipoamide, respectively.


Subject(s)
3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)/chemistry , Thermus thermophilus/enzymology , 3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)/metabolism , Amino Acid Sequence , Binding Sites , Caproates/chemistry , Caproates/metabolism , Crystallography, X-Ray , Humans , Ligands , Molecular Sequence Data , Protein Conformation , Pseudomonas putida/enzymology , Sequence Alignment , Thermus thermophilus/chemistry , Thermus thermophilus/metabolism
17.
Acta Crystallogr D Biol Crystallogr ; 59(Pt 9): 1610-8, 2003 Sep.
Article in English | MEDLINE | ID: mdl-12925792

ABSTRACT

The glycine-cleavage system is a multi-enzyme complex consisting of four different components (the P-, H-, T- and L-proteins). Recombinant H-protein corresponding to that from Thermus thermophilus HB8 has been overexpressed, purified and crystallized. Synchrotron radiation from BL44B2 at SPring-8 was used to collect a native data set to 2.5 A resolution. The crystals belonged to the hexagonal space group P6(5) and contained three molecules per asymmetric unit, with a solvent content of 39%. Because of the large number of molecules within a closely packed unit cell, this structure was solved by six-dimensional molecular replacement with the program EPMR using the pea H-protein structure as a search model and was refined to an R factor of 0.189 and a free R factor of 0.256. Comparison with the pea H-protein reveals two highly conserved regions surrounding the lipoyl-lysine arm. Both of these regions are negatively charged and each has additional properties that are conserved in H-proteins from many species, suggesting that these regions are involved in intermolecular interactions. One region has previously been proposed to constitute an interaction surface with T-protein, while the other may be involved in an interaction with P-protein. Meanwhile, the lipoyl-lysine arm of the T. thermophilus H-protein was found to be more flexible than that of the pea H-protein, supporting the hypothesis that H-protein does not form a stable complex with L-protein during the reaction.


Subject(s)
Crystallography, X-Ray/methods , Thermus thermophilus/chemistry , Binding Sites , Cloning, Molecular , Conserved Sequence , Multienzyme Complexes/chemistry , Protein Binding , Protein Conformation , Sequence Alignment
18.
Acta Crystallogr D Biol Crystallogr ; 59(Pt 3): 554-7, 2003 Mar.
Article in English | MEDLINE | ID: mdl-12595724

ABSTRACT

Thermus thermophilus (Tth) HB8 glycine decarboxylase (P-protein) is an alpha(2)beta(2) tetrameric enzyme with a total molecular mass of 200 kDa. The alpha- and beta-subunits of the Tth P-protein have been coexpressed in Escherichia coli and purified as a stable complex. Dynamic light-scattering measurements indicated the recombinant protein to be monodisperse and its size to be consistent with an alpha(2)beta(2) tetrameric composition. Crystals of the protein have been grown in polyethylene glycol 3350 using the vapour-diffusion method at 291 K. Synchrotron radiation from BL45XU at SPring-8 was used to measure a complete native data set to 2.4 A resolution. The crystals belong to the trigonal space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 89.5, c = 371.0 A. Estimation of the crystal packing (V(M) = 2.15 A(3) Da(-1)) and self-rotation function analysis suggest the presence of one alpha(2)beta(2) tetramer per asymmetric unit, with the molecules related by non-crystallographic twofold symmetry.


Subject(s)
Amino Acid Oxidoreductases/chemistry , Glycine/chemistry , Thermus thermophilus/enzymology , Amino Acid Oxidoreductases/biosynthesis , Amino Acid Oxidoreductases/isolation & purification , Crystallization , Crystallography, X-Ray , Electrophoresis, Polyacrylamide Gel , Glycine Dehydrogenase (Decarboxylating) , Light , Plasmids/genetics , Recombinant Proteins , Scattering, Radiation , X-Ray Diffraction
19.
J Am Chem Soc ; 124(44): 13139-53, 2002 Nov 06.
Article in English | MEDLINE | ID: mdl-12405843

ABSTRACT

The mechanism of Preferential Enrichment, an unusual enantiomeric resolution phenomenon observed upon recrystallization of a series of racemic crystals which are classified as a racemic mixed crystal with fairly ordered arrangement of the two enantiomers, has been studied. On the basis of the existence of polymorphs and the occurrence of the resulting polymorphic transition during crystallization from solution, the mechanism has been accounted for in terms of (1) a preferential homochiral molecular association to form one-dimensional chain structures in the supersaturated solution of the racemate or nonracemic sample with a low ee value, (2) a kinetic formation of a metastable crystalline phase retaining the homochiral chain structures in a process of nucleation, (3) a polymorphic transition from the metastable phase to a stable one followed by enantioselective liberation of the excess R (or S) enantiomers from the transformed crystal into solution at the beginning of crystal growth to result in a slight enrichment (up to 10% ee) of the opposite S (or R) enantiomer in the deposited crystals, together with an enantiomeric enrichment of the R (or S) enantiomer in the mother liquor, and (4) a chiral discrimination by the once formed S (or R)-rich stable crystalline phase in a process of the subsequent crystal growth, leading to a considerable enantiomeric enrichment of the R (or S) enantiomer up to 100% ee in the mother liquor. The processes (3) and (4) are considered to be directly responsible for an enrichment of one enantiomer in the mother liquor. The association mode of the two enantiomers in solution has been investigated by means of (i) the solubility measurement and (ii) the number-averaged molecular weight measurement in solution by vapor pressure osmometry, together with (iii) the molecular dynamics simulation of oligomer models. The polymorphic transition during crystallization has been observed visually and by means of the in situ FTIR technique and DSC measurement. Both metastable and stable crystals have been obtained, and their crystal structures have been elucidated by X-ray crystallographic analysis of their single crystals.


Subject(s)
Crystallization/methods , Stereoisomerism , Alkanesulfonates/isolation & purification , Crystallography, X-Ray , Models, Molecular , Quaternary Ammonium Compounds/isolation & purification , Solutions , X-Ray Diffraction
20.
J Org Chem ; 64(9): 3102-3105, 1999 Apr 30.
Article in English | MEDLINE | ID: mdl-11674408

ABSTRACT

The sterically bulky t-Bu-substituted derivatives of 1,1,2,2-tetraphenyl-3,8-dichlorobuta[b]naphthalene (5), trans-1,2-tert-butyl-1,2-diphenyl- (8) and 1,1-di-tert-butyl-2,2-diphenyl-3,8-dichlorocyclobuta[b]naphthalene (12), were prepared. X-ray analysis of 8 and 12 at 150 K showed that C-C bonds of 8 and 12 are 1.686 and 1.729 Å, respectively. The latter bond length is longer than that of 1.720 Å in 5 and is the longest one reliably determined to date.

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