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1.
Protein Expr Purif ; 219: 106487, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38657915

RESUMO

The bacterial Efe system functions as an importer of free Fe2+ into cells independently of iron-chelating compounds such as siderophores and consisted of iron-binding protein EfeO, peroxidase EfeB, and transmembrane permease EfeU. While we and other researchers reported crystal structures of EfeO and EfeB, that of EfeU remains undetermined. In this study, we constructed expression system of EfeU derived from Escherichia coli, selected E. coli Rosetta-gami 2 (DE3) as an expression host, and succeeded in purification of the proteins which were indicated to form an oligomer by blue native PAGE. We obtained preliminary data of the X-ray crystallography, suggesting that expression and purification methods we established in this study enable structural analysis of the bacterial Efe system.


Assuntos
Proteínas de Escherichia coli , Escherichia coli , Ferro , Escherichia coli/genética , Escherichia coli/metabolismo , Cristalografia por Raios X , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/isolamento & purificação , Ferro/metabolismo , Ferro/química , Expressão Gênica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/biossíntese , Proteínas de Ligação ao Ferro/química , Proteínas de Ligação ao Ferro/genética , Proteínas de Ligação ao Ferro/isolamento & purificação , Proteínas de Ligação ao Ferro/metabolismo
2.
Biochem Biophys Res Commun ; 594: 124-130, 2022 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-35081501

RESUMO

EfeUOB is a siderophore-independent iron uptake mechanism in bacteria. EfeU, EfeO, and EfeB are a permease, an iron-binding or electron-transfer protein, and a peroxidase, respectively. A Gram-negative bacterium, Sphingomonas sp. strain A1, encodes EfeU, EfeO, EfeB together with alginate-binding protein Algp7, a truncated EfeO-like protein (EfeOII), in the genome. The typical EfeO (EfeOI) consists of N-terminal cupredoxin and C-terminal M75 peptidase domains. Here, we detail the structure and function of bacterial EfeB and EfeO. Crystal structures of strain A1 EfeB and Escherichia coli EfeOI were determined at 2.30 Å and 1.85 Å resolutions, respectively. A molecule of heme involved in oxidase activity was bound to the C-terminal Dyp peroxidase domain of EfeB. Two domains of EfeOI were connected by a short loop, and a zinc ion was bound to four residues, Glu156, Glu159, Asp173, and Glu255, in the C-terminal M75 peptidase domain. These residues formed tetrahedron geometry suitable for metal binding and are well conserved among various EfeO proteins including Algp7 (EfeOII), although the metal-binding site (HxxE) is proposed in the C-terminal M75 peptidase domain. This is the first report on structure of a typical EfeO with two domains, postulating a novel metal-binding motif "ExxE-//-D-//-E" in the EfeO C-terminal M75 peptidase domain.


Assuntos
Proteínas de Transporte de Cátions/química , Proteínas de Escherichia coli/química , Heme/química , Ferro/química , Motivos de Aminoácidos , Azurina/química , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Transporte Biológico , Cristalografia por Raios X , Proteínas de Escherichia coli/metabolismo , Metais/química , Conformação Molecular , Oxirredutases/química , Ligação Proteica , Conformação Proteica , Domínios Proteicos , Estrutura Secundária de Proteína , Sphingomonas/metabolismo
3.
J Biol Chem ; 295(20): 6983-6991, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-32269076

RESUMO

Newly synthesized major histocompatibility complex (MHC) class I proteins are stabilized in the endoplasmic reticulum (ER) by binding 8-10-mer-long self-peptide antigens that are provided by transporter associated with antigen processing (TAP). These MHC class I:peptide complexes then exit the ER and reach the plasma membrane, serving to sustain the steady-state MHC class I expression on the cell surface. A novel subset of MHC class I molecules that preferentially bind lipid-containing ligands rather than conventional peptides was recently identified. The primate classical MHC class I allomorphs, Mamu-B*098 and Mamu-B*05104, are capable of binding the N-myristoylated 5-mer (C14-Gly-Gly-Ala-Ile-Ser) or 4-mer (C14-Gly-Gly-Ala-Ile) lipopeptides derived from the N-myristoylated SIV Nef protein, respectively, and of activating lipopeptide antigen-specific cytotoxic T lymphocytes. We herein demonstrate that Mamu-B*098 samples lysophosphatidylethanolamine and lysophosphatidylcholine containing up to a C20 fatty acid in the ER. The X-ray crystal structures of Mamu-B*098 and Mamu-B*05104 complexed with lysophospholipids at high resolution revealed that the B and D pockets in the antigen-binding grooves of these MHC class I molecules accommodate these lipids through a monoacylglycerol moiety. Consistent with the capacity to bind cellular lipid ligands, these two MHC class I molecules did not require TAP function for cell-surface expression. Collectively, these results indicate that peptide- and lipopeptide-presenting MHC class I subsets use distinct sources of endogenous ligands.


Assuntos
Antígenos de Histocompatibilidade Classe I/química , Lisofosfolipídeos/química , Animais , Sítios de Ligação , Cristalografia por Raios X , Antígenos de Histocompatibilidade Classe I/imunologia , Lipoilação/imunologia , Lisofosfolipídeos/imunologia , Macaca mulatta , Peptídeos/química , Peptídeos/imunologia , Estrutura Quaternária de Proteína , Produtos do Gene nef do Vírus da Imunodeficiência Humana/química , Produtos do Gene nef do Vírus da Imunodeficiência Humana/imunologia
4.
J Immunol ; 202(12): 3349-3358, 2019 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-31043477

RESUMO

Similar to host proteins, N-myristoylation occurs for viral proteins to dictate their pathological function. However, this lipid-modifying reaction creates a novel class of "lipopeptide" Ags targeted by host CTLs. The primate MHC class I-encoded protein, Mamu-B*098, was previously shown to bind N-myristoylated 5-mer peptides. Nevertheless, T cells exist that recognize even shorter lipopeptides, and much remains to be elucidated concerning the molecular mechanisms of lipopeptide presentation. We, in this study, demonstrate that the MHC class I allele, Mamu-B*05104, binds the N-myristoylated 4-mer peptide (C14-Gly-Gly-Ala-Ile) derived from the viral Nef protein for its presentation to CTLs. A phylogenetic tree analysis indicates that these classical MHC class I alleles are not closely associated; however, the high-resolution x-ray crystallographic analyses indicate that both molecules share lipid-binding structures defined by the exceptionally large, hydrophobic B pocket to accommodate the acylated glycine (G1) as an anchor. The C-terminal isoleucine (I4) of C14-Gly-Gly-Ala-Ile anchors at the F pocket, which is distinct from that of Mamu-B*098 and is virtually identical to that of the peptide-presenting MHC class I molecule, HLA-B51. The two central amino acid residues (G2 and A3) are only exposed externally for recognition by T cells, and the methyl side chain on A3 constitutes a major T cell epitope, underscoring that the epitopic diversity is highly limited for lipopeptides as compared with that for MHC class I-presented long peptides. These structural features suggest that lipopeptide-presenting MHC class I alleles comprise a distinct MHC class I subset that mediates an alternative pathway for CTL activation.


Assuntos
Autoantígenos/metabolismo , Epitopos de Linfócito T/metabolismo , Produtos do Gene nef/metabolismo , Antígenos de Histocompatibilidade Classe I/metabolismo , Lipopeptídeos/metabolismo , Peptídeos/metabolismo , Linfócitos T Citotóxicos/imunologia , Animais , Apresentação de Antígeno , Autoantígenos/química , Autoantígenos/imunologia , Cristalografia por Raios X , Epitopos de Linfócito T/imunologia , Produtos do Gene nef/química , Produtos do Gene nef/imunologia , Antígenos de Histocompatibilidade Classe I/genética , Humanos , Lipopeptídeos/química , Lipopeptídeos/imunologia , Ativação Linfocitária , Ácido Mirístico/química , Peptídeos/química , Peptídeos/imunologia , Filogenia , Primatas
5.
Biochem Biophys Res Commun ; 510(1): 177-183, 2019 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-30683313

RESUMO

Ceriporiopsis subvermispora (C. subvermispora), one of the white-rot fungi, is known as a selective lignin degrader of the woody biomass. Glutathione S-transferases (GSTs) are multifunctional enzymes that are capable of catalyzing the reactions involved in detoxification and metabolic pathways. In this study, a GST of C. subvermispora, named CsGST63524, was overexpressed in E. coli, and then purified by affinity, anion exchange, and size exclusion column chromatography. The crystal structures of the CsGST63524 in ligand-free and complex with GSH were refined at 2.45 and 2.50 Šresolutions, respectively. The sulfur atom of glutathione forms a hydrogen bond with Ser21 of CsGST63524, indicating it is a serine-type GST. Mutagenesis of Ser21 unexpectedly indicated that this serine residue is not essential for the enzymatic activity of CsGST63524. Comparative sequence and structural analyses, together with functional mutagenesis, newly identified the enzymatically important non-canonical amino acid residues, Asn23 and Tyr45, other than the serine residue.


Assuntos
Coriolaceae/enzimologia , Glutationa Transferase/química , Mutagênese , Aminoácidos/fisiologia , Asparagina , Cristalografia por Raios X , Proteínas Fúngicas/química , Glutationa/química , Glutationa Transferase/genética , Glutationa Transferase/isolamento & purificação , Ligantes , Serina , Tirosina
6.
Biochem Biophys Res Commun ; 493(2): 1095-1101, 2017 11 18.
Artigo em Inglês | MEDLINE | ID: mdl-28919419

RESUMO

The tripartite EfeUOB system functions as a low pH iron importer in Gram-negative bacteria. In the alginate-assimilating bacterium Sphingomonas sp. strain A1, an additional EfeO-like protein (Algp7) is encoded downstream of the efeUOB operon. Here we show the metal binding mode of Algp7, which carries a M_75 metallopeptidase motif. The Algp7 protein was purified from recombinant E. coli cells and was subsequently characterized using differential scanning fluorimetry, fluorescence spectrometry, atomic absorption spectroscopy, and X-ray crystallography. The fluorescence of a dye, SYPRO Orange, bound to denatured Algp7 in the absence and presence of metal ions was measured during heat treatment. The fluorescence profile of Algp7 in the presence of metals such as ferric, ferrous, and zinc ions, shifted to a higher temperature, suggesting that Algp7 binds these metal ions and that metal ion-bound Algp7 is more thermally stable than the ligand-free form. Algp7 was directly demonstrated to show an ability to bind copper ion by atomic absorption spectroscopy. Crystal structure of metal ion-bound Algp7 revealed that the metal ion is bound to the cleft surrounded by several acidic residues. Four residues, Glu79, Glu82, Asp96, and Glu178, distinct from the M_75 motif (His115xxGlu118), are coordinated to the metal ion. This is the first report to provide structural insights into metal binding by the bacterial EfeO element.


Assuntos
Alginatos/metabolismo , Proteínas de Bactérias/metabolismo , Ferro/metabolismo , Metais/metabolismo , Sphingomonas/metabolismo , Proteínas de Bactérias/química , Sítios de Ligação , Transporte Biológico , Cobre/metabolismo , Cristalografia por Raios X , Ácido Glucurônico/metabolismo , Infecções por Bactérias Gram-Negativas/microbiologia , Ácidos Hexurônicos/metabolismo , Modelos Moleculares , Conformação Proteica , Sphingomonas/química , Zinco/metabolismo
7.
J Biol Chem ; 292(38): 15681-15690, 2017 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-28768763

RESUMO

The Gram-negative bacterium Sphingomonas sp. A1 incorporates alginate into cells via the cell-surface pit without prior depolymerization by extracellular enzymes. Alginate import across cytoplasmic membranes thereby depends on the ATP-binding cassette transporter AlgM1M2SS (a heterotetramer of AlgM1, AlgM2, and AlgS), which cooperates with the periplasmic solute-binding protein AlgQ1 or AlgQ2; however, several details of AlgM1M2SS-mediated alginate import are not well-understood. Herein, we analyzed ATPase and transport activities of AlgM1M2SS after reconstitution into liposomes with AlgQ2 and alginate oligosaccharide substrates having different polymerization degrees (PDs). Longer alginate oligosaccharides (PD ≥ 5) stimulated the ATPase activity of AlgM1M2SS but were inert as substrates of AlgM1M2SS-mediated transport, indicating that AlgM1M2SS-mediated ATP hydrolysis can be stimulated independently of substrate transport. Using X-ray crystallography in the presence of AlgQ2 and long alginate oligosaccharides (PD 6-8) and with the humid air and glue-coating method, we determined the crystal structure of AlgM1M2SS in complex with oligosaccharide-bound AlgQ2 at 3.6 Å resolution. The structure of the ATP-binding cassette transporter in complex with non-transport ligand-bound periplasmic solute-binding protein revealed that AlgM1M2SS and AlgQ2 adopt inward-facing and closed conformations, respectively. These in vitro assays and structural analyses indicated that interactions between AlgM1M2SS in the inward-facing conformation and periplasmic ligand-bound AlgQ2 in the closed conformation induce ATP hydrolysis by the ATP-binding protein AlgS. We conclude that substrate-bound AlgQ2 in the closed conformation initially interacts with AlgM1M2SS, the AlgM1M2SS-AlgQ2 complex then forms, and this formation is followed by ATP hydrolysis.


Assuntos
Transportadores de Cassetes de Ligação de ATP/química , Transportadores de Cassetes de Ligação de ATP/metabolismo , Trifosfato de Adenosina/metabolismo , Alginatos/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Adenosina Trifosfatases/metabolismo , Alginatos/química , Transporte Biológico , Ácido Glucurônico/química , Ácido Glucurônico/metabolismo , Ácidos Hexurônicos/química , Ácidos Hexurônicos/metabolismo , Umidade , Hidrólise , Modelos Moleculares , Oligossacarídeos/química , Conformação Proteica
8.
ACS Nano ; 10(11): 10382-10388, 2016 11 22.
Artigo em Inglês | MEDLINE | ID: mdl-27934076

RESUMO

Rendering the geometry of protein-based assemblies controllable remains challenging. Protein shell-like nanocages represent particularly interesting targets for designed assembly. Here, we introduce an engineering strategy-key subunit interface redesign (KSIR)-that alters a natural subunit-subunit interface by selective deletion of a small number of "silent" amino acid residues (no participation in interfacial interactions) into one that triggers the generation of a non-native protein cage. We have applied KSIR to construct a non-native 48-mer nanocage from its native 24-mer recombinant human H-chain ferritin (rHuHF). This protein is a heteropolymer composed of equal numbers of two different subunits which are derived from one polypeptide. This strategy has allowed the study of conversion between protein nanocages with different geometries by re-engineering key subunit interfaces and the demonstration of the important role of the above-mentioned specific residues in providing geometric specificity for protein assembly.


Assuntos
Aminoácidos/química , Ferritinas/química , Sequência de Aminoácidos , Humanos , Nanocompostos
9.
Extremophiles ; 20(5): 723-31, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27377296

RESUMO

Oligopeptide-binding proteins (Opps) are part of the ATP-binding cassette system, playing a crucial role in nutrient uptake and sensing the external environment in bacteria, including hyperthermophiles. Opps serve as a binding platform for diverse peptides; however, how these peptides are recognized by Opps is still largely unknown and few crystal structures of Opps from hyperthermophiles have been determined. To facilitate such an understanding, the crystal structure of a putative Opp, OppA from Thermotoga maritima (TmOppA), was solved at 2.6-Å resolution in the open conformation. TmOppA is composed of three domains. The N-terminal domain consists of twelve strands, nine helices, and four 310 helices, and the C-terminal domain consists of five strands, ten helices, and one 310 helix. These two domains are connected by the linker domain, which consists of two strands, three helices, and three 310 helices. Based on structural comparisons of TmOppA with other OppAs and binding studies, we suggest that TmOppA might be a periplasmic Opp. The most distinct feature of TmOppA is the insertion of two helices, which are lacking in other OppAs. A cavity volume between the N-terminal and C-terminal domains is suggested to be responsible for binding peptides of various lengths.


Assuntos
Proteínas de Bactérias/química , Proteínas de Transporte/química , Lipoproteínas/química , Periplasma/metabolismo , Thermotoga maritima/química , Trifosfato de Adenosina/metabolismo , Motivos de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Lipoproteínas/genética , Lipoproteínas/metabolismo , Ligação Proteica , Thermotoga maritima/genética , Thermotoga maritima/metabolismo
10.
Acta Crystallogr D Biol Crystallogr ; 71(Pt 10): 2054-65, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26457429

RESUMO

The selection of correct metal ions with high fidelity against competing cellular cations is crucial for the function of many metalloenzymes; however, the understanding of the principles that govern metal selectivity is still incomplete. In this study, the crystal structure of the Tm1162 protein from Thermotoga maritima, a metallo-ß-lactamase, is reported. Several crystal structures of wild-type Tm1162 and its mutants were solved. Homologues of Tm1162 are widely distributed in bacteria and archaea, including several human pathogens. The monomer possesses an αß/ßα fold, with the core ß-strands having the ß-sheet sandwich structure common to the metallo-ß-lactamase superfamily. Tm1162 exists as a trimer in the crystal and this trimeric unit is likely to be present in solution. In the trimer, three active sites reside at the interface between subunits, suggesting that the oligomeric assembly is crucial for catalysis. A new type of structurally encoded heterodinuclear site has been identified by confirming the identity of nickel-containing heteronuclear sites in Tm1162 via X-ray absorption spectroscopy and anomalous difference Fourier maps. The second coordination sphere, including His8 and Glu73, maintains the side-chain orientations of histidines and stabilizes the metal-binding site. Nickel coordination was crucial for the oligomerization of Tm1162. The nickel-dependent and manganese-dependent ß-lactamase and phosphodiesterase activities of Tm1162 have also been characterized.


Assuntos
Níquel/química , Thermotoga maritima/enzimologia , beta-Lactamases/química , Sequência de Aminoácidos , Sítios de Ligação , Cristalografia por Raios X , Modelos Moleculares , Dados de Sequência Molecular , Níquel/metabolismo , Alinhamento de Sequência , Thermotoga maritima/química , Thermotoga maritima/metabolismo , Espectroscopia por Absorção de Raios X , beta-Lactamases/metabolismo
11.
Structure ; 23(9): 1643-1654, 2015 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-26235029

RESUMO

The acidic polysaccharide alginate represents a promising marine biomass for the microbial production of biofuels, although the molecular and structural characteristics of alginate transporters remain to be clarified. In Sphingomonas sp. A1, the ATP-binding cassette transporter AlgM1M2SS is responsible for the import of alginate across the cytoplasmic membrane. Here, we present the substrate-transport characteristics and quaternary structure of AlgM1M2SS. The addition of poly- or oligoalginate enhanced the ATPase activity of reconstituted AlgM1M2SS coupled with one of the periplasmic solute-binding proteins, AlgQ1 or AlgQ2. External fluorescence-labeled oligoalginates were specifically imported into AlgM1M2SS-containing proteoliposomes in the presence of AlgQ2, ATP, and Mg(2+). The crystal structure of AlgQ2-bound AlgM1M2SS adopts an inward-facing conformation. The interaction between AlgQ2 and AlgM1M2SS induces the formation of an alginate-binding tunnel-like structure accessible to the solvent. The translocation route inside the transmembrane domains contains charged residues suitable for the import of acidic saccharides.


Assuntos
Transportadores de Cassetes de Ligação de ATP/química , Transportadores de Cassetes de Ligação de ATP/metabolismo , Alginatos/metabolismo , Sphingomonas/enzimologia , Trifosfato de Adenosina/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Cristalografia por Raios X , Ácido Glucurônico/metabolismo , Ácidos Hexurônicos/metabolismo , Magnésio/metabolismo , Modelos Moleculares , Estrutura Quaternária de Proteína , Sphingomonas/química
12.
Protein Expr Purif ; 113: 44-50, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25959458

RESUMO

Moloney murine leukemia virus reverse transcriptase (MMLV RT) contains fingers, palm, thumb, and connection subdomains as well as an RNase H domain. The DNA polymerase active site resides in the palm subdomain, and the RNase H active site is located in the RNase H domain. The RNase H domain contains a positively charged α-helix called the C helix (H(594)GEIYRRR(601)), that is thought to be involved in substrate recognition. In this study, we expressed three versions of the RNase H domain in Escherichia coli, the wild-type domain (WT) (residues Ile498-Leu671) and two variants that lack the regions containing the C helix (Ile593-Leu603 and Gly595-Thr605, which we called ΔC1 and ΔC2, respectively) with a strep-tag at the N-terminus and a deca-histidine tag at the C-terminus. These peptides were purified from the cells by anion-exchange, Ni(2+) affinity, and Strep-Tactin affinity column chromatography, and then the tags were removed by proteolysis. In an RNase H assay using a 25-bp RNA-DNA heteroduplex, WT, ΔC1, and ΔC2 produced RNA fragments ranging from 7 to 16 nucleotides (nt) whereas the full-length MMLV RT (Thr24-Leu671) produced 14-20-nt RNA fragments, suggesting that elimination of the fingers, palm, thumb, and connection subdomains affects the binding of the RNase H domain to the RNA-DNA heteroduplex. The activity levels of WT, ΔC1, and ΔC2 were estimated to be 1%, 0.01%, and 0.01% of full-length MMLV RT activity, indicating that the C helix is important, but not critical, for the activity of the isolated RNase H domain.


Assuntos
Vírus da Leucemia Murina de Moloney/genética , DNA Polimerase Dirigida por RNA/metabolismo , Proteínas Recombinantes/metabolismo , Ribonuclease H/metabolismo , Proteínas Virais/metabolismo , Sequência de Aminoácidos , Sequência de Bases , Escherichia coli/genética , Dados de Sequência Molecular , Vírus da Leucemia Murina de Moloney/enzimologia , RNA/metabolismo , DNA Polimerase Dirigida por RNA/química , DNA Polimerase Dirigida por RNA/genética , DNA Polimerase Dirigida por RNA/isolamento & purificação , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Ribonuclease H/química , Ribonuclease H/genética , Ribonuclease H/isolamento & purificação , Proteínas Virais/química , Proteínas Virais/genética , Proteínas Virais/isolamento & purificação
13.
Acta Crystallogr F Struct Biol Commun ; 71(Pt 2): 132-5, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25664783

RESUMO

ß-Conglycinin is a major seed storage protein in soybeans, which are an important source of protein. The major subunits (α, α' and ß) of ß-conglycinin are sorted to protein-storage vacuoles in seed cells. Vacuolar sorting receptor (VSR) is an integral membrane protein that recognizes the sorting determinant of vacuolar proteins, including ß-conglycinin, and regulates their sorting process. Vacuolar sorting determinants of the α' and ß subunits of ß-conglycinin exist in their C-terminal peptides. Here, the preliminary X-ray diffraction analysis of the binding domain of soybean VSR crystallized with the peptide responsible for the sorting determinant in ß-conglycinin is reported. X-ray diffraction data were collected to a resolution of 3.5 Å. The crystals belonged to space group P3121, with unit-cell parameters a = b = 116.4, c = 86.1 Å.


Assuntos
Antígenos de Plantas/química , Globulinas/química , Glycine max/química , Receptores de Superfície Celular/química , Proteínas de Armazenamento de Sementes/química , Proteínas de Soja/química , Vacúolos/metabolismo , Cristalização , Cristalografia por Raios X , Eletroforese em Gel de Poliacrilamida , Peptídeos/química , Estrutura Terciária de Proteína , Transporte Proteico
14.
FEBS J ; 281(11): 2659-73, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24720693

RESUMO

UNLABELLED: Phenoloxidase (PO), which is classified as a type 3 copper protein, catalyzes the hydroxylation of monophenol to o-diphenol and subsequent oxidation to the corresponding o-quinone. The geometry and coordination environment of the active site of the arthropod PO are very similar to those of the arthropod hemocyanin (Hc). However, unlike the POs, Hc is an oxygen carrier in crustaceans, and does not possess PO activity in general. Recently, we identified a new type of proPO from a crustacean and designated it proPOß. This enzyme has many characteristics that are rather similar to those of Hc, such as its maturation, localization, and oligomeric state. Here, we determined the crystal structure of proPOß prepared from the hemolymph of kuruma prawns (Marsupenaeus japonicus) at 1.8-Å resolution. M. japonicus proPOß forms a homohexamer rather similar to that of arthropod Hc. The geometry of the active copper site in proPOß is nearly identical to that of arthropod Hc. Furthermore, the well-characterized 'place-holder' phenylalanine is present (Phe72). However, the accessibility to the active site differs in several ways. First, another phenylalanine, which shields the active site by interacting with a copper-coordinated histidine in crustacean Hc, is replaced by valine in the proPOß structure. Second, two tyrosines, Tyr208 and Tyr209, both of which are absent in Hc, show the alternative conformations and form a pathway providing access to the reaction center. Thus, the present crystal structure clarifies the similarities and differences in the activity of two closely related proteins, PO and Hc. DATABASE: Structural data are available in the RSCB protein data bank under the accession number 3WKY. ray crystallography (View interaction).


Assuntos
Artrópodes/enzimologia , Catecol Oxidase/metabolismo , Precursores Enzimáticos/metabolismo , Animais , Catecol Oxidase/química , Precursores Enzimáticos/química
15.
Artigo em Inglês | MEDLINE | ID: mdl-23908048

RESUMO

Glycinin is one of the most abundant storage-protein molecules in soybean seeds and is composed of five subunits (A1aB1b, A1bB2, A2B1a, A3B4 and A5A4B3). A1bB2 was purified from a mutant soybean cultivar containing glycinin composed of only A5A4B3 and A1bB2. At 281 K the protein formed hexagonal, rectangular and rod-shaped crystals in the first [0.1 M imidazole pH 8.0, 0.2 M MgCl2, 35%(v/v) MPD], second [0.1 M sodium citrate pH 5.6, 0.2 M ammonium acetate, 30%(v/v) MPD] and third (0.1 M phosphate-citrate pH 4.2, 2.0 M ammonium sulfate) crystallization conditions, respectively. X-ray diffraction data were collected to resolutions of 1.85, 1.85 and 2.5 Å from crystals of the three different shapes. The crystals belonged to space groups P6322, P21 and P1, with unit-cell parameters a = b = 143.60, c = 84.54 Å, a = 114.54, b = 105.82, c = 116.67 Å, ß = 94.99° and a = 94.45, b = 94.96, c = 100.66 Å, α = 107.02, ß = 108.44, γ = 110.71°, respectively. One, six and six subunits of A1bB2 were estimated to be present in the respective asymmetric units. The three-dimensional structure of the A1bB2 hexamer is currently being determined.


Assuntos
Globulinas/química , Globulinas/isolamento & purificação , Glycine max , Proteínas de Soja/química , Proteínas de Soja/isolamento & purificação , Cristalização , Cristalografia por Raios X , Globulinas/genética , Mutação/genética , Proteínas de Soja/genética
16.
Biochemistry ; 51(17): 3622-33, 2012 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-22486720

RESUMO

Alginate is a heteropolysaccharide that consists of ß-D-mannuronate (M) and α-L-guluronate (G). The Gram-negative bacterium Sphingomonas sp. A1 directly incorporates alginate into the cytoplasm through the periplasmic solute-binding protein (AlgQ1 and AlgQ2)-dependent ABC transporter (AlgM1-AlgM2/AlgS-AlgS). Two binding proteins with at least four subsites strongly recognize the nonreducing terminal residue of alginate at subsite 1. Here, we show the broad substrate preference of strain A1 solute-binding proteins for M and G present in alginate and demonstrate the structural determinants in binding proteins for heteropolysaccharide recognition through X-ray crystallography of four AlgQ1 structures in complex with saturated and unsaturated alginate oligosaccharides. Alginates with different M/G ratios were assimilated by strain A1 cells and bound to AlgQ1 and AlgQ2. Crystal structures of oligosaccharide-bound forms revealed that in addition to interaction between AlgQ1 and unsaturated oligosaccharides, the binding protein binds through hydrogen bonds to the C4 hydroxyl group of the saturated nonreducing terminal residue at subsite 1. The M residue of saturated oligosaccharides is predominantly accommodated at subsite 1 because of the strict binding of Ser-273 to the carboxyl group of the residue. In unsaturated trisaccharide (ΔGGG or ΔMMM)-bound AlgQ1, the protein interacts appropriately with substrate hydroxyl groups at subsites 2 and 3 to accommodate M or G, while substrate carboxyl groups are strictly recognized by the specific residues Tyr-129 at subsite 2 and Lys-22 at subsite 3. Because of this substrate recognition mechanism, strain A1 solute-binding proteins can bind heteropolysaccharide alginate with different M/G ratios.


Assuntos
Transportadores de Cassetes de Ligação de ATP/metabolismo , Adenosina Trifosfatases/metabolismo , Alginatos/metabolismo , Proteínas de Bactérias/metabolismo , Proteínas Periplásmicas/metabolismo , Sphingomonas/química , Transportadores de Cassetes de Ligação de ATP/química , Adenosina Trifosfatases/química , Aldeídos/química , Aldeídos/metabolismo , Alginatos/química , Proteínas de Bactérias/química , Ácido Glucurônico/química , Ácido Glucurônico/metabolismo , Ácidos Hexurônicos/química , Ácidos Hexurônicos/metabolismo , Proteínas Periplásmicas/química , Polissacarídeos/química , Polissacarídeos/metabolismo , Ligação Proteica
17.
J Biol Chem ; 286(44): 38691-38702, 2011 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-21926168

RESUMO

Protein glutaminase, which converts a protein glutamine residue to a glutamate residue, is expected to be useful as a new food-processing enzyme. The crystal structures of the mature and pro forms of the enzyme were refined at 1.15 and 1.73 Å resolution, respectively. The overall structure of the mature enzyme has a weak homology to the core domain of human transglutaminase-2. The catalytic triad (Cys-His-Asp) common to transglutaminases and cysteine proteases is located in the bottom of the active site pocket. The structure of the recombinant pro form shows that a short loop between S2 and S3 in the proregion covers and interacts with the active site of the mature region, mimicking the protein substrate of the enzyme. Ala-47 is located just above the pocket of the active site. Two mutant structures (A47Q-1 and A47Q-2) refined at 1.5 Å resolution were found to correspond to the enzyme-substrate complex and an S-acyl intermediate. Based on these structures, the catalytic mechanism of protein glutaminase is proposed.


Assuntos
Chryseobacterium/enzimologia , Glutaminase/química , Sequência de Aminoácidos , Catálise , Domínio Catalítico , Cristalização , Cristalografia por Raios X/métodos , Cisteína Proteases/química , Glutamina/química , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Mutação , Prolina/química , Ligação Proteica , Conformação Proteica , Transglutaminases/química
18.
Mol Cells ; 32(5): 431-5, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21912874

RESUMO

Phosphopantetheine adenylyltransferase (PPAT) catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) to form dephospho-CoA (dPCoA) and pyrophosphate in the Coenzyme A (CoA) biosynthetic pathway. Importantly, PPATs are the potential target for developing antibiotics because bacterial and mammalian PPATs share little sequence homology. Previous structural studies revealed the mechanism of the recognizing substrates and products. The binding modes of ATP, ADP, Ppant, and dPCoA are highly similar in all known structures, whereas the binding modes of CoA or 3'-phosphoadenosine 5'-phosphosulfate binding are novel. To provide further structural information on ligand binding by PPATs, the crystal structure of PPAT from Enterococcus faecalis was solved in three forms: (i) apo form, (ii) binary complex with ATP, and (iii) binary complex with pantetheine. The substrate analog, pantetheine, binds to the active site in a similar manner to Ppant. The new structural information reported in this study including pantetheine as a potent inhibitor of PPAT will supplement the existing structural data and should be useful for structure-based antibacterial discovery against PPATs.


Assuntos
Trifosfato de Adenosina/química , Coenzima A/química , Enterococcus faecalis/enzimologia , Nucleotidiltransferases/química , Panteteína/química , Trifosfato de Adenosina/metabolismo , Coenzima A/metabolismo , Cristalografia por Raios X , Ligantes , Modelos Moleculares , Panteteína/análogos & derivados , Panteteína/metabolismo , Estrutura Quaternária de Proteína
19.
Biochem Biophys Res Commun ; 400(1): 94-9, 2010 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-20705053

RESUMO

Ferritins are ubiquitous iron storage proteins. Recently, we identified a novel metal-binding site, transit site, in the crystal structure of phytoferritin. To elucidate the function of the transit site in ferritin from other species, we prepared transit-site-deficient mutants of human H ferritin, E140A and E140Q, and their iron oxidation kinetics was analyzed. The initial velocities of iron oxidization were reduced in the variants, especially in E140Q. The crystal structure of E140Q showed that the side chain of the mutated Gln140 was fixed by a hydrogen bond, whereas that of native Glu140 was flexible. These results suggest that the conserved transit site also has a function to assist with the metal ion sequestration to the ferroxidase site in ferritins from vertebrates.


Assuntos
Ceruloplasmina/metabolismo , Ferritinas/metabolismo , Ferro/metabolismo , Ceruloplasmina/química , Ceruloplasmina/genética , Ferritinas/química , Ferritinas/genética , Humanos , Oxirredução , Oxirredutases , Conformação Proteica
20.
Biosci Biotechnol Biochem ; 74(8): 1631-4, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-20699573

RESUMO

Basic 7S globulin, a cysteine-rich protein from soybean seeds, consists of subunits containing 27 kD and 16 kD chains linked by disulfide bonding. Three differently sized subunits of the basic 7S globulin were detected and partially separated by SP Sepharose chromatography. The basic 7S globulin was characterized as a member of a superfamily of structurally related but functionally distinct proteins descended from a specific group of plant aspartic proteinases.


Assuntos
Antígenos de Plantas/química , Antígenos de Plantas/metabolismo , Evolução Molecular , Globulinas/química , Globulinas/metabolismo , Glycine max , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo , Proteínas de Armazenamento de Sementes/química , Proteínas de Armazenamento de Sementes/metabolismo , Proteínas de Soja/química , Proteínas de Soja/metabolismo , Sequência de Aminoácidos , Antígenos de Plantas/genética , Ácido Aspártico Proteases/metabolismo , Globulinas/genética , Dados de Sequência Molecular , Filogenia , Subunidades Proteicas/genética , Proteínas de Armazenamento de Sementes/genética , Proteínas de Soja/genética
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