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Santos J, Fernández Villamil SH, Delfino JM, Valsecchi WM. Structural differences between hypoxanthine phosphoribosyltransferase family members highlight opportunities for antiparasitic drug design in neglected diseases. Arch Biochem Biophys 2023; 737:109550. [PMID: 36796662 DOI: 10.1016/j.abb.2023.109550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
Approaches to identify novel druggable targets for treating neglected diseases include computational studies that predict possible interactions of drugs and their molecular targets. Hypoxanthine phosphoribosyltransferase (HPRT) plays a central role in the purine salvage pathway. This enzyme is essential for the survival of the protozoan parasite T. cruzi, the causal agent of Chagas disease, and other parasites related to neglected diseases. Here we found dissimilar functional behaviours between TcHPRT and the human homologue, HsHPRT, in the presence of substrate analogues that can lie in differences in their oligomeric assemblies and structural features. To shed light on this issue, we carried out a comparative structural analysis between both enzymes. Our results show that HsHPRT is considerably more resistant to controlled proteolysis than TcHPRT. Moreover, we observed a variation in the length of two key loops depending on the structural arrangement of each protein (groups D1T1 and D1T1'). Such variations might be involved in inter-subunit communication or influencing the oligomeric state. Besides, to understand the molecular basis that govern D1T1 and D1T1' folding groups, we explored the distribution of charges on the interaction surfaces of TcHPRT and HsHPRT, respectively. To know whether the rigidity degree bears effect on the active site, we studied the flexibility of both proteins. The analysis performed here illuminates the underlying reasons and significance behind each protein's preference for one or the other quaternary arrangement that can be exploited for therapeutic approaches.
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Affiliation(s)
- J Santos
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - S H Fernández Villamil
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Argentina; Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Argentina
| | - J M Delfino
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Argentina
| | - W M Valsecchi
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Argentina.
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2
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Parihar PS, Pratap JV. The L.donovani Hypoxanthine-guanine phosphoribosyl transferase (HGPRT) oligomer is distinct from the human homolog. Biochem Biophys Res Commun 2020; 532:499-504. [DOI: 10.1016/j.bbrc.2020.08.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 11/26/2022]
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3
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Dickman R, Mitchell SA, Figueiredo AM, Hansen DF, Tabor AB. Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B. J Org Chem 2019; 84:11493-11512. [PMID: 31464129 PMCID: PMC6759747 DOI: 10.1021/acs.joc.9b01253] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 12/12/2022]
Abstract
In response to the growing threat posed by antibiotic-resistant bacterial strains, extensive research is currently focused on developing antimicrobial agents that target lipid II, a vital precursor in the biosynthesis of bacterial cell walls. The lantibiotic nisin and related peptides display unique and highly selective binding to lipid II. A key feature of the nisin-lipid II interaction is the formation of a cage-like complex between the pyrophosphate moiety of lipid II and the two thioether-bridged rings, rings A and B, at the N-terminus of nisin. To understand the important structural factors underlying this highly selective molecular recognition, we have used solid-phase peptide synthesis to prepare individual ring A and B structures from nisin, the related lantibiotic mutacin, and synthetic analogues. Through NMR studies of these rings, we have demonstrated that ring A is preorganized to adopt the correct conformation for binding lipid II in solution and that individual amino acid substitutions in ring A have little effect on the conformation. We have also analyzed the turn structures adopted by these thioether-bridged peptides and show that they do not adopt the tight α-turn or β-turn structures typically found in proteins.
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Affiliation(s)
- Rachael Dickman
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Serena A. Mitchell
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Angelo M. Figueiredo
- Institute
of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K.
| | - D. Flemming Hansen
- Institute
of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K.
| | - Alethea B. Tabor
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
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4
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Terán D, Doleželová E, Keough DT, Hocková D, Zíková A, Guddat LW. Crystal structures of Trypanosoma brucei hypoxanthine - guanine - xanthine phosphoribosyltransferase in complex with IMP, GMP and XMP. FEBS J 2019; 286:4721-4736. [PMID: 31287615 DOI: 10.1111/febs.14987] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 04/16/2019] [Accepted: 07/06/2019] [Indexed: 11/27/2022]
Abstract
The 6-oxopurine phosphoribosyltransferases (PRTs) are drug targets for the treatment of parasitic diseases. This is due to the fact that parasites are auxotrophic for the 6-oxopurine bases relying on salvage enzymes for the synthesis of their 6-oxopurine nucleoside monophosphates. In Trypanosoma brucei, the parasite that is the aetiological agent for sleeping sickness, there are three 6-oxopurine PRT isoforms. Two are specific for hypoxanthine and guanine, whilst the third, characterized here, uses all three naturally occurring bases with similar efficiency. Here, we have determined crystal structures for TbrHGXPRT in complex with GMP, XMP and IMP to investigate the structural basis for substrate specificity. The results show that Y201 and E208, not commonly observed within the purine binding pocket of 6-oxopurine PRTs, contribute to the versatility of this enzyme. The structures further show that a nearby water can act as an adaptor to facilitate the binding of XMP and GMP. When GMP binds, a water can accept a proton from the 2-amino group but when XMP binds, the equivalent water can donate its proton to the 2-oxo group. However, when IMP is bound, no water molecule is observed at that location. DATABASE: Coordinates and structure factors were submitted to the Protein Data Bank and have accession codes of 6MXB, 6MXC, 6MXD and 6MXG for the TbrHGXPRT.XMP complex, TbrHGXPRT.GMP complex, TbrHGXPRT.IMP complex, and TbrHGPRT.XMP complex, respectively.
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Affiliation(s)
- David Terán
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Eva Doleželová
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Dianne T Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Dana Hocková
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Alena Zíková
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Luke W Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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5
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Kubota T, Tani O, Yamaguchi T, Namatame I, Sakashita H, Furukawa K, Yamasaki K. Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase from Trypanosoma brucei. FEBS Open Bio 2018; 8:680-691. [PMID: 29632820 PMCID: PMC5881531 DOI: 10.1002/2211-5463.12403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 01/29/2023] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a flavin‐binding enzyme essential for pyrimidine biosynthesis, which converts dihydroorotate to orotate. Three‐dimensional structures of cytosolic DHODH of parasitic protozoa are of interest in drug discovery for neglected tropical diseases, especially because these enzymes possess significantly different structural and functional properties from the membrane‐associated human enzyme. The existing crystal structures of the flavin mononucleotide (FMN)‐bound DHODHs reveal a number of interactions stabilizing FMN. However, to understand the binding mechanism correctly, it is necessary to compare the structures of the FMN‐bound and FMN‐free forms, because the protein moiety of the former is not necessarily the same as the latter. Here, we prepared the FMN‐free DHODH of Trypanosoma brucei using an Escherichia coli overexpression system. Although this apoform lacks enzymatic activity, simple incubation with FMN activated the enzyme. It was stable enough to be crystallized, enabling us to determine its structure by X‐ray crystallography at 1.6 Å resolution. We also determined the FMN‐bound form at 1.8 Å resolution. Although the two structures have essentially the same scaffold, we observed flipping of a peptide‐bond plane in the vicinity of the FMN‐binding site, accompanied by an alternative hydrogen‐bonding pattern. Comparisons of B factors of the protein main chain revealed that binding of FMN decreased flexibility of most of the residues at the FMN‐binding site, but increased flexibility of a lid‐like loop structure over the active center. This increase was ascribed to a conformational change in an FMN‐contacting residue, Asn195, which induced a rearrangement of a hydrogen‐bond network of the residues comprising the lid.
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Affiliation(s)
- Tomomi Kubota
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Osamu Tani
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | | | | | - Hitoshi Sakashita
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Koji Furukawa
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Kazuhiko Yamasaki
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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6
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Crystal structures and inhibition of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltransferase. Sci Rep 2016; 6:35894. [PMID: 27786284 PMCID: PMC5081515 DOI: 10.1038/srep35894] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/06/2016] [Indexed: 01/29/2023] Open
Abstract
Human African Trypanosomiasis (HAT) is a life-threatening infectious disease caused by the protozoan parasite, Trypanosoma brucei (Tbr). Due to the debilitating side effects of the current therapeutics and the emergence of resistance to these drugs, new medications for this disease need to be developed. One potential new drug target is 6-oxopurine phosphoribosyltransferase (PRT), an enzyme central to the purine salvage pathway and whose activity is critical for the production of the nucleotides (GMP and IMP) required for DNA/RNA synthesis within this protozoan parasite. Here, the first crystal structures of this enzyme have been determined, these in complex with GMP and IMP and with three acyclic nucleoside phosphonate (ANP) inhibitors. The Ki values for GMP and IMP are 30.5 μM and 77 μM, respectively. Two of the ANPs have Ki values considerably lower than for the nucleotides, 2.3 μM (with guanine as base) and 15.8 μM (with hypoxanthine as base). The crystal structures show that when two of the ANPs bind, they induce an unusual conformation change to the loop where the reaction product, pyrophosphate, is expected to bind. This and other structural differences between the Tbr and human enzymes suggest selective inhibitors for the Tbr enzyme can be designed.
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Karmakar T, Roy S, Balaram H, Balasubramanian S. Structural and dynamical correlations in PfHGXPRT oligomers: A molecular dynamics simulation study. J Biomol Struct Dyn 2016; 34:1590-605. [PMID: 26441001 DOI: 10.1080/07391102.2015.1085441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PfHGXPRT is a key enzyme involved in purine nucleotide salvage pathway of the malarial parasite, Plasmodium falciparum. Atomistic molecular dynamics simulations have been performed on two types of PfHGXPRT dimers (D1 and D3) and its tetramer in their apo and ligand-bound states. A significant event in the catalytic cycle is the dynamics of a gate that provides access for the ligand molecules to the reaction center. The gate is formed by loops II and IV, the former being the most flexible. Large amplitude conformational changes have been observed in active site loop II. Upon complete occupancy of the active site, loop II gets stabilized due to specific interactions between its residues and the ligand molecules. Remote loop, X, is seen to be less fluxional in the D3 dimer than in D1 which is rationalized as due to the greater number of inter-subunit contacts in the former. The presence of ligand molecules in subunits of the tetramer further reduces the flexibility of loop X epitomizing a communication between this region and the active sites in the tetramer. These observations are in accordance with the outcomes of several experimental investigations. Participation of loop X in the oligomerization process has also been discerned. Between the two types of dimers in solution, D1 tetramerizes readily and thus would not be present as free dimers. We conjecture an equilibrium to exist between D3 and the tetramer in solution; upon binding of the ligand molecules to the D3 dimer, this equilibrium shifts toward the tetramer.
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Affiliation(s)
- Tarak Karmakar
- a Chemistry and Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Sourav Roy
- b Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Hemalatha Balaram
- b Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Sundaram Balasubramanian
- a Chemistry and Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
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8
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Zhang N, Gong X, Lu M, Chen X, Qin X, Ge H. Crystal structures of Apo and GMP bound hypoxanthine-guanine phosphoribosyltransferase from Legionella pneumophila and the implications in gouty arthritis. J Struct Biol 2016; 194:311-6. [PMID: 26968365 DOI: 10.1016/j.jsb.2016.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 01/10/2023]
Abstract
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) (EC 2.4.2.8) reversibly catalyzes the transfer of the 5-phophoribosyl group from 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP) to hypoxanthine or guanine to form inosine monophosphate (IMP) or guanosine monophosphate (GMP) in the purine salvage pathway. To investigate the catalytic mechanism of this enzyme in the intracellular pathogen Legionella pneumophila, we determined the crystal structures of the L. pneumophila HGPRT (LpHGPRT) both in its apo-form and in complex with GMP. The structures reveal that LpHGPRT comprises a core domain and a hood domain which are packed together to create a cavity for GMP-binding and the enzymatic catalysis. The binding of GMP induces conformational changes of the stable loop II. This new binding site is closely related to the Gout arthritis-linked human HGPRT mutation site (Ser103Arg). Finally, these structures of LpHGPRT provide insights into the catalytic mechanism of HGPRT.
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Affiliation(s)
- Nannan Zhang
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Xiaojian Gong
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Min Lu
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Xiaofang Chen
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Ximing Qin
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Honghua Ge
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China; Modern Experiment Technology Center, Anhui University, Hefei, Anhui 230601, China.
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9
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Roy S, Karmakar T, S. Prahlada Rao V, K. Nagappa L, Balasubramanian S, Balaram H. Slow ligand-induced conformational switch increases the catalytic rate in Plasmodium falciparum hypoxanthine guanine xanthine phosphoribosyltransferase. MOLECULAR BIOSYSTEMS 2015; 11:1410-24. [DOI: 10.1039/c5mb00136f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coupled events of ligand-induced isomerization and oligomerization in catalysis by PfHGXPRT.
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Affiliation(s)
- Sourav Roy
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Tarak Karmakar
- Chemistry and Physics of Materials Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Vasudeva S. Prahlada Rao
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Lakshmeesha K. Nagappa
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
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