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1.
J Biol Chem ; 296: 100263, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33837744

RESUMEN

The development of a targeted therapy would significantly improve the treatment of periodontitis and its associated diseases including Alzheimer's disease, rheumatoid arthritis, and cardiovascular diseases. Glutaminyl cyclases (QCs) from the oral pathogens Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia represent attractive target enzymes for small-molecule inhibitor development, as their action is likely to stabilize essential periplasmic and outer membrane proteins by N-terminal pyroglutamination. In contrast to other microbial QCs that utilize the so-called type I enzymes, these oral pathogens possess sequences corresponding to type II QCs, observed hitherto only in animals. However, whether differences between these bacteroidal QCs and animal QCs are sufficient to enable development of selective inhibitors is not clear. To learn more, we recombinantly expressed all three QCs. They exhibit comparable catalytic efficiencies and are inhibited by metal chelators. Crystal structures of the enzymes from P. gingivalis (PgQC) and T. forsythia (TfQC) reveal a tertiary structure composed of an eight-stranded ß-sheet surrounded by seven α-helices, typical of animal type II QCs. In each case, an active site Zn ion is tetrahedrally coordinated by conserved residues. Nevertheless, significant differences to mammalian enzymes are found around the active site of the bacteroidal enzymes. Application of a PgQC-selective inhibitor described here for the first time results in growth inhibition of two P. gingivalis clinical isolates in a dose-dependent manner. The insights gained by these studies will assist in the development of highly specific small-molecule bacteroidal QC inhibitors, paving the way for alternative therapies against periodontitis and associated diseases.


Asunto(s)
Aminoaciltransferasas/química , Periodontitis/microbiología , Porphyromonas gingivalis/enzimología , Prevotella intermedia/enzimología , Aminoaciltransferasas/antagonistas & inhibidores , Aminoaciltransferasas/genética , Aminoaciltransferasas/ultraestructura , Dominio Catalítico/efectos de los fármacos , Cristalografía por Rayos X , Humanos , Periodontitis/tratamiento farmacológico , Periodontitis/genética , Porphyromonas gingivalis/patogenicidad , Prevotella intermedia/patogenicidad , Estructura Terciaria de Proteína/efectos de los fármacos , Ácido Pirrolidona Carboxílico/química , Ácido Pirrolidona Carboxílico/metabolismo , Tannerella forsythia/enzimología , Tannerella forsythia/patogenicidad
2.
J Biol Chem ; 2021 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-33402424

RESUMEN

The development of a targeted therapy would significantly improve the treatment of periodontitis and its associated diseases including Alzheimer Disease, rheumatoid arthritis, and cardiovascular diseases. Glutaminyl cyclases (QCs) from the oral pathogens Porphyromonas gingivalis, Tannerella forsythia and Prevotella intermedia represent attractive target enzymes for small-molecule inhibitor development, as their action is likely to stabilize essential periplasmic and outer membrane proteins by N-terminal pyroglutamination. In contrast to other microbial QCs that utilize so-called type I enzymes, these oral pathogens possess sequences corresponding to type II QCs, observed hitherto only in animals. However, whether differences between these bacteroidal QCs and animal QCs are sufficient to enable development of selective inhibitors is not clear. To learn more, we recombinantly expressed all three QCs. They exhibit comparable catalytic efficiencies and are inhibited by metal chelators. Crystal structures  of the enzymes from P. gingivalis (PgQC) and T. forsythia (TfQC) reveal a tertiary structure composed of an eight-stranded ß-sheet surrounded by seven α-helices, typical of animal type II QCs. In each case, an active site Zn ion is tetrahedrally coordinated by conserved residues. Nevertheless, significant differences to mammalian enzymes are found around the active site of the bacteroidal enzymes. Application of a PgQC-selective inhibitor described here for the first time results in growth inhibition of two P. gingivalis clinical isolates in a dose dependent manner. The insights gained by these studies will assist in the development of highly specific small-molecule bacteroidal QC inhibitors, paving the way for alternative therapies against periodontitis and associated diseases.

3.
Int J Mol Sci ; 22(11)2021 May 26.
Artículo en Inglés | MEDLINE | ID: mdl-34073350

RESUMEN

The astacin protease Meprin ß represents an emerging target for drug development due to its potential involvement in disorders such as acute and chronic kidney injury and fibrosis. Here, we elaborate on the structural basis of inhibition by a specific Meprin ß inhibitor. Our analysis of the crystal structure suggests different binding modes of the inhibitor to the active site. This flexibility is caused, at least in part, by movement of the C-terminal region of the protease domain (CTD). The CTD movement narrows the active site cleft upon inhibitor binding. Compared with other astacin proteases, among these the highly homologous isoenzyme Meprin α, differences in the subsites account for the unique selectivity of the inhibitor. Although the inhibitor shows substantial flexibility in orientation within the active site, the structural data as well as binding analyses, including molecular dynamics simulations, support a contribution of electrostatic interactions, presumably by arginine residues, to binding and specificity. Collectively, the results presented here and previously support an induced fit and substantial movement of the CTD upon ligand binding and, possibly, during catalysis. To the best of our knowledge, we here present the first structure of a Meprin ß holoenzyme containing a zinc ion and a specific inhibitor bound to the active site. The structural data will guide rational drug design and the discovery of highly potent Meprin inhibitors.


Asunto(s)
Ácidos Hidroxámicos/química , Metaloendopeptidasas/antagonistas & inhibidores , Metaloendopeptidasas/química , Simulación de Dinámica Molecular , Inhibidores de Proteasas/química , Humanos , Relación Estructura-Actividad
4.
J Biol Chem ; 292(30): 12713-12724, 2017 07 28.
Artículo en Inglés | MEDLINE | ID: mdl-28623233

RESUMEN

Alzheimer disease is associated with deposition of the amyloidogenic peptide Aß in the brain. Passive immunization using Aß-specific antibodies has been demonstrated to reduce amyloid deposition both in vitro and in vivo Because N-terminally truncated pyroglutamate (pE)-modified Aß species (AßpE3) exhibit enhanced aggregation potential and propensity to form toxic oligomers, they represent particularly attractive targets for antibody therapy. Here we present three separate monoclonal antibodies that specifically recognize AßpE3 with affinities of 1-10 nm and inhibit AßpE3 fibril formation in vitro. In vivo application of one of these resulted in improved memory in AßpE3 oligomer-treated mice. Crystal structures of Fab-AßpE3 complexes revealed two distinct binding modes for the peptide. Juxtaposition of pyroglutamate pE3 and the F4 side chain (the "pEF head") confers a pronounced bulky hydrophobic nature to the AßpE3 N terminus that might explain the enhanced aggregation properties of the modified peptide. The deep burial of the pEF head by two of the antibodies explains their high target specificity and low cross-reactivity, making them promising candidates for the development of clinical antibodies.


Asunto(s)
Enfermedad de Alzheimer/inmunología , Enfermedad de Alzheimer/terapia , Péptidos beta-Amiloides/inmunología , Anticuerpos Monoclonales/química , Anticuerpos Monoclonales/inmunología , Inmunoterapia , Ácido Pirrolidona Carboxílico/inmunología , Péptidos beta-Amiloides/química , Animales , Células Cultivadas , Ratones
5.
Proc Natl Acad Sci U S A ; 111(17): 6281-6, 2014 Apr 29.
Artículo en Inglés | MEDLINE | ID: mdl-24733933

RESUMEN

Drosophila Toll receptors are involved in embryonic development and the immune response of adult flies. In both processes, the only known Toll receptor ligand is the human nerve growth factor-like cystine knot protein Spätzle. Here we present the crystal structure of a 1:1 (nonsignaling) complex of the full-length Toll receptor ectodomain (ECD) with the Spätzle cystine knot domain dimer. The ECD is divided into two leucine-rich repeat (LRR) domains, each of which is capped by cysteine-rich domains. Spätzle binds to the concave surface of the membrane-distal LRR domain, in contrast to the flanking ligand interactions observed for mammalian Toll-like receptors, with asymmetric contributions from each Spätzle protomer. The structure allows rationalization of existing genetic and biochemical data and provides a framework for targeting the immune systems of insects of economic importance, as well as a variety of invertebrate disease vectors.


Asunto(s)
Proteínas de Drosophila/metabolismo , Drosophila melanogaster/crecimiento & desarrollo , Drosophila melanogaster/inmunología , Inmunidad Innata , Transducción de Señal , Receptores Toll-Like/metabolismo , Animales , Proteínas de Drosophila/química , Humanos , Modelos Moleculares , Unión Proteica , Multimerización de Proteína , Estructura Terciaria de Proteína , Receptores Toll-Like/química
6.
Mol Microbiol ; 98(4): 743-59, 2015 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-26235546

RESUMEN

Phage shock protein A (PspA) belongs to the highy conserved PspA/IM30 family and is a key component of the stress inducible Psp system in Escherichia coli. One of its central roles is the regulatory interaction with the transcriptional activator of this system, the σ(54) enhancer-binding protein PspF, a member of the AAA+ protein family. The PspA/F regulatory system has been intensively studied and serves as a paradigm for AAA+ enzyme regulation by trans-acting factors. However, the molecular mechanism of how exactly PspA controls the activity of PspF and hence σ(54) -dependent expression of the psp genes is still unclear. To approach this question, we identified the minimal PspF-interacting domain of PspA, solved its structure, determined its affinity to PspF and the dissociation kinetics, identified residues that are potentially important for PspF regulation and analyzed effects of their mutation on PspF in vivo and in vitro. Our data indicate that several characteristics of AAA+ regulation in the PspA·F complex resemble those of the AAA+ unfoldase ClpB, with both proteins being regulated by a structurally highly conserved coiled-coil domain. The convergent evolution of both regulatory domains points to a general mechanism to control AAA+ activity for divergent physiologic tasks via coiled-coil domains.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Proteínas de Choque Térmico/química , Proteínas de Choque Térmico/metabolismo , Transactivadores/metabolismo , Proteínas Bacterianas/genética , Endopeptidasa Clp , Escherichia coli/fisiología , Proteínas de Escherichia coli/metabolismo , Proteínas de Escherichia coli/fisiología , Regulación Bacteriana de la Expresión Génica , Proteínas de Choque Térmico/genética , Regiones Promotoras Genéticas , Unión Proteica , Factor sigma/genética , Factor sigma/metabolismo , Transactivadores/genética , Transcripción Genética
7.
Biochemistry ; 54(42): 6454-61, 2015 Oct 27.
Artículo en Inglés | MEDLINE | ID: mdl-26435421

RESUMEN

Human vitamin K epoxide reductase (hVKOR) is an integral membrane protein responsible for the maintenance of reduced vitamin K pools, a prerequisite for the action of γ-glutamyl carboxylase and hence for hemostasis. Here we describe the recombinant expression of hVKOR as an insoluble fusion protein in Escherichia coli, followed by purification and chemical cleavage under denaturing conditions. In vitro renaturation and reconstitution of purified solubilized hVKOR in phospholipids could be established to yield active protein. Crucially, the renatured enzyme is inhibited by the powerful coumarin anticoagulant warfarin, and we demonstrate that enzyme activity depends on lipid composition. The completely synthetic system for protein production allows a rational investigation of the multiple variables in membrane protein folding and paves the way for the provision of pure, active membrane protein for structural studies.


Asunto(s)
Vitamina K Epóxido Reductasas/química , Vitamina K Epóxido Reductasas/metabolismo , Inhibidores Enzimáticos/farmacología , Humanos , Técnicas In Vitro , Cinética , Lípidos de la Membrana/química , Lípidos de la Membrana/metabolismo , Proteínas de la Membrana/química , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Modelos Moleculares , Fosfolípidos/química , Fosfolípidos/metabolismo , Pliegue de Proteína , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Vitamina K Epóxido Reductasas/genética , Warfarina/farmacología
8.
Proc Natl Acad Sci U S A ; 109(31): 12503-8, 2012 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-22814377

RESUMEN

Oligomers are intermediates of the ß-amyloid (Aß) peptide fibrillogenic pathway and are putative pathogenic culprits in Alzheimer's disease (AD). Here we report the biotechnological generation and biochemical characterization of an oligomer-specific antibody fragment, KW1. KW1 not only discriminates between oligomers and other Aß conformations, such as fibrils or disaggregated peptide; it also differentiates between different types of Aß oligomers, such as those formed by Aß (1-40) and Aß (1-42) peptide. This high selectivity of binding contrasts sharply with many other conformational antibodies that interact with a large number of structurally analogous but sequentially different antigens. X-ray crystallography, NMR spectroscopy, and peptide array measurements imply that KW1 recognizes oligomers through a hydrophobic and significantly aromatic surface motif that includes Aß residues 18-20. KW1-positive oligomers occur in human AD brain samples and induce synaptic dysfunctions in living brain tissues. Bivalent KW1 potently neutralizes this effect and interferes with Aß assembly. By altering a specific step of the fibrillogenic cascade, it prevents the formation of mature Aß fibrils and induces the accumulation of nonfibrillar aggregates. Our data illuminate significant mechanistic differences in oligomeric and fibril recognition and suggest the considerable potential of KW1 in future studies to detect or inhibit specific types of Aß conformers.


Asunto(s)
Péptidos beta-Amiloides/química , Fragmentos de Péptidos/química , Multimerización de Proteína , Secuencias de Aminoácidos , Anticuerpos Monoclonales , Cristalografía por Rayos X , Humanos , Resonancia Magnética Nuclear Biomolecular , Estructura Cuaternaria de Proteína
9.
Angew Chem Int Ed Engl ; 53(11): 3024-8, 2014 Mar 10.
Artículo en Inglés | MEDLINE | ID: mdl-24520050

RESUMEN

Although site-specific incorporation of artificial functionalities into proteins is an important tool in both basic and applied research, it can be a major challenge to protein chemists. Enzymatic protein modification is an attractive goal due to the inherent regio- and stereoselectivity of enzymes, yet their specificity remains a problem. As a result of the intrinsic reversibility of enzymatic reactions, proteinases can in principle catalyze ligation reactions. While this makes them attractive tools for site-specific protein bioconjugation, competing hydrolysis reactions limits their general use. Here we describe the design and application of a highly specific trypsin variant for the selective modification of N-terminal residues of diverse proteins with various reagents. The modification proceeds quantitatively under native (aqueous) conditions. We show that the variant has a disordered zymogen-like activation domain, effectively suppressing the hydrolysis reaction, which is converted to an active conformation in the presence of appropriate substrates.


Asunto(s)
Proteínas/metabolismo , Biocatálisis , Ciclofilinas/química , Ciclofilinas/metabolismo , Procesamiento Proteico-Postraduccional , Estructura Terciaria de Proteína , Proteínas/química , Proteolisis , Estereoisomerismo , Especificidad por Sustrato , Tripsina/química , Tripsina/metabolismo
10.
Trends Biochem Sci ; 34(6): 303-10, 2009 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-19446460

RESUMEN

G-protein-coupled receptors (GPCRs) represent the largest constellation of validated drug targets. Crystal structures of class A GPCRs have facilitated major advances in understanding the principles underlying GPCR activation. By contrast, relatively little is known about class B GPCRs, a family of receptors for a variety of therapeutically relevant peptide hormones. Encouraging progress has recently been made through the structural elucidation of several extracellular hormone-binding domains of class B GPCRs in complex with their natural ligands or synthetic analogues. The structures reveal similar modes of ligand binding, with concomitant alpha-helical structuring of the ligand. The latter suggests an attractive mechanical model for class B GPCR activation.


Asunto(s)
Hormonas Peptídicas/metabolismo , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/fisiología , Secuencia de Aminoácidos , Animales , Humanos , Ligandos , Modelos Biológicos , Datos de Secuencia Molecular , Péptidos/química , Conformación Proteica , Pliegue de Proteína , Estructura Secundaria de Proteína , Homología de Secuencia de Aminoácido
11.
Commun Biol ; 7(1): 907, 2024 Jul 27.
Artículo en Inglés | MEDLINE | ID: mdl-39068227

RESUMEN

Affilin proteins, artificial binding proteins based on the ubiquitin scaffold, have been generated by directed protein evolution to yield de-novo variants that bind the extra-domain B (EDB) of oncofetal fibronectin, an established marker of tumor neovasculature. The crystal structures of two EDB-specific Affilin variants reveal a striking structural plasticity of the ubiquitin scaffold, characterised by ß-strand slippage, leading to different negative register shifts of the ß5 strands. This process recruits amino acid residues from ß5 towards the N-terminus to an adjacent loop region and subsequent residues into ß5, respectively, remodeling the binding interface and leading to target specificity and affinity. Protein backbone alterations resulting from ß-strand register shifts, as seen in the ubiquitin fold, can pose additional challenges to protein engineering as structural evidence of these events is still limited and they are difficult to predict. However, they can surface under the selection pressure of directed evolution and suggest that backbone plasticity allowing ß-strand slippages can increase structural diversity, enhancing the evolutionary potential of a protein scaffold.


Asunto(s)
Fibronectinas , Ubiquitina , Fibronectinas/metabolismo , Fibronectinas/química , Fibronectinas/genética , Ubiquitina/metabolismo , Humanos , Unión Proteica , Conformación Proteica en Lámina beta , Modelos Moleculares , Cristalografía por Rayos X , Ingeniería de Proteínas
12.
Biol Chem ; 394(8): 1091-6, 2013 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-23729564

RESUMEN

Drosophila Toll receptors are involved in embryonic development and in the immune response of adult flies. In both processes, the Toll receptor ligand is the NGF-like cystine knot protein Spätzle. Here we present the expression of Toll receptor ectodomain in Schneider cells at high yields and demonstrate a high affinity interaction with the refolded and trypsin-processed Spätzle cystine knot domain dimer. Poorly and anisotropically diffracting crystals of the complex could be improved by deglycosylation and dehydration, paving the way for structural analyses of the Toll-Spätzle interaction.


Asunto(s)
Proteínas de Drosophila/metabolismo , Drosophila/metabolismo , Receptores Toll-Like/metabolismo , Secuencia de Aminoácidos , Animales , Línea Celular , Clonación Molecular , Cristalización , Drosophila/química , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Expresión Génica , Datos de Secuencia Molecular , Multimerización de Proteína , Replegamiento Proteico , Estructura Terciaria de Proteína , Receptores Toll-Like/química , Receptores Toll-Like/genética
13.
Nat Chem Biol ; 7(10): 678-84, 2011 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-21857661

RESUMEN

We examined the catalytic cycle of transaldolase (TAL) from Thermoplasma acidophilum by cryocrystallography and were able to structurally characterize--for the first time, to our knowledge--different genuine TAL reaction intermediates. These include the Schiff base adducts formed between the catalytic lysine and the donor ketose substrates fructose-6-phosphate and sedoheptulose-7-phosphate as well as the Michaelis complex with acceptor aldose erythrose-4-phosphate. These structural snapshots necessitate a revision of the accepted reaction mechanism with respect to functional roles of active site residues, and they further reveal fundamental insights into the general structural features of enzymatic Schiff base intermediates and the role of conformational dynamics in enzyme catalysis, substrate binding and discrimination. A nonplanar arrangement of the substituents around the Schiff base double bond was observed, suggesting that a structurally encoded reactant-state destabilization is a driving force of catalysis. Protein dynamics and the intrinsic hydrogen-bonding pattern appear to be crucial for selective recognition and binding of ketose as first substrate.


Asunto(s)
Bases de Schiff/metabolismo , Thermoplasma/enzimología , Transaldolasa/metabolismo , Biocatálisis , Dominio Catalítico , Cristalografía por Rayos X , Modelos Moleculares , Estructura Molecular , Bases de Schiff/química , Especificidad por Sustrato , Transaldolasa/química
14.
Biochemistry ; 51(37): 7383-92, 2012 Sep 18.
Artículo en Inglés | MEDLINE | ID: mdl-22897232

RESUMEN

Glutaminyl cyclases (QCs), which catalyze the formation of pyroglutamic acid (pGlu) at the N-terminus of a variety of peptides and proteins, have attracted particular attention for their potential role in Alzheimer's disease. In a transgenic Drosophila melanogaster (Dm) fruit fly model, oral application of the potent competitive QC inhibitor PBD150 was shown to reduce the burden of pGlu-modified Aß. In contrast to mammals such as humans and rodents, there are at least three DmQC species, one of which (isoDromeQC) is localized to mitochondria, whereas DromeQC and an isoDromeQC splice variant possess signal peptides for secretion. Here we present the recombinant expression, characterization, and crystal structure determination of mature DromeQC and isoDromeQC, revealing an overall fold similar to that of mammalian QCs. In the case of isoDromeQC, the putative extended substrate binding site might be affected by the proximity of the N-terminal residues. PBD150 inhibition of DromeQC is roughly 1 order of magnitude weaker than that of the human and murine QCs. The inhibitor binds to isoDromeQC in a fashion similar to that observed for human QCs, whereas it adopts alternative binding modes in a DromeQC variant lacking the conserved cysteines near the active center and shows a disordered dimethoxyphenyl moiety in wild-type DromeQC, providing an explanation for the lower affinity. Our biophysical and structural data suggest that isoDromeQC and human QC are similar with regard to functional aspects. The two Dm enzymes represent a suitable model for further in-depth analysis of the catalytic mechanism of animal QCs, and isoDromeQC might serve as a model system for the structure-based design of potential AD therapeutics.


Asunto(s)
Aminoaciltransferasas/química , Proteínas de Drosophila/química , Proteínas Mitocondriales/química , Enfermedad de Alzheimer/tratamiento farmacológico , Enfermedad de Alzheimer/enzimología , Enfermedad de Alzheimer/genética , Aminoaciltransferasas/antagonistas & inhibidores , Aminoaciltransferasas/genética , Aminoaciltransferasas/metabolismo , Animales , Proteínas de Drosophila/antagonistas & inhibidores , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/uso terapéutico , Humanos , Ratones , Proteínas Mitocondriales/genética , Proteínas Mitocondriales/metabolismo , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Homología Estructural de Proteína , Relación Estructura-Actividad , Tomografía Computarizada por Rayos X
15.
Biochemistry ; 50(28): 6280-8, 2011 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-21671571

RESUMEN

Formation of N-terminal pyroglutamate (pGlu or pE) from glutaminyl or glutamyl precursors is catalyzed by glutaminyl cyclases (QC). As the formation of pGlu-amyloid has been linked with Alzheimer's disease, inhibitors of QCs are currently the subject of intense development. Here, we report three crystal structures of N-glycosylated mammalian QC from humans (hQC) and mice (mQC). Whereas the overall structures of the enzymes are similar to those reported previously, two surface loops in the neighborhood of the active center exhibit conformational variability. Furthermore, two conserved cysteine residues form a disulfide bond at the base of the active center that was not present in previous reports of hQC structure. Site-directed mutagenesis suggests a structure-stabilizing role of the disulfide bond. At the entrance to the active center, the conserved tryptophan residue, W(207), which displayed multiple orientations in previous structure, shows a single conformation in both glycosylated human and murine QCs. Although mutagenesis of W(207) into leucine or glutamine altered substrate conversion significantly, the binding constants of inhibitors such as the highly potent PQ50 (PBD150) were minimally affected. The crystal structure of PQ50 bound to the active center of murine QC reveals principal binding determinants provided by the catalytic zinc ion and a hydrophobic funnel. This study presents a first comparison of two mammalian QCs containing typical, conserved post-translational modifications.


Asunto(s)
Aminoaciltransferasas/química , Aminoaciltransferasas/metabolismo , Secuencia de Aminoácidos , Aminoaciltransferasas/genética , Animales , Bovinos , Secuencia Conservada , Cristalografía por Rayos X , Activación Enzimática/genética , Escherichia coli/enzimología , Escherichia coli/genética , Glicosilación , Humanos , Ratones , Datos de Secuencia Molecular , Pichia/enzimología , Pichia/genética , Conformación Proteica , Procesamiento Proteico-Postraduccional/genética , Ratas , Ovinos
16.
J Biol Chem ; 285(41): 31559-70, 2010 Oct 08.
Artículo en Inglés | MEDLINE | ID: mdl-20667822

RESUMEN

The crystal structure of human transketolase (TKT), a thiamine diphosphate (ThDP) and Ca(2+)-dependent enzyme that catalyzes the interketol transfer between ketoses and aldoses as part of the pentose phosphate pathway, has been determined to 1.75 Å resolution. The recombinantly produced protein crystallized in space group C2 containing one monomer in the asymmetric unit. Two monomers form the homodimeric biological assembly with two identical active sites at the dimer interface. Although the protomer exhibits the typical three (α/ß)-domain structure and topology reported for TKTs from other species, structural differences are observed for several loop regions and the linker that connects the PP and Pyr domain. The cofactor and substrate binding sites of human TKT bear high resemblance to those of other TKTs but also feature unique properties, including two lysines and a serine that interact with the ß-phosphate of ThDP. Furthermore, Gln(189) spans over the thiazolium moiety of ThDP and replaces an isoleucine found in most non-mammalian TKTs. The side chain of Gln(428) forms a hydrogen bond with the 4'-amino group of ThDP and replaces a histidine that is invariant in all non-mammalian TKTs. All other amino acids involved in substrate binding and catalysis are strictly conserved. Besides a steady-state kinetic analysis, microscopic equilibria of the donor half-reaction were characterized by an NMR-based intermediate analysis. These studies reveal that formation of the central 1,2-dihydroxyethyl-ThDP carbanion-enamine intermediate is thermodynamically favored with increasing carbon chain length of the donor ketose substrate. Based on the structure of human transketolase and sequence alignments, putative functional properties of the related transketolase-like proteins TKTL1 and -2 are discussed in light of recent findings suggesting that TKTL1 plays a role in cancerogenesis.


Asunto(s)
Multimerización de Proteína/fisiología , Transcetolasa/química , Cristalografía por Rayos X , Humanos , Cinética , Resonancia Magnética Nuclear Biomolecular , Estructura Cuaternaria de Proteína , Estructura Secundaria de Proteína , Transcetolasa/metabolismo
17.
J Mol Recognit ; 24(1): 23-34, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-20140889

RESUMEN

The Bcl-2 inhibitor FKBP38 is regulated by the Ca(2+)-sensor calmodulin (CaM). Here we show a hitherto unknown low-affinity cation-binding site in the FKBP domain of FKBP38, which may afford an additional level of regulation based on electrostatic interactions. Fluorescence titration experiments indicate that in particular the physiologically relevant Ca(2+) ion binds to this site. NMR-based chemical shift perturbation data locate this cation-interaction site within the ß5-α1 loop (Leu90-Ile96) of the FKBP domain, which contains the acidic Asp92 and Asp94 side-chains. Binding constants were subsequently determined for K(+), Mg(2+), Ca(2+), and La(3+), indicating that the net charge and the radius of the ion influences the binding interaction. X-ray diffraction data furthermore show that the conformation of the ß5-α1 loop is influenced by the presence of a positively charged guanidinium group belonging to a neighboring FKBP38 molecule in the crystal lattice. The position of the cation-binding site has been further elucidated based on pseudocontact shift data obtained by NMR via titration with Tb(3+). Elimination of the Ca(2+)-binding capacity by substitution of the respective aspartate residues in a D92N/D94N double-substituted variant reduces the Bcl-2 affinity of the FKBP38(35-153)/CaM complex to the same degree as the presence of Ca(2+) in the wild-type protein. Hence, this charge-sensitive site in the FKBP domain participates in the regulation of FKBP38 function by enabling electrostatic interactions with ligand proteins and/or salt ions such as Ca(2+).


Asunto(s)
Dominio Catalítico , Proteínas Proto-Oncogénicas c-bcl-2/metabolismo , Proteínas de Unión a Tacrolimus/química , Proteínas de Unión a Tacrolimus/metabolismo , Secuencia de Aminoácidos , Asparagina/metabolismo , Sitios de Unión , Calcio/química , Calcio/metabolismo , Cationes/química , Cationes/metabolismo , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Unión Proteica , Estructura Terciaria de Proteína/fisiología , Alineación de Secuencia , Electricidad Estática , Proteínas de Unión a Tacrolimus/genética
18.
Artículo en Inglés | MEDLINE | ID: mdl-21543867

RESUMEN

The metabolic enzyme transaldolase from Thermoplasma acidophilum was recombinantly expressed in Escherichia coli and could be crystallized in two polymorphic forms. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 6000 as precipitant. Native data sets for crystal forms 1 and 2 were collected in-house to resolutions of 3.0 and 2.7 Å, respectively. Crystal form 1 belonged to the orthorhombic space group C222(1) with five monomers per asymmetric unit and crystal form 2 belonged to the monoclinic space group P2(1) with ten monomers per asymmetric unit.


Asunto(s)
Thermoplasma/enzimología , Transaldolasa/química , Cristalización , Cristalografía por Rayos X
19.
Biochemistry ; 49(37): 8197-212, 2010 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-20715795

RESUMEN

Pyruvate decarboxylase (PDC) catalyzes the nonoxidative decarboxylation of pyruvate into acetaldehyde and carbon dioxide and requires thiamin diphosphate (ThDP) and a divalent cation as cofactors. Recent studies have permitted the assignment of functional roles of active site residues; however, the underlying reaction mechanisms of elementary steps have remained hypothetical. Here, a kinetic and thermodynamic single-step analysis in conjunction with X-ray crystallographic studies of PDC from Zymomonas mobilis implicates active site residue Glu473 (located on the re-face of the ThDP thiazolium nucleus) in facilitating both decarboxylation of 2-lactyl-ThDP and protonation of the 2-hydroxyethyl-ThDP carbanion/enamine intermediate. Variants carrying either an isofunctional (Glu473Asp) or isosteric (Glu473Gln) substitution exhibit a residual catalytic activity of less than 0.1% but accumulate different intermediates at the steady state. Whereas the predecarboxylation intermediate 2-lactyl-ThDP is accumulated in Glu473Asp because of a 3000-fold slower decarboxylation compared to that of the wild-type enzyme, Glu473Gln is not impaired in decarboxylation but generates a long-lived 2-hydroxyethyl-ThDP carbanion/enamine postdecarboxylation intermediate. CD spectroscopic analysis of the protonic and tautomeric equilibria of the cocatalytic aminopyrimidine part of ThDP indicates that an acidic residue is required at position 473 for proper substrate binding. Wild-type PDC and the Glu473Asp variant bind the substrate analogue acetylphosphinate with the same affinity, implying a similar stabilization of the predecarboxylation intermediate analogue on the enzyme, whereas Glu473Gln fails to bind the analogue. The X-ray crystallographic structure of 2-lactyl-ThDP trapped in the decarboxylation-deficient variant Glu473Asp reveals a common stereochemistry of the intermediate C2α stereocenter; however, the scissile C2α-C(carboxylate) bond deviates by ∼25-30° from the perpendicular "maximum overlap" orientation relative to the thiazolium ring plane as commonly observed in ThDP enzymes. Because a reactant-state stabilization of the predecarboxylation intermediate can be excluded to account for the slower decarboxylation, the data suggest a strong stereoelectronic effect for the transition state of decarboxylation as supported by additional DFT studies on models. To the best of our knowledge, this is a very rare example in which the magnitude of a stereoelectronic effect could be experimentally estimated for an enzymatic system. Given that variant Glu473Gln is not decarboxylation-deficient, electrostatic stress can be excluded as a driving force for decarboxylation. The apparent dual function of Glu473 further suggests that decarboxylation and protonation of the incipient carbanion are committed and presumably proceed in the same transition state.


Asunto(s)
Aminas/química , Tiamina Pirofosfato/química , Sitios de Unión , Catálisis , Cristalografía por Rayos X , Descarboxilación , Ácido Glutámico/metabolismo , Termodinámica , Tiamina Pirofosfato/metabolismo , Rayos X , Zymomonas/enzimología , Zymomonas/genética , Zymomonas/metabolismo
20.
Biol Chem ; 391(12): 1419-28, 2010 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-20868223

RESUMEN

Although enzymes responsible for the cyclization of amino-terminal glutamine residues are present in both plant and mammal species, none have yet been characterized in bacteria. Based on low sequence homologies to plant glutaminyl cyclases (QCs), we cloned the coding sequences of putative microbial QCs from Zymomonas mobilis (ZmQC) and Myxococcus xanthus (MxQC). The two recombinant enzymes exhibited distinct QC activity, with specificity constants k(cat)/K(m) of 1.47±0.33 mm⁻¹ s⁻¹ (ZmQC) and 142±32.7 mm⁻¹ s⁻¹ (MxQC) towards the fluorescent substrate glutamine-7-amino-4-methyl-coumarine. The measured pH-rate profile of the second order rate constant displayed an interesting deviation towards the acidic limb of the pH chart in the case of ZmQC, whereas MxQC showed maximum activity in the mild alkaline pH range. Analysis of the enzyme variants ZmQCGlu46Gln and MxQCGln46Glu show that the exchanged residues play a significant role in the pH behaviour of the respective enzymes. In addition, we determined the three dimensional crystal structures of both enzymes. The tertiary structure is defined by a five-bladed ß-propeller anchored by a core cation. The structures corroborate the putative location of the active site and confirm the proposed relation between bacterial and plant glutaminyl cyclases.


Asunto(s)
Aminoaciltransferasas/química , Proteínas Bacterianas/química , Myxococcus xanthus/enzimología , Zymomonas/enzimología , Secuencia de Aminoácidos , Aminoaciltransferasas/genética , Aminoaciltransferasas/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Catálisis , Dominio Catalítico , Clonación Molecular , Genoma Bacteriano , Concentración de Iones de Hidrógeno , Cinética , Datos de Secuencia Molecular , Myxococcus xanthus/metabolismo , Conformación Proteica , Especificidad por Sustrato , Zymomonas/metabolismo
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