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Agrahari AK, Krishna Priya M, Praveen Kumar M, Tayubi IA, Siva R, Prabhu Christopher B, George Priya Doss C, Zayed H. Understanding the structure-function relationship of HPRT1 missense mutations in association with Lesch-Nyhan disease and HPRT1-related gout by in silico mutational analysis. Comput Biol Med 2019; 107:161-171. [PMID: 30831305 DOI: 10.1016/j.compbiomed.2019.02.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Abstract
The nucleotide salvage pathway is used to recycle degraded nucleotides (purines and pyrimidines); one of the enzymes that helps to recycle purines is hypoxanthine guanine phosphoribosyl transferase 1 (HGPRT1). Therefore, defects in this enzyme lead to the accumulation of DNA and nucleotide lesions and hence replication errors and genetic disorders. Missense mutations in hypoxanthine phosphoribosyl transferase 1 (HPRT1) are associated with deficiencies such as Lesch-Nyhan disease and chronic gout, which have manifestations such as arthritis, neurodegeneration, and cognitive disorders. In the present study, we collected 88 non-synonymous single nucleotide polymorphisms (nsSNPs) from the UniProt, dbSNP, ExAC, and ClinVar databases. We used a series of sequence-based and structure-based in silico tools to prioritize and characterize the most pathogenic and stabilizing or destabilizing nsSNPs. Moreover, to obtain the structural impact of the pathogenic mutations, we mapped the mutations to the crystal structure of the HPRT protein. We further subjected these mutant proteins to a 50 ns molecular dynamics simulation (MDS). The MDS trajectory showed that all mutant proteins altered the structural conformation and dynamic behavior of the HPRT protein and corroborated its association with LND and gout. This study provides essential information regarding the use of HPRT protein mutants as potential targets for therapeutic development.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - M Krishna Priya
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - Medapalli Praveen Kumar
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - Iftikhar Aslam Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Rabigh, 21911, Saudi Arabia
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | | | - C George Priya Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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Ceballos-Picot I, Augé F, Fu R, Olivier-Bandini A, Cahu J, Chabrol B, Aral B, de Martinville B, Lecain JP, Jinnah HA. Phenotypic variation among seven members of one family with deficiency of hypoxanthine-guanine phosphoribosyltransferase. Mol Genet Metab 2013; 110:268-74. [PMID: 24075303 PMCID: PMC3830450 DOI: 10.1016/j.ymgme.2013.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/29/2013] [Accepted: 08/29/2013] [Indexed: 11/26/2022]
Abstract
We describe a family of seven boys affected by Lesch-Nyhan disease with various phenotypes. Further investigations revealed a mutation c.203T>C in the gene encoding HGprt of all members, with substitution of leucine to proline at residue 68 (p.Leu68Pro). Thus patients from this family display a wide variety of symptoms although sharing the same mutation. Mutant HGprt enzyme was prepared by site-directed mutagenesis and the kinetics of the enzyme revealed that the catalytic activity of the mutant was reduced, in association with marked reductions in the affinity towards phosphoribosylpyrophosphate (PRPP). Its Km for PRPP was increased 215-fold with hypoxanthine as substrate and 40-fold with guanine as substrate with associated reduced catalytic potential. Molecular modeling confirmed that the most prominent defect was the dramatically reduced affinity towards PRPP. Our studies suggest that the p.Leu68Pro mutation has a strong impact on PRPP binding and on stability of the active conformation. This suggests that factors other than HGprt activity per se may influence the phenotype of Lesch-Nyhan patients.
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Affiliation(s)
- Irène Ceballos-Picot
- Department of Metabolic Biochemistry, Hôpital Necker-Enfants Malades, AP-HP, 149 rue de Sèvres, 75015 Paris, France; School of Medicine, Paris Descartes University Sorbonne Paris Cité, 15 rue de l'Ecole de Médecine, 75006 Paris, France.
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Fu R, Ceballos-Picot I, Torres RJ, Larovere LE, Yamada Y, Nguyen KV, Hegde M, Visser JE, Schretlen DJ, Nyhan WL, Puig JG, O'Neill PJ, Jinnah HA. Genotype-phenotype correlations in neurogenetics: Lesch-Nyhan disease as a model disorder. ACTA ACUST UNITED AC 2013; 137:1282-303. [PMID: 23975452 DOI: 10.1093/brain/awt202] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Establishing meaningful relationships between genetic variations and clinical disease is a fundamental goal for all human genetic disorders. However, these genotype-phenotype correlations remain incompletely characterized and sometimes conflicting for many diseases. Lesch-Nyhan disease is an X-linked recessive disorder that is caused by a wide variety of mutations in the HPRT1 gene. The gene encodes hypoxanthine-guanine phosphoribosyl transferase, an enzyme involved in purine metabolism. The fine structure of enzyme has been established by crystallography studies, and its function can be measured with very precise biochemical assays. This rich knowledge of genetic alterations in the gene and their functional effect on its protein product provides a powerful model for exploring factors that influence genotype-phenotype correlations. The present study summarizes 615 known genetic mutations, their influence on the gene product, and their relationship to the clinical phenotype. In general, the results are compatible with the concept that the overall severity of the disease depends on how mutations ultimately influence enzyme activity. However, careful evaluation of exceptions to this concept point to several additional genetic and non-genetic factors that influence genotype-phenotype correlations. These factors are not unique to Lesch-Nyhan disease, and are relevant to most other genetic diseases. The disease therefore serves as a valuable model for understanding the challenges associated with establishing genotype-phenotype correlations for other disorders.
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Affiliation(s)
- Rong Fu
- 1 Departments of Neurology, Human Genetics and Paediatrics; Emory University, Atlanta GA, USA
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Kadaveru K, Vyas J, Schiller MR. Viral infection and human disease--insights from minimotifs. FRONT BIOSCI-LANDMRK 2008; 13:6455-71. [PMID: 18508672 DOI: 10.2741/3166] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Short functional peptide motifs cooperate in many molecular functions including protein interactions, protein trafficking, and posttranslational modifications. Viruses exploit these motifs as a principal mechanism for hijacking cells and many motifs are necessary for the viral life-cycle. A virus can accommodate many short motifs in its small genome size providing a plethora of ways for the virus to acquire host molecular machinery. Host enzymes that act on motifs such as kinases, proteases, and lipidation enzymes, as well as protein interaction domains, are commonly mutated in human disease, suggesting that the short peptide motif targets of these enzymes may also be mutated in disease; however, this is not observed. How can we explain why viruses have evolved to be so dependent on motifs, yet these motifs, in general do not seem to be as necessary for human viability? We propose that short motifs are used at the system level. This system architecture allows viruses to exploit a motif, whereas the viability of the host is not affected by mutation of a single motif.
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Affiliation(s)
- Krishna Kadaveru
- University of Connecticut Health Center, Department of Molecular, Microbial, and Structural Biology, Biological Systems Modeling Group, 263 Farmington Ave., Farmington, CT, 06030-3305, USA
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Zoref-Shani E, Bromberg Y, Hirsch J, Feinstein S, Frishberg Y, Sperling O. Clinical and biochemical manifestations and molecular characterization of the mutation HPRT Jerusalem. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:1165-8. [PMID: 15571222 DOI: 10.1081/ncn-200027436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A novel point mutation (I137T) was identified in the hypoxanthine-guanine phosphoribosyltransferase (HPRT) encoding gene, in a patient with partial deficiency of the enzyme. The mutation, ATT to ACT (substitution of isoleucine to threonine), occurred at codon 137, which is within the region encoding the binding site for 5-phosphoribosyl-1-pyrophosphate (PRPP). The mutation caused decreased affinity for PRPP, manifested clinically as a Lesch-Nyhan variant (excessive purine production and delayed acquisition of language skills). The partial HPRT deficiency could be detected only by measuring HPRT activity in intact fibroblasts (uptake of hypoxanthine into nucleotides).
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Affiliation(s)
- E Zoref-Shani
- Department of Clinical Biochemistry, Tel-Aviv University, Tel-Aviv, Israel
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Jinnah HA, Harris JC, Nyhan WL, O'Neill JP. The spectrum of mutations causing HPRT deficiency: an update. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:1153-60. [PMID: 15571220 DOI: 10.1081/ncn-200027400] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mutations in the gene encoding hypoxanthine-guanine phosphoribosyltransferase (HPRT) cause Lesch-Nyhan disease, which is characterized by hyperuricemia, severe motor disability, and self-injurious behavior. Mutations in the same gene also cause less severe clinical phenotypes with only some portions of the full syndrome. A large database of 271 mutations associated with both full and partial clinical phenotypes was recently compiled. Since the original database was assembled, 31 additional mutations have been identified, bringing the new total to 302. The results demonstrate a very heterogeneous collection of mutations for both LND and its partial syndromes. The differences between LND and the partial phenotypes cannot be explained by differences in the locations of mutations, but the partial phenotypes are more likely to have mutations predicted to allow some residual enzyme function. The reasons for some apparent exceptions to this proposal are addressed.
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Affiliation(s)
- H A Jinnah
- Department of Neurology, Johns Hopkins Hospital, Baltimore, Maryland 21287, USA
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Cattaneo D, Tankiewicz A, Merlini S, Perico N, Remuzzi G. Pharmacogenetics and pharmacogenomics of immunosuppressive agents: perspective for individualized therapy. Per Med 2004; 1:53-62. [DOI: 10.1517/17410541.1.1.53] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Immunosuppressive therapy has markedly improved over the past years with the advent of highly potent and rationally targeted immunosuppressive agents. Since these drugs are characterized by a narrow therapeutic index, major efforts have been carried out to define therapeutic windows based on the blood levels of each immunosuppressant, and relating those concentrations to clinical events. Although pharmacokinetic-based approaches are currently used as useful tools to guide drug dosing, they present several limitations. Pharmacogenomics – a science that studies the inherited basis of differences between individual responses to drugs in order to identify the best dose and therapy for each patient – might represent a complementary support. Preliminary studies that have focused on polymorphisms of genes encoding enzymes involved in drug metabolism, drug distribution, and pharmacological target, have shown promising results. Indeed, pharmacogenomics holds promise for improvement in the ability to individualize pharmacological therapy based on the patient’s genetic profile.
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Affiliation(s)
- Dario Cattaneo
- Mario Negri Institute, Department of Medicine and Transplantation Ospedali Riuniti di Bergamo, Mario Negri Institute for Pharmacological Research, Via Gavazzeni 11- 24125 Bergamo, Italy.
| | - Anna Tankiewicz
- Medical University of Bialystok, Department of Pharmacodynamics, Medical University of Bialystok, Poland
| | - Simona Merlini
- Mario Negri Institute, Department of Medicine and Transplantation Ospedali Riuniti di Bergamo, Mario Negri Institute for Pharmacological Research, Via Gavazzeni 11- 24125 Bergamo, Italy
| | - Norberto Perico
- Mario Negri Institute, Department of Medicine and Transplantation Ospedali Riuniti di Bergamo, Mario Negri Institute for Pharmacological Research, Via Gavazzeni 11- 24125 Bergamo, Italy
| | - Giuseppe Remuzzi
- Mario Negri Institute, Department of Medicine and Transplantation Ospedali Riuniti di Bergamo, Mario Negri Institute for Pharmacological Research, Via Gavazzeni 11- 24125 Bergamo, Italy
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Dussol B, Ceballos-Picot I, Aral B, Castera V, Philip N, Berland Y. Kelley-Seegmiller syndrome due to a new variant of the hypoxanthine-guanine phosphoribosyltransferase (I136T) encoding gene (HPRT Marseille). J Inherit Metab Dis 2004; 27:543-5. [PMID: 15334740 DOI: 10.1023/b:boli.0000037399.72152.a9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A patient with hyperuricaemia and gouty arthritis due to a new variant of hypoxanthine-guanine phosphoribosyltransferase is described. The mutation (I136T, HPRT Marseille) is in the phosphoribosylpyrophosphate-binding region of the gene and leads to almost total loss of enzyme activity in erythrocytes, with 5% in lymphocytes. Nevertheless, the patient showed no neurological abnormality.
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Affiliation(s)
- B Dussol
- Service de Néphrologie, Hôpital de la Conception, 147 Bd Baille, 13385 Marseille Cedex 05, France.
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