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1.
Nat Commun ; 15(1): 3248, 2024 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-38622112

RESUMEN

5,10-methylenetetrahydrofolate reductase (MTHFR) commits folate-derived one-carbon units to generate the methyl-donor S-adenosyl-L-methionine (SAM). Eukaryotic MTHFR appends to the well-conserved catalytic domain (CD) a unique regulatory domain (RD) that confers feedback inhibition by SAM. Here we determine the cryo-electron microscopy structures of human MTHFR bound to SAM and its demethylated product S-adenosyl-L-homocysteine (SAH). In the active state, with the RD bound to a single SAH, the CD is flexible and exposes its active site for catalysis. However, in the inhibited state the RD pocket is remodelled, exposing a second SAM-binding site that was previously occluded. Dual-SAM bound MTHFR demonstrates a substantially rearranged inter-domain linker that reorients the CD, inserts a loop into the active site, positions Tyr404 to bind the cofactor FAD, and blocks substrate access. Our data therefore explain the long-distance regulatory mechanism of MTHFR inhibition, underpinned by the transition between dual-SAM and single-SAH binding in response to cellular methylation status.


Asunto(s)
Metilenotetrahidrofolato Reductasa (NADPH2) , S-Adenosilmetionina , Humanos , Regulación Alostérica , Metilenotetrahidrofolato Reductasa (NADPH2)/química , Microscopía por Crioelectrón , S-Adenosilmetionina/metabolismo , Metilación
2.
Nat Commun ; 15(1): 2931, 2024 Apr 04.
Artículo en Inglés | MEDLINE | ID: mdl-38575566

RESUMEN

Cystathionine beta-synthase (CBS) is an essential metabolic enzyme across all domains of life for the production of glutathione, cysteine, and hydrogen sulfide. Appended to the conserved catalytic domain of human CBS is a regulatory domain that modulates activity by S-adenosyl-L-methionine (SAM) and promotes oligomerisation. Here we show using cryo-electron microscopy that full-length human CBS in the basal and SAM-bound activated states polymerises as filaments mediated by a conserved regulatory domain loop. In the basal state, CBS regulatory domains sterically block the catalytic domain active site, resulting in a low-activity filament with three CBS dimers per turn. This steric block is removed when in the activated state, one SAM molecule binds to the regulatory domain, forming a high-activity filament with two CBS dimers per turn. These large conformational changes result in a central filament of SAM-stabilised regulatory domains at the core, decorated with highly flexible catalytic domains. Polymerisation stabilises CBS and reduces thermal denaturation. In PC-3 cells, we observed nutrient-responsive CBS filamentation that disassembles when methionine is depleted and reversed in the presence of SAM. Together our findings extend our understanding of CBS enzyme regulation, and open new avenues for investigating the pathogenic mechanism and therapeutic opportunities for CBS-associated disorders.


Asunto(s)
Cistationina betasintasa , Metionina , Humanos , Cistationina betasintasa/metabolismo , Microscopía por Crioelectrón , S-Adenosilmetionina/metabolismo , Dominio Catalítico
3.
Eur J Hum Genet ; 31(10): 1190-1194, 2023 10.
Artículo en Inglés | MEDLINE | ID: mdl-37558808

RESUMEN

Biallelic hypomorphic variants in PRORP have been recently described as causing the autosomal recessive disorder combined oxidative phosphorylation deficiency type 54 (COXPD54). COXPD54 encompasses a phenotypic spectrum of sensorineural hearing loss and ovarian insufficiency (Perrault syndrome) to leukodystrophy. Here, we report three additional families with homozygous missense PRORP variants with pleiotropic phenotypes. Each missense variant altered a highly conserved residue within the metallonuclease domain. In vitro mitochondrial tRNA processing assays with recombinant TRMT10C, SDR5C1 and PRORP indicated two COXPD54-associated PRORP variants, c.1159A>G (p.Thr387Ala) and c.1241C>T (p.Ala414Val), decreased pre-tRNAIle cleavage, consistent with both variants impacting tRNA processing. No significant decrease in tRNA processing was observed with PRORP c.1093T>C (p.Tyr365His), which was identified in an individual with leukodystrophy. These data provide independent evidence that PRORP variants are associated with COXPD54 and that the assessment of 5' leader mitochondrial tRNA processing is a valuable assay for the functional analysis and clinical interpretation of novel PRORP variants.


Asunto(s)
Pérdida Auditiva Sensorineural , Enfermedades Mitocondriales , Ribonucleasa P , Femenino , Humanos , Genotipo , Pérdida Auditiva Sensorineural/genética , Homocigoto , Enfermedades Mitocondriales/genética , ARN de Transferencia , Ribonucleasa P/genética
4.
J Inherit Metab Dis ; 46(3): 406-420, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-36680553

RESUMEN

Vitamin B12 (cobalamin, Cbl) is required as a cofactor by two human enzymes, 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) and methylmalonyl-CoA mutase (MMUT). Within the body, a vast array of transporters, enzymes and chaperones are required for the generation and delivery of these cofactor forms. How they perform these functions is dictated by the structure and interactions of the proteins involved, the molecular bases of which are only now being elucidated. In this review, we highlight recent insights into human Cbl metabolism and address open questions in the field by employing a protein structure and interactome based perspective. We discuss how three very similar proteins-haptocorrin, intrinsic factor and transcobalamin-exploit slight structural differences and unique ligand receptor interactions to effect selective Cbl absorption and internalisation. We describe recent advances in the understanding of how endocytosed Cbl is transported across the lysosomal membrane and the implications of the recently solved ABCD4 structure. We detail how MMACHC and MMADHC cooperate to modify and target cytosolic Cbl to the client enzymes MTR and MMUT using ingenious modifications to an ancient nitroreductase fold, and how MTR and MMUT link with their accessory enzymes to sustainably harness the supernucleophilic potential of Cbl. Finally, we provide an outlook on how future studies may combine structural and interactome based approaches and incorporate knowledge of post-translational modifications to bring further insights.


Asunto(s)
Metilmalonil-CoA Mutasa , Vitamina B 12 , Humanos , Vitamina B 12/metabolismo , Metilmalonil-CoA Mutasa/metabolismo , Transporte Biológico , Chaperonas Moleculares , Transportadoras de Casetes de Unión a ATP/metabolismo , Oxidorreductasas/metabolismo
5.
Nat Struct Mol Biol ; 29(7): 628-638, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35835870

RESUMEN

Glycogen synthase (GYS1) is the central enzyme in muscle glycogen biosynthesis. GYS1 activity is inhibited by phosphorylation of its amino (N) and carboxyl (C) termini, which is relieved by allosteric activation of glucose-6-phosphate (Glc6P). We present cryo-EM structures at 3.0-4.0 Å resolution of phosphorylated human GYS1, in complex with a minimal interacting region of glycogenin, in the inhibited, activated and catalytically competent states. Phosphorylations of specific terminal residues are sensed by different arginine clusters, locking the GYS1 tetramer in an inhibited state via intersubunit interactions. The Glc6P activator promotes conformational change by disrupting these interactions and increases the flexibility of GYS1, such that it is poised to adopt a catalytically competent state when the sugar donor UDP-glucose (UDP-glc) binds. We also identify an inhibited-like conformation that has not transitioned into the activated state, in which the locking interaction of phosphorylation with the arginine cluster impedes subsequent conformational changes due to Glc6P binding. Our results address longstanding questions regarding the mechanism of human GYS1 regulation.


Asunto(s)
Glucosa-6-Fosfato , Glucógeno Sintasa , Arginina/metabolismo , Glucosa-6-Fosfato/metabolismo , Glucógeno Sintasa/química , Glucógeno Sintasa/metabolismo , Humanos , Fosforilación , Uridina Difosfato/metabolismo
6.
J Pers Med ; 11(2)2021 Feb 07.
Artículo en Inglés | MEDLINE | ID: mdl-33562227

RESUMEN

Galactosemia is a rare inherited metabolic disease resulting from mutations in the four genes which encode enzymes involved in the metabolism of galactose. The current therapy, the removal of galactose from the diet, is inadequate. Consequently, many patients suffer lifelong physical and cognitive disability. The phenotype varies from almost asymptomatic to life-threatening disability. The fundamental biochemical cause of the disease is a decrease in enzymatic activity due to failure of the affected protein to fold and/or function correctly. Many novel therapies have been proposed for the treatment of galactosemia. Often, these are designed to treat the symptoms and not the fundamental cause. Pharmacological chaperones (PC) (small molecules which correct the folding of misfolded proteins) represent an exciting potential therapy for galactosemia. In theory, they would restore enzyme function, thus preventing downstream pathological consequences. In practice, no PCs have been identified for potential application in galactosemia. Here, we review the biochemical basis of the disease, identify opportunities for the application of PCs and describe how these might be discovered. We will conclude by considering some of the clinical issues which will affect the future use of PCs in the treatment of galactosemia.

7.
IUCrJ ; 7(Pt 4): 693-706, 2020 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-32695416

RESUMEN

DHTKD1 is a lesser-studied E1 enzyme among the family of 2-oxoacid de-hydrogenases. In complex with E2 (di-hydro-lipo-amide succinyltransferase, DLST) and E3 (dihydrolipo-amide de-hydrogenase, DLD) components, DHTKD1 is involved in lysine and tryptophan catabolism by catalysing the oxidative de-carboxyl-ation of 2-oxoadipate (2OA) in mitochondria. Here, the 1.9 Šresolution crystal structure of human DHTKD1 is solved in complex with the thi-amine diphosphate co-factor. The structure reveals how the DHTKD1 active site is modelled upon the well characterized homologue 2-oxoglutarate (2OG) de-hydrogenase but engineered specifically to accommodate its preference for the longer substrate of 2OA over 2OG. A 4.7 Šresolution reconstruction of the human DLST catalytic core is also generated by single-particle electron microscopy, revealing a 24-mer cubic scaffold for assembling DHTKD1 and DLD protomers into a megacomplex. It is further demonstrated that missense DHTKD1 variants causing the inborn error of 2-amino-adipic and 2-oxoadipic aciduria impact on the complex formation, either directly by disrupting the interaction with DLST, or indirectly through destabilizing the DHTKD1 protein. This study provides the starting framework for developing DHTKD1 modulators to probe the intricate mitochondrial energy metabolism.

8.
Cell Mol Life Sci ; 77(1): 3-18, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31748913

RESUMEN

Homologous recombination (HR) is a pathway to faithfully repair DNA double-strand breaks (DSBs). At the core of this pathway is a DNA recombinase, which, as a nucleoprotein filament on ssDNA, pairs with homologous DNA as a template to repair the damaged site. In eukaryotes Rad51 is the recombinase capable of carrying out essential steps including strand invasion, homology search on the sister chromatid and strand exchange. Importantly, a tightly regulated process involving many protein factors has evolved to ensure proper localisation of this DNA repair machinery and its correct timing within the cell cycle. Dysregulation of any of the proteins involved can result in unchecked DNA damage, leading to uncontrolled cell division and cancer. Indeed, many are tumour suppressors and are key targets in the development of new cancer therapies. Over the past 40 years, our structural and mechanistic understanding of homologous recombination has steadily increased with notable recent advancements due to the advances in single particle cryo electron microscopy. These have resulted in higher resolution structural models of the signalling proteins ATM (ataxia telangiectasia mutated), and ATR (ataxia telangiectasia and Rad3-related protein), along with various structures of Rad51. However, structural information of the other major players involved, such as BRCA1 (breast cancer type 1 susceptibility protein) and BRCA2 (breast cancer type 2 susceptibility protein), has been limited to crystal structures of isolated domains and low-resolution electron microscopy reconstructions of the full-length proteins. Here we summarise the current structural understanding of homologous recombination, focusing on key proteins in recruitment and signalling events as well as the mediators for the Rad51 recombinase.


Asunto(s)
Daño del ADN , Mapas de Interacción de Proteínas , Reparación del ADN por Recombinación , Animales , Proteínas de la Ataxia Telangiectasia Mutada/química , Proteínas de la Ataxia Telangiectasia Mutada/metabolismo , Proteína BRCA1/química , Proteína BRCA1/metabolismo , Proteína BRCA2/química , Proteína BRCA2/metabolismo , ADN/química , ADN/genética , Humanos , Modelos Moleculares , Conformación Proteica , Recombinasa Rad51/química , Recombinasa Rad51/metabolismo
9.
Nature ; 571(7766): 521-527, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-31270457

RESUMEN

The integrity of genomes is constantly threatened by problems encountered by the replication fork. BRCA1, BRCA2 and a subset of Fanconi anaemia proteins protect stalled replication forks from degradation by nucleases, through pathways that involve RAD51. The contribution and regulation of BRCA1 in replication fork protection, and how this role relates to its role in homologous recombination, is unclear. Here we show that BRCA1 in complex with BARD1, and not the canonical BRCA1-PALB2 interaction, is required for fork protection. BRCA1-BARD1 is regulated by a conformational change mediated by the phosphorylation-directed prolyl isomerase PIN1. PIN1 activity enhances BRCA1-BARD1 interaction with RAD51, thereby increasing the presence of RAD51 at stalled replication structures. We identify genetic variants of BRCA1-BARD1 in patients with cancer that exhibit poor protection of nascent strands but retain homologous recombination proficiency, thus defining domains of BRCA1-BARD1 that are required for fork protection and associated with cancer development. Together, these findings reveal a BRCA1-mediated pathway that governs replication fork protection.


Asunto(s)
Proteína BRCA1/química , Proteína BRCA1/metabolismo , Replicación del ADN , Proteínas Supresoras de Tumor/metabolismo , Ubiquitina-Proteína Ligasas/metabolismo , Proteína BRCA1/genética , Línea Celular Tumoral , Replicación del ADN/genética , Inestabilidad Genómica/genética , Humanos , Isomerismo , Mutación , Peptidilprolil Isomerasa de Interacción con NIMA/metabolismo , Fosforilación , Fosfoserina/metabolismo , Unión Proteica , Recombinasa Rad51/metabolismo
10.
Sci Rep ; 6: 23748, 2016 Apr 06.
Artículo en Inglés | MEDLINE | ID: mdl-27049649

RESUMEN

The multi-domain enzyme phenylalanine hydroxylase (PAH) catalyzes the hydroxylation of dietary I-phenylalanine (Phe) to I-tyrosine. Inherited mutations that result in PAH enzyme deficiency are the genetic cause of the autosomal recessive disorder phenylketonuria. Phe is the substrate for the PAH active site, but also an allosteric ligand that increases enzyme activity. Phe has been proposed to bind, in addition to the catalytic domain, a site at the PAH N-terminal regulatory domain (PAH-RD), to activate the enzyme via an unclear mechanism. Here we report the crystal structure of human PAH-RD bound with Phe at 1.8 Å resolution, revealing a homodimer of ACT folds with Phe bound at the dimer interface. This work delivers the structural evidence to support previous solution studies that a binding site exists in the RD for Phe, and that Phe binding results in dimerization of PAH-RD. Consistent with our structural observation, a disease-associated PAH mutant impaired in Phe binding disrupts the monomer:dimer equilibrium of PAH-RD. Our data therefore support an emerging model of PAH allosteric regulation, whereby Phe binds to PAH-RD and mediates the dimerization of regulatory modules that would bring about conformational changes to activate the enzyme.


Asunto(s)
Fenilalanina Hidroxilasa/química , Fenilalanina Hidroxilasa/metabolismo , Fenilalanina/metabolismo , Regulación Alostérica , Sitios de Unión , Humanos , Ligandos , Modelos Moleculares , Unión Proteica , Conformación Proteica , Multimerización de Proteína , Dispersión del Ángulo Pequeño
11.
Hum Mol Genet ; 25(11): 2234-2244, 2016 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-27005423

RESUMEN

Classic galactosemia is a potentially lethal disease caused by the dysfunction of galactose 1-phosphate uridylyltransferase (GALT). Over 300 disease-associated GALT mutations have been reported, with the majority being missense changes, although a better understanding of their underlying molecular effects has been hindered by the lack of structural information for the human enzyme. Here, we present the 1.9 Å resolution crystal structure of human GALT (hGALT) ternary complex, revealing a homodimer arrangement that contains a covalent uridylylated intermediate and glucose-1-phosphate in the active site, as well as a structural zinc-binding site, per monomer. hGALT reveals significant structural differences from bacterial GALT homologues in metal ligation and dimer interactions, and therefore is a zbetter model for understanding the molecular consequences of disease mutations. Both uridylylation and zinc binding influence the stability and aggregation tendency of hGALT. This has implications for disease-associated variants where p.Gln188Arg, the most commonly detected, increases the rate of aggregation in the absence of zinc likely due to its reduced ability to form the uridylylated intermediate. As such our structure serves as a template in the future design of pharmacological chaperone therapies and opens new concepts about the roles of metal binding and activity in protein misfolding by disease-associated mutants.


Asunto(s)
Galactosemias/genética , Relación Estructura-Actividad , Factores Complejos Ternarios/química , UTP-Hexosa-1-Fosfato Uridililtransferasa/genética , Sitios de Unión/genética , Dominio Catalítico/genética , Cristalografía por Rayos X , Galactosa/química , Galactosa/metabolismo , Galactosemias/metabolismo , Galactosemias/patología , Humanos , Cinética , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Mutación , Conformación Proteica , Factores Complejos Ternarios/genética , UTP-Hexosa-1-Fosfato Uridililtransferasa/química
12.
J Biol Chem ; 290(49): 29167-77, 2015 Dec 04.
Artículo en Inglés | MEDLINE | ID: mdl-26483544

RESUMEN

Conversion of vitamin B12 (cobalamin, Cbl) into the cofactor forms methyl-Cbl (MeCbl) and adenosyl-Cbl (AdoCbl) is required for the function of two crucial enzymes, mitochondrial methylmalonyl-CoA mutase and cytosolic methionine synthase, respectively. The intracellular proteins MMACHC and MMADHC play important roles in processing and targeting the Cbl cofactor to its destination enzymes, and recent evidence suggests that they may interact while performing these essential trafficking functions. To better understand the molecular basis of this interaction, we have mapped the crucial protein regions required, indicate that Cbl is likely processed by MMACHC prior to interaction with MMADHC, and identify patient mutations on both proteins that interfere with complex formation, via different mechanisms. We further report the crystal structure of the MMADHC C-terminal region at 2.2 Å resolution, revealing a modified nitroreductase fold with surprising homology to MMACHC despite their poor sequence conservation. Because MMADHC demonstrates no known enzymatic activity, we propose it as the first protein known to repurpose the nitroreductase fold solely for protein-protein interaction. Using small angle x-ray scattering, we reveal the MMACHC-MMADHC complex as a 1:1 heterodimer and provide a structural model of this interaction, where the interaction region overlaps with the MMACHC-Cbl binding site. Together, our findings provide novel structural evidence and mechanistic insight into an essential biological process, whereby an intracellular "trafficking chaperone" highly specific for a trace element cofactor functions via protein-protein interaction, which is disrupted by inherited disease mutations.


Asunto(s)
Proteínas Portadoras/química , Proteínas de Transporte de Membrana Mitocondrial/química , Vitamina B 12/química , Secuencia de Aminoácidos , Animales , Sitios de Unión , Proteínas Portadoras/genética , Cristalografía por Rayos X , Humanos , Péptidos y Proteínas de Señalización Intracelular , Enfermedades Metabólicas/metabolismo , Ratones , Proteínas de Transporte de Membrana Mitocondrial/genética , Chaperonas Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Mutación , Nitrorreductasas/química , Oxidorreductasas , Fenotipo , Unión Proteica , Mapeo de Interacción de Proteínas , Multimerización de Proteína , Estructura Secundaria de Proteína , Transporte de Proteínas , Proteínas Recombinantes/química , Homología de Secuencia de Aminoácido
13.
Hum Mol Genet ; 24(20): 5667-76, 2015 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-26199317

RESUMEN

Glycogen branching enzyme 1 (GBE1) plays an essential role in glycogen biosynthesis by generating α-1,6-glucosidic branches from α-1,4-linked glucose chains, to increase solubility of the glycogen polymer. Mutations in the GBE1 gene lead to the heterogeneous early-onset glycogen storage disorder type IV (GSDIV) or the late-onset adult polyglucosan body disease (APBD). To better understand this essential enzyme, we crystallized human GBE1 in the apo form, and in complex with a tetra- or hepta-saccharide. The GBE1 structure reveals a conserved amylase core that houses the active centre for the branching reaction and harbours almost all GSDIV and APBD mutations. A non-catalytic binding cleft, proximal to the site of the common APBD mutation p.Y329S, was found to bind the tetra- and hepta-saccharides and may represent a higher-affinity site employed to anchor the complex glycogen substrate for the branching reaction. Expression of recombinant GBE1-p.Y329S resulted in drastically reduced protein yield and solubility compared with wild type, suggesting this disease allele causes protein misfolding and may be amenable to small molecule stabilization. To explore this, we generated a structural model of GBE1-p.Y329S and designed peptides ab initio to stabilize the mutation. As proof-of-principle, we evaluated treatment of one tetra-peptide, Leu-Thr-Lys-Glu, in APBD patient cells. We demonstrate intracellular transport of this peptide, its binding and stabilization of GBE1-p.Y329S, and 2-fold increased mutant enzymatic activity compared with untreated patient cells. Together, our data provide the rationale and starting point for the screening of small molecule chaperones, which could become novel therapies for this disease.


Asunto(s)
Sistema de la Enzima Desramificadora del Glucógeno/química , Sistema de la Enzima Desramificadora del Glucógeno/genética , Enfermedad del Almacenamiento de Glucógeno Tipo IV/enzimología , Enfermedad del Almacenamiento de Glucógeno/enzimología , Mutación Missense , Enfermedades del Sistema Nervioso/enzimología , Péptidos/uso terapéutico , Secuencia de Aminoácidos , Biología Computacional , Sistema de la Enzima Desramificadora del Glucógeno/efectos de los fármacos , Sistema de la Enzima Desramificadora del Glucógeno/metabolismo , Enfermedad del Almacenamiento de Glucógeno/tratamiento farmacológico , Enfermedad del Almacenamiento de Glucógeno/genética , Enfermedad del Almacenamiento de Glucógeno Tipo IV/genética , Humanos , Datos de Secuencia Molecular , Enfermedades del Sistema Nervioso/tratamiento farmacológico , Enfermedades del Sistema Nervioso/genética , Estructura Terciaria de Proteína , Alineación de Secuencia
14.
J Biol Chem ; 289(52): 36018-30, 2014 Dec 26.
Artículo en Inglés | MEDLINE | ID: mdl-25336647

RESUMEN

Cystathionine ß-synthase (CBS) is a key enzyme in sulfur metabolism, and its inherited deficiency causes homocystinuria. Mammalian CBS is modulated by the binding of S-adenosyl-l-methionine (AdoMet) to its regulatory domain, which activates its catalytic domain. To investigate the underlying mechanism, we performed x-ray crystallography, mutagenesis, and mass spectrometry (MS) on human CBS. The 1.7 Å structure of a AdoMet-bound CBS regulatory domain shows one AdoMet molecule per monomer, at the interface between two constituent modules (CBS-1, CBS-2). AdoMet binding is accompanied by a reorientation between the two modules, relative to the AdoMet-free basal state, to form interactions with AdoMet via residues verified by mutagenesis to be important for AdoMet binding (Phe(443), Asp(444), Gln(445), and Asp(538)) and for AdoMet-driven inter-domain communication (Phe(443), Asp(538)). The observed structural change is further supported by ion mobility MS, showing that as-purified CBS exists in two conformational populations, which converged to one in the presence of AdoMet. We therefore propose that AdoMet-induced conformational change alters the interface and arrangement between the catalytic and regulatory domains within the CBS oligomer, thereby increasing the accessibility of the enzyme active site for catalysis.


Asunto(s)
Cistationina betasintasa/química , S-Adenosilmetionina/química , Dominio Catalítico , Cristalografía por Rayos X , Humanos , Enlace de Hidrógeno , Modelos Moleculares , Unión Proteica , Estructura Secundaria de Proteína
15.
Gene ; 524(2): 95-104, 2013 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-23644136

RESUMEN

The enzyme UDP-galactose 4'-epimerase (GALE) catalyses the reversible epimerisation of both UDP-galactose and UDP-N-acetyl-galactosamine. Deficiency of the human enzyme (hGALE) is associated with type III galactosemia. The majority of known mutations in hGALE are missense and private thus making clinical guidance difficult. In this study a bioinformatics approach was employed to analyse the structural effects due to each mutation using both the UDP-glucose and UDP-N-acetylglucosamine bound structures of the wild-type protein. Changes to the enzyme's overall stability, substrate/cofactor binding and propensity to aggregate were also predicted. These predictions were found to be in good agreement with previous in vitro and in vivo studies when data was available and allowed for the differentiation of those mutants that severely impair the enzyme's activity against UDP-galactose. Next this combination of techniques were applied to another twenty-six reported variants from the NCBI dbSNP database that have yet to be studied to predict their effects. This identified p.I14T, p.R184H and p.G302R as likely severely impairing mutations. Although severely impaired mutants were predicted to decrease the protein's stability, overall predicted stability changes only weakly correlated with residual activity against UDP-galactose. This suggests other protein functions such as changes in cofactor and substrate binding may also contribute to the mechanism of impairment. Finally this investigation shows that this combination of different in silico approaches is useful in predicting the effects of mutations and that it could be the basis of an initial prediction of likely clinical severity when new hGALE mutants are discovered.


Asunto(s)
Galactosemias/genética , Mutación Missense , UDPglucosa 4-Epimerasa/genética , Secuencia de Aminoácidos , Biología Computacional , Bases de Datos Genéticas , Activación Enzimática , Estabilidad de Enzimas , Galactosemias/clasificación , Galactosemias/enzimología , Predisposición Genética a la Enfermedad , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Polimorfismo de Nucleótido Simple , Valor Predictivo de las Pruebas , Pliegue de Proteína , Estructura Secundaria de Proteína , Índice de Severidad de la Enfermedad , Especificidad por Sustrato , UDPglucosa 4-Epimerasa/metabolismo , Uridina Difosfato Galactosa/metabolismo , Uridina Difosfato N-Acetilglucosamina/metabolismo
16.
Biochim Biophys Acta ; 1832(8): 1279-93, 2013 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-23583749

RESUMEN

Type I galactosemia is a genetic disorder that is caused by the impairment of galactose-1-phosphate uridylyltransferase (GALT; EC 2.7.7.12). Although a large number of mutations have been detected through genetic screening of the human GALT (hGALT) locus, for many it is not known how they cause their effects. The majority of these mutations are missense, with predicted substitutions scattered throughout the enzyme structure and thus causing impairment by other means rather than direct alterations to the active site. To clarify the fundamental, molecular basis of hGALT impairment we studied five disease-associated variants p.D28Y, p.L74P, p.F171S, p.F194L and p.R333G using both a yeast model and purified, recombinant proteins. In a yeast expression system there was a correlation between lysate activity and the ability to rescue growth in the presence of galactose, except for p.R333G. Kinetic analysis of the purified proteins quantified each variant's level of enzymatic impairment and demonstrated that this was largely due to altered substrate binding. Increased surface hydrophobicity, altered thermal stability and changes in proteolytic sensitivity were also detected. Our results demonstrate that hGALT requires a level of flexibility to function optimally and that altered folding is the underlying reason of impairment in all the variants tested here. This indicates that misfolding is a common, molecular basis of hGALT deficiency and suggests the potential of pharmacological chaperones and proteostasis regulators as novel therapeutic approaches for type I galactosemia.


Asunto(s)
Galactosemias/enzimología , Deficiencias en la Proteostasis/enzimología , UDP-Glucosa-Hexosa-1-Fosfato Uridiltransferasa/química , UDP-Glucosa-Hexosa-1-Fosfato Uridiltransferasa/metabolismo , Galactosemias/etiología , Galactosemias/genética , Humanos , Cinética , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Mutación , Unión Proteica , Desnaturalización Proteica , Deficiencias en la Proteostasis/etiología , Deficiencias en la Proteostasis/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , UDP-Glucosa-Hexosa-1-Fosfato Uridiltransferasa/genética
17.
Biochim Biophys Acta ; 1822(10): 1516-26, 2012 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-22613355

RESUMEN

Deficiency of UDP-galactose 4'-epimerase is implicated in type III galactosemia. Two variants, p.K161N-hGALE and p.D175N-hGALE, have been previously found in combination with other alleles in patients with a mild form of the disease. Both variants were studied in vivo and in vitro and showed different levels of impairment. p.K161N-hGALE was severely impaired with substantially reduced enzymatic activity, increased thermal stability, reduced cofactor binding and no ability to rescue the galactose-sensitivity of gal10-null yeast. Interestingly p.K161N-hGALE showed less impairment of activity with UDP-N-acetylgalactosamine in comparison to UDP-galactose. Differential scanning fluorimetry revealed that p.K161N-hGALE was more stable than the wild-type protein and only changed stability in the presence of UDP-N-acetylglucosamine and NAD(+). p.D175N-hGALE essentially rescued the galactose-sensitivity of gal10-null yeast, was less stable than the wild-type protein but showed increased stability in the presence of substrates and cofactor. We postulate that p.K161N-hGALE causes its effects by abolishing an important interaction between the protein and the cofactor, whereas p.D175N-hGALE is predicted to remove a stabilizing salt bridge between the ends of two α-helices that contain residues that interact with NAD(+). These results suggest that the cofactor binding is dynamic and that its loss results in significant structural changes that may be important in disease causation.


Asunto(s)
Coenzimas/metabolismo , Galactosemias/enzimología , Unión Proteica/genética , UDPglucosa 4-Epimerasa/química , UDPglucosa 4-Epimerasa/genética , UDPglucosa 4-Epimerasa/metabolismo , Alelos , Coenzimas/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas Fúngicas/metabolismo , Galactosa/genética , Galactosa/metabolismo , Galactosemias/genética , Humanos , Cinética , Modelos Moleculares , NAD/genética , NAD/metabolismo , Péptido Hidrolasas/genética , Péptido Hidrolasas/metabolismo , Desnaturalización Proteica , Multimerización de Proteína , Estructura Secundaria de Proteína/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Relación Estructura-Actividad , Uridina Difosfato N-Acetilglucosamina/genética , Uridina Difosfato N-Acetilglucosamina/metabolismo , Levaduras/genética , Levaduras/metabolismo
18.
Chem Biol Drug Des ; 80(2): 173-81, 2012 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-22487100

RESUMEN

During the past century, several epidemics of human African trypanosomiasis, a deadly disease caused by the protist Trypanosoma brucei, have afflicted sub-Saharan Africa. Over 10 000 new victims are reported each year, with hundreds of thousands more at risk. As current drug treatments are either highly toxic or ineffective, novel trypanocides are urgently needed. The T. brucei galactose synthesis pathway is one potential therapeutic target. Although galactose is essential for T. brucei survival, the parasite lacks the transporters required to intake galactose from the environment. UDP-galactose 4'-epimerase (TbGalE) is responsible for the epimerization of UDP-glucose to UDP-galactose and is therefore of great interest to medicinal chemists. Using molecular dynamics simulations, we investigate the atomistic motions of TbGalE in both the apo and holo states. The sampled conformations and protein dynamics depend not only on the presence of a UDP-sugar ligand, but also on the chirality of the UDP-sugar C4 atom. This dependence provides important insights into TbGalE function and may help guide future computer-aided drug discovery efforts targeting this protein.


Asunto(s)
Simulación de Dinámica Molecular , Trypanosoma brucei brucei/enzimología , Tripanosomiasis Africana/parasitología , UDPglucosa 4-Epimerasa/química , Regulación Alostérica , Sitios de Unión , Diseño de Fármacos , Humanos , Enlace de Hidrógeno , Ligandos , Conformación Proteica , Trypanosoma brucei brucei/química , Trypanosoma brucei brucei/metabolismo , UDPglucosa 4-Epimerasa/metabolismo
19.
IUBMB Life ; 63(11): 949-54, 2011 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-21960482

RESUMEN

Type I galactosemia results from reduced galactose 1-phosphate uridylyltransferase (GALT) activity. Signs of disease include damage to the eyes, brain, liver, and ovaries. However, the exact nature and severity of the pathology depends on the mutation(s) in the patient's genes and his/her environment. Considerable enzymological and structural knowledge has been accumulated and this provides a basis to explain, at a biochemical level, impairment in the enzyme in the more than 230 disease-associated variants, which have been described. The most common variant, Q188R, occurs close to the active site and the dimer interface. The substitution probably disrupts both UDP-sugar binding and homodimer stability. Other alterations, for example K285N, occur close to the surface of the enzyme and most likely affect the folding and stability of the enzyme. There are a number of unanswered questions in the field, which require resolution. These include the possibility that the main enzymes of galactose metabolism form a supramolecular complex and the need for a high resolution crystal structure of human GALT.


Asunto(s)
Galactosemias/genética , UTP-Hexosa-1-Fosfato Uridililtransferasa/genética , Alelos , Animales , Dominio Catalítico , Galactosemias/enzimología , Humanos , Modelos Moleculares , Mutación Missense , UTP-Hexosa-1-Fosfato Uridililtransferasa/química
20.
IUBMB Life ; 63(9): 694-700, 2011 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-21793161

RESUMEN

Reduced galactose 1-phosphate uridylyltransferase (GALT) activity is associated with the genetic disease type I galactosemia. This results in an increase in the cellular concentration of galactose 1-phosphate. The accumulation of this toxic metabolite, combined with aberrant glycoprotein and glycolipid biosynthesis, is likely to be the major factor in molecular pathology. The mechanism of GALT was established through classical enzymological methods to be a substituted enzyme in which the reaction with UDP-glucose results in the formation of a covalent, UMP-histidine adduct in the active site. The uridylated enzyme can then react with galactose 1-phosphate to form UDP-galactose. The structure of the enzyme from Escherichia coli reveals a homodimer containing one zinc (II) and one iron (II) ion per subunit. This enzymological and structural knowledge provides the basis for understanding the biochemistry of this critical step in the Leloir pathway. However, a high-resolution crystal structure of human GALT is required to assist greater understanding of the effects of disease-associated mutations.


Asunto(s)
Escherichia coli/enzimología , Galactosemias/enzimología , Modelos Moleculares , UTP-Hexosa-1-Fosfato Uridililtransferasa/química , UTP-Hexosa-1-Fosfato Uridililtransferasa/metabolismo , Galactosafosfatos/metabolismo , Humanos , Redes y Vías Metabólicas/fisiología , Estructura Molecular
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