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1.
FEBS J ; 291(3): 510-526, 2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-37863644

RESUMO

Hydroxymethylbilane synthase (HMBS), involved in haem biosynthesis, catalyses the head-to-tail coupling of four porphobilinogens (PBGs) via a dipyrromethane (DPM) cofactor. DPM is composed of two PBGs, and a hexapyrrole is built before the tetrapyrrolic 1-hydroxymethylbilane product is released. During this elongation, stable enzyme (E) intermediates are formed from the holoenzyme, with additional PBG substrates (S): ES, ES2 , ES3 and ES4 . Native PAGE and mass spectrometry of the acute intermittent porphyria (AIP)-associated HMBS variant p.Arg167Gln demonstrated an increased amount of ES3 . Kinetic parameters indicated catalytic dysfunction, however, the product release was not entirely prevented. Isolation and crystal structure analysis of the ES3 intermediate (PDB: 8PND) showed that a pentapyrrole was fully retained within the active site, revealing that polypyrrole elongation proceeds within the active site via a third interaction site, intermediate pyrrole site 3 (IPS3). The AIP-associated HMBS variant p.Arg195Cys, located on the opposite side to p.Arg167Gln in the active site, accumulated the ES4 intermediate in the presence of excess PBG, implying that product hydrolysis was obstructed. Arg167 is thus involved in all elongation steps and is a determinant for the rate of enzyme catalysis, whereas Arg195 is important for releasing the product. Moreover, by substituting residues in the vicinity of IPS3, our results indicate that a fully retained hexapyrrole could be hydrolysed in a novel site in proximity of the IPS3.


Assuntos
Hidroximetilbilano Sintase , Porfiria Aguda Intermitente , Humanos , Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/genética , Hidroximetilbilano Sintase/metabolismo , Polímeros , Pirróis , Domínio Catalítico , Mutação
2.
Am J Hum Genet ; 110(10): 1769-1786, 2023 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-37729906

RESUMO

Defects in hydroxymethylbilane synthase (HMBS) can cause acute intermittent porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ∼⅓ of clinical HMBS variants are missense variants, and most clinically reported HMBS missense variants are designated as "variants of uncertain significance" (VUSs). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino acid substitutions. The resulting variant effect maps generally agreed with biochemical expectations and provide further evidence that HMBS can function as a monomer. Additionally, the maps implicated specific residues as having roles in active site dynamics, which was further supported by molecular dynamics simulations. Most importantly, these maps can help discriminate pathogenic from benign HMBS variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.


Assuntos
Hidroximetilbilano Sintase , Porfiria Aguda Intermitente , Humanos , Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/genética , Hidroximetilbilano Sintase/metabolismo , Mutação de Sentido Incorreto/genética , Porfiria Aguda Intermitente/diagnóstico , Porfiria Aguda Intermitente/genética , Substituição de Aminoácidos , Simulação de Dinâmica Molecular
3.
FEBS Open Bio ; 12(12): 2136-2146, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36115019

RESUMO

Hydroxymethylbilane synthase (HMBS) is the third enzyme involved in haem biosynthesis, in which it catalyses the formation of tetrapyrrole 1-hydroxymethylbilane (HMB). In this process, HMBS binds four consecutive substrate molecules, creating the enzyme-intermediate complexes ES, ES2 , ES3 and ES4 . Pathogenic variants in the HMBS gene are associated with the dominantly inherited disorder acute intermittent porphyria. In this study, we have characterised the p.R26H variant to shed light on the role of Arg26 in the elongation mechanism of HMBS and to provide insights into its effect on the enzyme. With selected biophysical methods, we have been able to show that p.R26H forms a single enzyme-intermediate complex in the ES2 -state. We were also able to demonstrate that the p.R26H variant results in an inactive enzyme, which is unable to produce the HMB product.


Assuntos
Hidroximetilbilano Sintase , Porfiria Aguda Intermitente , Humanos , Hidroximetilbilano Sintase/genética , Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/metabolismo , Porfiria Aguda Intermitente/genética
4.
Acta Crystallogr F Struct Biol Commun ; 77(Pt 11): 388-398, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34726177

RESUMO

The enzyme hydroxymethylbilane synthase (HMBS; EC 4.3.1.8), also known as porphobilinogen deaminase, catalyses the stepwise addition of four molecules of porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane. Thirty years of crystal structures are surveyed in this topical review. These crystal structures aim at the elucidation of the structural basis of the complex reaction mechanism involving the formation of tetrapyrrole from individual porphobilinogen units. The consistency between the various structures is assessed. This includes an evaluation of the precision of each molecular model and what was not modelled. A survey is also made of the crystallization conditions used in the context of the operational pH of the enzyme. The combination of 3D structural techniques, seeking accuracy, has also been a feature of this research effort. Thus, SAXS, NMR and computational molecular dynamics have also been applied. The general framework is also a considerable chemistry research effort to understand the function of the enzyme and its medical pathologies in acute intermittent porphyria (AIP). Mutational studies and their impact on the catalytic reaction provide insight into the basis of AIP and are also invaluable for guiding the understanding of the crystal structure results. Future directions for research on HMBS are described, including the need to determine the protonation states of key amino-acid residues identified as being catalytically important. The question remains - what is the molecular engine for this complex reaction? Thermal fluctuations are the only suggestion thus far.


Assuntos
Hidroximetilbilano Sintase , Simulação de Dinâmica Molecular , Cristalografia por Raios X , Hidroximetilbilano Sintase/química , Espalhamento a Baixo Ângulo , Difração de Raios X
5.
Int J Mol Sci ; 22(20)2021 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-34681668

RESUMO

Acute intermittent porphyria (AIP) is an autosomal dominant genetic disease caused by a lack or decrease in hydroxymethylbilane synthase (HMBS) activity. It is characterized by acute nerve and visceral attacks caused by factors in the process of heme synthesis. The penetrance rate of this disease is low, and the heterogeneity is strong. Here, we reported two novel HMBS mutations from two unrelated Chinese AIP patients and confirmed the pathogenicity of these two mutations. We found the HMBS c.760-771+2delCTGAGGCACCTGGTinsGCTGCATCGCTGAA and HMBS c.88-1G>C mutations by second-generation sequencing and Sanger sequencing. The in vitro expression analysis showed that these mutations caused abnormal HMBS mRNA splicing and premature termination or partial missing of HMBS protein. Homologous modeling analysis showed that the HMBS mutants lacked the amino acids which are crucial for the enzyme activity or the protein stability. Consistently, enzyme activity analysis confirmed that the HMBS mutants' overexpression cells exhibited the reduced enzyme activity compared with the HMBS wildtype overexpression cells. Our study identified and confirmed two novel pathogenic HMBS mutations which will expand the molecular heterogeneity of AIP and provide further scientific basis for the clinical diagnosis of AIP.


Assuntos
Hidroximetilbilano Sintase/genética , Porfiria Aguda Intermitente/diagnóstico , Processamento Alternativo , Sequência de Aminoácidos , Povo Asiático/genética , China , Genótipo , Células HEK293 , Humanos , Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/metabolismo , Linhagem , Polimorfismo Genético , Porfiria Aguda Intermitente/genética , Estrutura Terciária de Proteína , Alinhamento de Sequência
6.
Acta Crystallogr A Found Adv ; 77(Pt 3): 173-185, 2021 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-33944796

RESUMO

The distinctive features of the physics-based probes used in understanding the structure of matter focusing on biological sciences, but not exclusively, are described in the modern context. This is set in a wider scope of holistic biology and the scepticism about `reductionism', what is called the `molecular level', and how to respond constructively. These topics will be set alongside the principles of accuracy and precision, and their boundaries. The combination of probes and their application together is the usual way of realizing accuracy. The distinction between precision and accuracy can be blurred by the predictive force of a precise structure, thereby lending confidence in its potential accuracy. These descriptions will be applied to the comparison of cryo and room-temperature protein crystal structures as well as the solid state of a crystal and the same molecules studied by small-angle X-ray scattering in solution and by electron microscopy on a sample grid. Examples will include: time-resolved X-ray Laue crystallography of an enzyme Michaelis complex formed directly in a crystal equivalent to in vivo; a new iodoplatin for radiation therapy predicted from studies of platin crystal structures; and the field of colouration of carotenoids, as an effective assay of function, i.e. their colouration, when unbound and bound to a protein. The complementarity of probes, as well as their combinatory use, is then at the foundation of real (biologically relevant), probe-artefacts-free, structure-function studies. The foundations of our methodologies are being transformed by colossal improvements in technologies of X-ray and neutron sources and their beamline instruments, as well as improved electron microscopes and NMR spectrometers. The success of protein structure prediction from gene sequence recently reported by CASP14 also opens new doors to change and extend the foundations of the structural sciences.


Assuntos
Elétrons , Hidroximetilbilano Sintase/química , Compostos Organometálicos/química , Cristalografia por Raios X , Hidroximetilbilano Sintase/metabolismo , Espectroscopia de Ressonância Magnética , Estrutura Molecular
7.
Biochem J ; 478(5): 1023-1042, 2021 03 12.
Artigo em Inglês | MEDLINE | ID: mdl-33600566

RESUMO

Hydroxymethylbilane synthase (HMBS), which is involved in the heme biosynthesis pathway, has a dipyrromethane cofactor and combines four porphobilinogen (PBG) molecules to form a linear tetrapyrrole, hydroxymethylbilane. Enzyme kinetic study of human HMBS using a PBG-derivative, 2-iodoporphobilinogen (2-I-PBG), exhibited noncompetitive inhibition with the inhibition constant being 5.4 ± 0.3 µM. To elucidate the reaction mechanism of HMBS in detail, crystal structure analysis of 2-I-PBG-bound holo-HMBS and its reaction intermediate possessing two PBG molecules (ES2), and inhibitor-free ES2 was performed at 2.40, 2.31, and 1.79 Šresolution, respectively. Their overall structures are similar to that of inhibitor-free holo-HMBS, and the differences are limited near the active site. In both 2-I-PBG-bound structures, 2-I-PBG is located near the terminus of the cofactor or the tetrapyrrole chain. The propionate group of 2-I-PBG interacts with the side chain of Arg173, and its acetate group is associated with the side chains of Arg26 and Ser28. Furthermore, the aminomethyl group and pyrrole nitrogen of 2-I-PBG form hydrogen bonds with the side chains of Gln34 and Asp99, respectively. These amino acid residues form a single substrate-binding site, where each of the four PBG molecules covalently binds to the cofactor (or oligopyrrole chain) consecutively, ultimately forming a hexapyrrole chain. Molecular dynamics simulation of the ES2 intermediate suggested that the thermal fluctuation of the lid and cofactor-binding loops causes substrate recruitment and oligopyrrole chain shift needed for consecutive condensation. Finally, the hexapyrrole chain is hydrolyzed self-catalytically to produce hydroxymethylbilane.


Assuntos
Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/metabolismo , Porfobilinogênio/metabolismo , Uroporfirinogênios/metabolismo , Catálise , Domínio Catalítico , Cristalografia por Raios X , Humanos , Simulação de Dinâmica Molecular , Conformação Proteica , Domínios Proteicos , Especificidade por Substrato
8.
Int J Mol Sci ; 22(2)2021 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-33445488

RESUMO

Acute intermittent porphyria (AIP) is an autosomal dominant inherited disease with low clinical penetrance, caused by mutations in the hydroxymethylbilane synthase (HMBS) gene, which encodes the third enzyme in the haem biosynthesis pathway. In susceptible HMBS mutation carriers, triggering factors such as hormonal changes and commonly used drugs induce an overproduction and accumulation of toxic haem precursors in the liver. Clinically, this presents as acute attacks characterised by severe abdominal pain and a wide array of neurological and psychiatric symptoms, and, in the long-term setting, the development of primary liver cancer, hypertension and kidney failure. Treatment options are few, and therapies preventing the development of symptomatic disease and long-term complications are non-existent. Here, we provide an overview of the disorder and treatments already in use in clinical practice, in addition to other therapies under development or in the pipeline. We also introduce the pathomechanistic effects of HMBS mutations, and present and discuss emerging therapeutic options based on HMBS stabilisation and the regulation of proteostasis. These are novel mechanistic therapeutic approaches with the potential of prophylactic correction of the disease by totally or partially recovering the enzyme functionality. The present scenario appears promising for upcoming patient-tailored interventions in AIP.


Assuntos
Porfiria Aguda Intermitente/terapia , Alelos , Animais , Terapia Combinada , Gerenciamento Clínico , Suscetibilidade a Doenças , Predisposição Genética para Doença , Heme/metabolismo , Humanos , Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/genética , Redes e Vias Metabólicas , Mutação , Porfiria Aguda Intermitente/diagnóstico , Porfiria Aguda Intermitente/etiologia , Relação Estrutura-Atividade , Resultado do Tratamento
9.
Phys Chem Chem Phys ; 21(15): 7932-7940, 2019 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-30918925

RESUMO

Hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthesis pathway, catalyzes the formation of 1-hydroxymethylbilane (HMB) by a stepwise polymerization of four molecules of porphobilinogen (PBG) using the dipyrromethane (DPM) cofactor. The mechanism by which HMBS polymerizes four units of PBG has not been elucidated to date. In vitro and in silico studies on HMBS have suggested certain residues with catalytic importance, but their specific role in the catalysis is unclear. To understand the catalytic mechanism of HMBS, quantum mechanical (QM) calculations were performed on model systems obtained from the active site of the human HMBS enzyme. The addition of one molecule of PBG to the DPM cofactor is carried out in four steps: (1) protonation of the substrate, PBG; (2) deamination of PBG; (3) electrophilic addition of the deaminated substrate to the terminal pyrrole ring of the enzyme-bound DPM cofactor and (4) deprotonation of the carbon atom at the α-position of the second ring of DPM. Based on the energy profiles from the QM calculations on cluster models, R26 is proposed to be the best suitable proton donor to the PBG moiety, which aids in the deamination of the substrate. During the electrophilic addition step, the intermediate formed is stabilized by the carboxylate side chain of the D99 residue. In the final deprotonation step, an extra proton from the second ring of DPM is transferred to R26 via the carboxylate side chain of D99, thus completing one cycle of the catalytic mechanism. The residues in the cluster model seem to play an important role in obtaining accurate energy barriers. All the stationary points along the reaction pathway have been characterized using QM calculations. The rate limiting step for the complete mechanism is found to be the deamination of the PBG moiety. The results of this study provide a detailed understanding of the catalytic mechanism and would help design future studies aimed at modulating the activity of HMBS.


Assuntos
Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/metabolismo , Modelos Químicos , Catálise , Humanos
10.
Biochim Biophys Acta Gen Subj ; 1862(9): 1948-1955, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-29908816

RESUMO

Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor. We present crystal structures for two human PBGD intermediates: PBGD loaded with the cofactor and with the reaction intermediate containing two additional substrate pyrrole rings. These results, combined with SAXS and NMR experiments, allow us to propose a mechanism for the reaction progression that requires less structural rearrangements than previously suggested: the enzyme slides a flexible loop over the growing-product active site cavity. The structures and the mechanism proposed for this essential reaction explain how a set of missense mutations result in acute intermittent porphyria.


Assuntos
Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/metabolismo , Pirróis/química , Pirróis/metabolismo , Catálise , Domínio Catalítico , Cristalografia por Raios X , Humanos , Polimerização , Porfobilinogênio/química , Porfobilinogênio/metabolismo , Conformação Proteica , Uroporfirinogênios/química , Uroporfirinogênios/metabolismo
11.
Proc Natl Acad Sci U S A ; 115(17): E4071-E4080, 2018 04 24.
Artigo em Inglês | MEDLINE | ID: mdl-29632172

RESUMO

Hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway, catalyzes the head-to-tail condensation of four molecules of porphobilinogen (PBG) to form the linear tetrapyrrole 1-hydroxymethylbilane (HMB). Mutations in human HMBS (hHMBS) cause acute intermittent porphyria (AIP), an autosomal-dominant disorder characterized by life-threatening neurovisceral attacks. Although the 3D structure of hHMBS has been reported, the mechanism of the stepwise polymerization of four PBG molecules to form HMB remains unknown. Moreover, the specific roles of each of the critical active-site residues in the stepwise enzymatic mechanism and the dynamic behavior of hHMBS during catalysis have not been investigated. Here, we report atomistic studies of HMB stepwise synthesis by using molecular dynamics (MD) simulations, mutagenesis, and in vitro expression analyses. These studies revealed that the hHMBS active-site loop movement and cofactor turn created space for the elongating pyrrole chain. Twenty-seven residues around the active site and water molecules interacted to stabilize the large, negatively charged, elongating polypyrrole. Mutagenesis of these active-site residues altered the binding site, hindered cofactor binding, decreased catalysis, impaired ligand exit, and/or destabilized the enzyme. Based on intermediate stages of chain elongation, R26 and R167 were the strongest candidates for proton transfer to deaminate the incoming PBG molecules. Unbiased random acceleration MD simulations identified R167 as a gatekeeper and facilitator of HMB egress through the space between the enzyme's domains and the active-site loop. These studies identified the specific active-site residues involved in each step of pyrrole elongation, thereby providing the molecular bases of the active-site mutations causing AIP.


Assuntos
Hidroximetilbilano Sintase/química , Simulação de Dinâmica Molecular , Mutação de Sentido Incorreto , Porfiria Aguda Intermitente/enzimologia , Pirróis/química , Substituição de Aminoácidos , Humanos , Hidroximetilbilano Sintase/genética , Hidroximetilbilano Sintase/metabolismo , Porfiria Aguda Intermitente/genética , Estrutura Secundária de Proteína , Pirróis/metabolismo
12.
ACS Chem Biol ; 13(3): 750-760, 2018 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-29360345

RESUMO

Porphobilinogen deaminase (PBGD) is an enzyme that catalyzes the formation of hydroxymethylbilane, a tetrapyrrole intermediate, during heme biosynthesis through the stepwise polymerization of four molecules of porphobilinogen. PBGD from Vibrio cholerae was expressed in Escherichia coli and characterized in this study. Unexpectedly, spectroscopic measurements revealed that PBGD bound one equivalent of heme with a dissociation constant of 0.33 ± 0.01 µM. The absorption and resonance Raman spectra suggested that heme is a mixture of the 5-coordinate and 6-coordinate hemes. Mutational studies indicated that the 5-coordinate heme possessed Cys105 as a heme axial ligand, and His227 was coordinated to form the 6-coordinate heme. Upon heme binding, the deamination activity decreased by approximately 15%. The crystal structure of PBGD revealed that His227 was located near Cys105, but the side chain of His227 did not point toward Cys105. The addition of the cyanide ion to heme-PBGD abolished the effect of heme binding on the enzymatic activity. Therefore, coordination of His227 to heme appeared to induce reorientation of the domains containing Cys105, leading to a decrease in the enzymatic activity. This is the first report indicating that the PBGD activity is controlled by heme, the final product of heme biosynthesis. This finding improves our understanding of the mechanism by which heme biosynthesis is regulated.


Assuntos
Heme/biossíntese , Hidroximetilbilano Sintase/metabolismo , Uroporfirinogênios/biossíntese , Vibrio cholerae/metabolismo , Cristalografia por Raios X , Escherichia coli/genética , Heme/metabolismo , Hidroximetilbilano Sintase/química , Ligação Proteica , Análise Espectral Raman , Vibrio cholerae/enzimologia
13.
Acta Crystallogr F Struct Biol Commun ; 73(Pt 11): 612-620, 2017 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-29095155

RESUMO

The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) in the active site which is covalently linked to a conserved cysteine residue through a thioether bridge. The substrate molecules are linked to the cofactor in a stepwise head-to-tail manner during the reaction, which is catalysed by a conserved aspartate residue: Asp82 in the B. megaterium enzyme. Three mutations have been made affecting Asp82 (D82A, D82E and D82N) and their crystal structures have been determined at resolutions of 2.7, 1.8 and 1.9 Å, respectively. These structures reveal that whilst the D82E mutant possesses the DPM cofactor, in the D82N and D82A mutants the cofactor is likely to be missing, incompletely assembled or disordered. Comparison of the mutant PBGD structures with that of the wild-type enzyme shows that there are significant domain movements and suggests that the enzyme adopts `open' and `closed' conformations, potentially in response to substrate binding.


Assuntos
Bacillus megaterium/enzimologia , Hidroximetilbilano Sintase/química , Mutação , Tetrapirróis/metabolismo , Sítios de Ligação , Catálise , Domínio Catalítico , Cristalização , Cristalografia por Raios X , Hidroximetilbilano Sintase/genética , Hidroximetilbilano Sintase/metabolismo , Conformação Proteica , Domínios Proteicos
14.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 3): 744-51, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24598743

RESUMO

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.


Assuntos
Bacillus megaterium/enzimologia , Hidroximetilbilano Sintase/química , Porfobilinogênio/análogos & derivados , Sequência de Aminoácidos , Bacillus megaterium/metabolismo , Cristalização , Cristalografia por Raios X , Hidroximetilbilano Sintase/metabolismo , Dados de Sequência Molecular , Oxirredução , Porfobilinogênio/química , Porfobilinogênio/metabolismo
15.
Artigo em Inglês | MEDLINE | ID: mdl-23908040

RESUMO

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Expression in Escherichia coli of a His-tagged form of Bacillus megaterium PBGD permitted the crystallization and preliminary X-ray analysis of the enzyme from this species at high resolution.


Assuntos
Bacillus megaterium/enzimologia , Proteínas de Bactérias/química , Hidroximetilbilano Sintase/química , Tetrapirróis/química , Cristalização , Cristalografia por Raios X
16.
Biosci Rep ; 33(4)2013 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-23815679

RESUMO

The autosomal dominantly inherited disease AIP (acute intermittent porphyria) is caused by mutations in HMBS [hydroxymethylbilane synthase; also known as PBG (porphobilinogen) deaminase], the third enzyme in the haem biosynthesis pathway. Enzyme-intermediates with increasing number of PBG molecules are formed during the catalysis of HMBS. In this work, we studied the two uncharacterized mutants K132N and V215E comparative with wt (wild-type) HMBS and to the previously reported AIP-associated mutants R116W, R167W and R173W. These mainly present defects in conformational stability (R116W), enzyme kinetics (R167W) or both (R173W). A combination of native PAGE, CD, DSF (differential scanning fluorimetry) and ion-exchange chromatography was used to study conformational stability and activity of the recombinant enzymes. We also investigated the distribution of intermediates corresponding to specific elongation stages. It is well known that the thermostability of HMBS increases when the DPM (dipyrromethane) cofactor binds to the apoenzyme and the holoenzyme is formed. Interestingly, a decrease in thermal stability was measured concomitant to elongation of the pyrrole chain, indicating a loosening of the structure prior to product release. No conformational or kinetic defect was observed for the K132N mutant, whereas V215E presented lower conformational stability and probably a perturbed elongation process. This is in accordance with the high association of V215E with AIP. Our results contribute to interpret the molecular mechanisms for dysfunction of HMBS mutants and to establish genotype-phenotype relations for AIP.


Assuntos
Hidroximetilbilano Sintase/química , Mutação de Sentido Incorreto , Porfiria Aguda Intermitente/enzimologia , Estabilidade Enzimática , Escherichia coli , Estudos de Associação Genética , Humanos , Hidroximetilbilano Sintase/biossíntese , Hidroximetilbilano Sintase/genética , Fenótipo , Porfiria Aguda Intermitente/genética , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Temperatura de Transição
17.
Acta Crystallogr D Biol Crystallogr ; 69(Pt 3): 471-85, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23519422

RESUMO

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step of the haem- and chlorophyll-biosynthesis pathways in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The active site possesses an unusual dipyrromethane cofactor which is extended during the reaction by the sequential addition of the four substrate molecules. The cofactor is linked covalently to the enzyme through a thioether bridge to the invariant Cys254. Until recently, structural data have only been available for the Escherichia coli and human forms of the enzyme. The expression of a codon-optimized gene for PBGD from Arabidopsis thaliana (thale cress) has permitted for the first time the X-ray analysis of the enzyme from a higher plant species at 1.45 Šresolution. The A. thaliana structure differs appreciably from the E. coli and human forms of the enzyme in that the active site is shielded by an extensive well defined loop region (residues 60-70) formed by highly conserved residues. This loop is completely disordered and uncharacterized in the E. coli and human PBGD structures. The new structure establishes that the dipyrromethane cofactor of the enzyme has become oxidized to the dipyrromethenone form, with both pyrrole groups approximately coplanar. Modelling of an intermediate of the elongation process into the active site suggests that the interactions observed between the two pyrrole rings of the cofactor and the active-site residues are highly specific and are most likely to represent the catalytically relevant binding mode. During the elongation cycle, it is thought that domain movements cause the bound cofactor and polypyrrole intermediates to move past the catalytic machinery in a stepwise manner, thus permitting the binding of additional substrate moieties and completion of the tetrapyrrole product. Such a model would allow the condensation reactions to be driven by the extensive interactions that are observed between the enzyme and the dipyrromethane cofactor, coupled with acid-base catalysis provided by the invariant aspartate residue Asp95.


Assuntos
Proteínas de Arabidopsis/química , Arabidopsis/enzimologia , Domínio Catalítico , Hidroximetilbilano Sintase/química , Tetrapirróis/química , Apoenzimas/química , Cristalografia por Raios X , Ligação Proteica
18.
Acta Crystallogr Sect F Struct Biol Cryst Commun ; 68(Pt 12): 1491-3, 2012 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-23192030

RESUMO

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step of the haem-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Since PBGD catalyses a reaction which is common to the biosynthesis of both haem and chlorophyll, structural studies of a plant PBGD enzyme offer great potential for the discovery of novel herbicides. Until recently, structural data have only been available for the Escherichia coli and human forms of the enzyme. Expression in E. coli of a codon-optimized gene for Arabidopsis thaliana PBGD has permitted for the first time the crystallization and preliminary X-ray analysis of the enzyme from a plant species at high resolution.


Assuntos
Proteínas de Arabidopsis/química , Arabidopsis/enzimologia , Hidroximetilbilano Sintase/química , Tetrapirróis/biossíntese , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Cristalização , Cristalografia por Raios X , Escherichia coli/genética , Escherichia coli/metabolismo , Hidroximetilbilano Sintase/metabolismo , Modelos Moleculares , Porfobilinogênio/química , Porfobilinogênio/metabolismo , Conformação Proteica , Tetrapirróis/química
19.
Hum Mol Genet ; 19(4): 584-96, 2010 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-19934113

RESUMO

Human acute intermittent porphyria (AIP), the most common acute hepatic porphyria, is an autosomal dominant inborn error of heme biosynthesis due to the half-normal activity of hydroxymethylbilane synthase (HMB-synthase). Here, we describe the first naturally occurring animal model of AIP in four unrelated cat lines who presented phenotypically as congenital erythropoietic porphyria (CEP). Affected cats had erythrodontia, brownish urine, fluorescent bones, and markedly elevated urinary uroporphyrin (URO) and coproporphyrin (COPRO) consistent with CEP. However, their uroporphyrinogen-III-synthase (URO-synthase) activities (deficient in CEP) were normal. Notably, affected cats had half-normal HMB-synthase activities and elevated urinary 5-aminolevulinic acid (ALA) and porphobilinogen (PBG), the deficient enzyme and accumulated metabolites in human AIP. Sequencing the feline HMB-synthase gene revealed different mutations in each line: a duplication (c.189dupT), an in-frame 3 bp deletion (c.842_844delGAG) identical to that causing human AIP and two missense mutations, c.250G>A (p.A84T) and c.445C>T (p.R149W). Prokaryotic expression of mutations c.842_844delGAG and c.445C>T resulted in mutant enzymes with <1% wild-type activity, whereas c.250G>A expressed a stable enzyme with approximately 35% of wild-type activity. The discolored teeth from the affected cats contained markedly elevated URO I and III, accounting for the CEP-like phenocopy. In three lines, the phenotype was an autosomal dominant trait, while affected cats with the c.250G>A (p.A84T) mutation were homozygous, a unique recessive form of AIP. These animal models may permit further investigation of the pathogenesis of the acute, life-threatening neurological attacks in human AIP and the evaluation of therapeutic strategies. GenBank Accession Numbers: GQ850461-GQ850464.


Assuntos
Doenças do Gato/enzimologia , Gatos/genética , Modelos Animais de Doenças , Hidroximetilbilano Sintase/genética , Mutação , Porfiria Aguda Intermitente/enzimologia , Porfiria Eritropoética/enzimologia , Animais , Osso e Ossos/metabolismo , Doenças do Gato/genética , Doenças do Gato/metabolismo , Gatos/metabolismo , Coproporfirinas/urina , Feminino , Humanos , Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/metabolismo , Masculino , Modelos Moleculares , Dados de Sequência Molecular , Porfiria Aguda Intermitente/genética , Porfiria Aguda Intermitente/metabolismo , Porfiria Eritropoética/genética , Porfiria Eritropoética/metabolismo , Porfirinas/metabolismo , Dente/metabolismo , Uroporfirinas/urina
20.
Cell Mol Biol (Noisy-le-grand) ; 55(2): 55-63, 2009 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-19656452

RESUMO

Acute intermittent porphyria (AIP), the most common acute hepatic porphyria, is an autosomal dominant disorder with low penetrance that results from a partial deficiency of hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway. The disease is clinically characterized by acute neurovisceral attacks that are precipitated by several factors including certain drugs, steroid hormones, alcohol and fasting. Early diagnosis and counselling are essential to prevent attacks, being mutation analysis the most reliable method to identify asymptomatic carriers in AIP families. In this study we have investigated the molecular defect in 15 unrelated Spanish AIP patients. Mutation analysis of the HMBS gene revealed a total of fourteen mutations including six novel ones, two of them were on the same allele in one patient. The novel mutations were three missense (R26L, R173G and D178H), two frameshift (c.749_765dup and c.874insC) and one intronic deletion (IVS12+3_+11delAGGGCCTGT). RT-PCR and sequencing demonstrated that the intronic mutation caused abnormal splicing and exon 12 skipping. Prokaryotic expression of the novel missense mutations showed that only D178H had significant residual activity. These findings will facilitate the accurate identification of presymptomatic AIP carriers in these families and they further emphasize the molecular heterogeneity of AIP in Spain.


Assuntos
Hidroximetilbilano Sintase/genética , Porfiria Aguda Intermitente/genética , População Branca/genética , Adulto , Idoso , Alelos , Feminino , Mutação da Fase de Leitura , Deleção de Genes , Humanos , Hidroximetilbilano Sintase/química , Hidroximetilbilano Sintase/metabolismo , Masculino , Pessoa de Meia-Idade , Mutação de Sentido Incorreto , Polimorfismo Genético , Porfiria Aguda Intermitente/enzimologia , Estabilidade Proteica , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Análise de Sequência de DNA , Espanha , Temperatura
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