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Agarwal P, Meena S, Meena LS. Comprehensive analysis of GTP cyclohydrolase I activity in Mycobacterium tuberculosis H 37 Rv via in silico studies. Biotechnol Appl Biochem 2020; 68:756-768. [PMID: 32691412 DOI: 10.1002/bab.1988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/14/2020] [Indexed: 11/06/2022]
Abstract
GTP cyclohydrolase I enzyme (GTPCH-I) is a rate limiting enzyme in the biosynthesis pathway of tetrahydrobiopterin (BH4) and tetrahydrofolate (THF) compounds; latter being are an essential compounds involved in many biological functions. This enzyme has been evaluated structurally and functionally in many organisms to understand its putative role in cell processes, kinetics, regulations, drug targeting in infectious diseases, pain sensitivity in humans, and so on. In Mycobacterium tuberculosis (a human pathogen causing tuberculosis), this GTPCH-I activity has been predicted to be present in Rv3609c gene (folE) of H37 Rv strain, which till date has not been studied in detail. In order to understand in depth, the structure and function of folE protein in M. tuberculosis H37 Rv, in silico study was designed by using many different bioinformatics tools. Comparative and structural analysis predicts that Rv3609c gene is similar to folE protein ortholog of Listeria monocytogenes (cause food born disease), and uses zinc ion as a cofactor for its catalysis. Result shows that mutation of folE protein at 52th residue from tyrosine to glycine or variation in pH and temperature can lead to high destability in protein structure. Studies here have also predicted about the functional regions and interacting partners involved with folE protein. This study has provided clues to carry out experimentally the analysis of folE protein in mycobacteria and if found suitable will be used for drug targeting.
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Affiliation(s)
- Preeti Agarwal
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
| | - Swati Meena
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
| | - Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
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Wang H, Yang B, Hao G, Feng Y, Chen H, Feng L, Zhao J, Zhang H, Chen YQ, Wang L, Chen W. Biochemical characterization of the tetrahydrobiopterin synthesis pathway in the oleaginous fungus Mortierella alpina. MICROBIOLOGY (READING, ENGLAND) 2011; 157:3059-3070. [PMID: 21852350 PMCID: PMC4811656 DOI: 10.1099/mic.0.051847-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/10/2011] [Accepted: 08/17/2011] [Indexed: 11/18/2022]
Abstract
We characterized the de novo biosynthetic pathway of tetrahydrobiopterin (BH₄) in the lipid-producing fungus Mortierella alpina. The BH₄ cofactor is essential for various cell processes, and is probably present in every cell or tissue of higher organisms. Genes encoding two copies of GTP cyclohydrolase I (GTPCH-1 and GTPCH-2) for the conversion of GTP to dihydroneopterin triphosphate (H₂-NTP), 6-pyruvoyltetrahydropterin synthase (PTPS) for the conversion of H₂-NTP to 6-pyruvoyltetrahydropterin (PPH₄), and sepiapterin reductase (SR) for the conversion of PPH₄ to BH₄, were expressed heterologously in Escherichia coli. The recombinant enzymes were produced as His-tagged fusion proteins and were purified to homogeneity to investigate their enzymic activities. Enzyme products were analysed by HPLC and electrospray ionization-MS. Kinetic parameters and other properties of GTPCH, PTPS and SR were investigated. Physiological roles of BH₄ in M. alpina are discussed, and comparative analyses between GTPCH, PTPS and SR proteins and other homologous proteins were performed. The presence of two functional GTPCH enzymes has, as far as we are aware, not been reported previously, reflecting the unique ability of this fungus to synthesize both BH₄ and folate, using the GTPCH product as a common substrate. To our knowledge, this study is the first to report the comprehensive characterization of a BH₄ biosynthesis pathway in a fungus.
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Affiliation(s)
- Hongchao Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Guangfei Hao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Yun Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin 300457, PR China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Lu Feng
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin 300457, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Yong Q. Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin Economic-Technological Development Area, Tianjin 300457, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
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Supangat S, Park SO, Seo KH, Lee SY, Park YS, Lee KH. Role of Phe-99 and Trp-196 of sepiapterin reductase from Chlorobium tepidum in the production of L-threo-tetrahydrobiopterin. Acta Biochim Biophys Sin (Shanghai) 2008; 40:513-8. [PMID: 18542834 DOI: 10.1111/j.1745-7270.2008.00422.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Sepiapterin reductase from Chlorobium tepidum (cSR) catalyzes the synthesis of a distinct tetrahydrobiopterin (BH4), L-threo-BH4, different from the mammalian enzyme product. The 3-D crystal structure of cSR has revealed that the product configuration is determined solely by the substrate binding mode within the well-conserved catalytic triads. In cSR, the sepiapterin is stacked between two aromatic side chains of Phe-99 and Trp-196 and rotated approximately 180 degrees C around the active site from the position in mouse sepiapterin reductase. To confirm their roles in substrate binding, we mutated Phe-99 and/or Trp-196 to alanine (F99A, W196A) by site-directed mutagenesis and comparatively examined substrate binding of the purified proteins by kinetics analysis and differential scanning calorimetry. These mutants had higher Km values than the wild type. Remarkably, the W196A mutation resulted in a higher Km increase compared with the F99A mutation. Consistent with the results, the melting temperature (Tm) in the presence of sepiapterin was lower in the mutant proteins and the worst was W196A. These findings indicate that the two residues are indispensable for substrate binding in cSR, and Trp-196 is more important than Phe-99 for different stereoisomer production.
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Affiliation(s)
- Supangat Supangat
- Division of Applied Life Science, BK21 Program, Gyeongsang National University, Jinju 660-701, Korea
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Noiriel A, Naponelli V, Bozzo GG, Gregory JF, Hanson AD. Folate salvage in plants: pterin aldehyde reduction is mediated by multiple non-specific aldehyde reductases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 51:378-89. [PMID: 17550420 DOI: 10.1111/j.1365-313x.2007.03143.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Folates undergo oxidative cleavage in vivo, releasing a pterin aldehyde fragment that can be re-used in folate synthesis if the aldehyde group is reduced. High levels of NADPH-dependent reductase activity against pterin-6-aldehyde and its dihydro form were detected in Arabidopsis, pea and other plants; modeling predicted that the activity would maintain in vivo pterin aldehyde pools at extremely low levels (<0.2 pmol g(-1) FW). Subcellular fractionation showed that the pea leaf activity is mainly cytosolic, and anion exchange chromatography revealed multiple isoforms, all of which catalyzed reduction of other aldehydes. Arabidopsis seed activity likewise comprised various isoforms. An Arabidopsis gene (At1g10310) encoding a pterin aldehyde reductase was identified by searching the short-chain dehydrogenase/reductase family for proteins predicted to be NADPH-linked, and sharing conserved residues with reductases that mediate analogous reactions. The recombinant protein behaved as a dimer in size exclusion chromatography. In addition to pterin aldehydes, it catalyzed the reduction of diverse aromatic and aliphatic aldehydes: Vmax values varied <5-fold, but Km values ranged from 3.6 microm to 1.7 mm, those for pterin-6-aldehyde and dihydropterin-6-aldehyde being 36 and 56 microm, respectively. Activity with dihydropterin-6-aldehyde was unusually high at 0 degrees C. The At1g10310 transcript was most abundant in seeds, but, as expected for multiple isoforms, inactivating the At1g10310 gene caused only a minor change in seed pterin aldehyde reductase activity. We conclude that pterin aldehyde salvage in plants involves multiple, generalist NADPH-linked reductases, and that the At1g10310 enzyme is typical of these and hence suitable for use in engineering studies of folate turnover.
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Affiliation(s)
- Alexandre Noiriel
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
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Supangat S, Seo KH, Choi YK, Park YS, Son D, Han CD, Lee KH. Structure of Chlorobium tepidum sepiapterin reductase complex reveals the novel substrate binding mode for stereospecific production of L-threo-tetrahydrobiopterin. J Biol Chem 2006; 281:2249-56. [PMID: 16308317 DOI: 10.1074/jbc.m509343200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sepiapterin reductase (SR) is involved in the last step of tetrahydrobiopterin (BH(4)) biosynthesis by reducing the di-keto group of 6-pyruvoyl tetrahydropterin. Chlorobium tepidum SR (cSR) generates a distinct BH(4) product, L-threo-BH(4) (6R-(1'S,2'S)-5,6,7,8-BH(4)), whereas animal enzymes produce L-erythro-BH(4) (6R-(1'R,2'S)-5,6,7,8-BH(4)) although it has high amino acid sequence similarities to the other animal enzymes. To elucidate the structural basis for the different reaction stereospecificities, we have determined the three-dimensional structures of cSR alone and complexed with NADP and sepiapterin at 2.1 and 1.7 A resolution, respectively. The overall folding of the cSR, the binding site for the cofactor NADP(H), and the positions of active site residues were quite similar to the mouse and the human SR. However, significant differences were found in the substrate binding region of the cSR. In comparison to the mouse SR complex, the sepiapterin in the cSR is rotated about 180 degrees around the active site and bound between two aromatic side chains of Trp-196 and Phe-99 so that its pterin ring is shifted to the opposite side, but its side chain position is not changed. The swiveled sepiapterin binding results in the conversion of the side chain configuration, exposing the opposite face for hydride transfer from NADPH. The different sepiapterin binding mode within the conserved catalytic architecture presents a novel strategy of switching the reaction stereospecificities in the same protein fold.
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Affiliation(s)
- Supangat Supangat
- Division of Applied Life Science, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea
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Choi YK, Park JS, Kong JS, Morio T, Park YS. D-threo-tetrahydrobiopterin is synthesized via 1'-oxo-2'-D-hydroxypropyl-tetrahydropterin in Dictyostelium discoideum Ax2. FEBS Lett 2005; 579:3085-9. [PMID: 15896778 DOI: 10.1016/j.febslet.2005.04.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Revised: 04/20/2005] [Accepted: 04/21/2005] [Indexed: 11/24/2022]
Abstract
The biosynthesis of D-threo-tetrahydrobiopterin (DH4, tetrahydrodictyopterin) in Dictyostelium discoideum Ax2 was investigated through the mutant disrupted in the gene encoding sepiapterin reductase (SR) by insertional inactivation. The mutant cells, being completely devoid of SR protein, showed 18.1% of L-erythro-tetrahydrobiopterin (BH4) and 0.6% of DH4 productions in the wild type cells. The mutant cells were also identified to excrete D- and L-sepiapterin, which were presumed to originate from intracellular 1'-oxo-2'-D-hydroxypropyl- and 1'-oxo-2'-L-hydroxypropyl-tetrahydropterin (H4-pterin), respectively. Furthermore, in a coupled assay with Dictyostelium SR, the mutant cell extract exhibited a novel enzyme activity converting 6-pyruvoyltetrahydropterin to 1'-oxo-2'-D-hydroxypropyl-H4-pterin. These results are clear demonstration of the in vivo synthesis of DH4 via 1'-oxo-2'-D-hydroxypropyl-H4-pterin as well as an alternative synthesis of BH4 and DH4 in the complete absence of SR.
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Affiliation(s)
- Yong Kee Choi
- School of Biotechnology and Biomedical Science, Inje University, Kimhae 621-749, Korea
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Supangat S, Choi YK, Park YS, Son D, Han CD, Lee KH. Expression, purification, crystallization and preliminary X-ray analysis of sepiapterin reductase from Chlorobium tepidum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:202-4. [PMID: 16510994 PMCID: PMC1952253 DOI: 10.1107/s174430910403444x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Accepted: 12/29/2004] [Indexed: 11/11/2022]
Abstract
Sepiapterin reductase from Chlorobium tepidum (CT-SR) produces L-threo-tetrahydrobiopterin, an isomer of tetrahydrobiopterin, in the last step of de novo synthesis initiating from GTP. Native CT-SR and a selenomethionine (SeMet) derivative of CT-SR have been crystallized by the hanging-drop vapour-diffusion method using PEG 400 as precipitant. CT-SR crystals belong to space group R32, with unit-cell parameters a = b = 201.142, c = 210.184 A, and contain four molecules in the asymmetric unit. Diffraction data were collected to 2.1 A resolution using synchrotron radiation. The structure of CT-SR has been determined using MAD phasing. There is one CT-SR tetramer in the asymmetric unit formed by two closely interacting CT-SR dimers. The solvent content is calculated to be about 67.2%.
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Affiliation(s)
- Supangat Supangat
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-711, South Korea
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-711, South Korea
| | - Yong Kee Choi
- School of Biotechnology and Biomedical Science, Inje University, Kimhae 621-749, South Korea
| | - Young Shik Park
- School of Biotechnology and Biomedical Science, Inje University, Kimhae 621-749, South Korea
| | - Daeyoung Son
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-711, South Korea
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-711, South Korea
| | - Chang-deok Han
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-711, South Korea
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-711, South Korea
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-711, South Korea
| | - Kon Ho Lee
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-711, South Korea
- Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-711, South Korea
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-711, South Korea
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