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Han X, Chen CC, Kuo CJ, Huang CH, Zheng Y, Ko TP, Zhu Z, Feng X, Wang K, Oldfield E, Wang AHJ, Liang PH, Guo RT, Ma Y. Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms. Proteins 2015; 83:37-45. [PMID: 24895191 PMCID: PMC4256133 DOI: 10.1002/prot.24618] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 05/12/2014] [Accepted: 05/27/2014] [Indexed: 01/07/2023]
Abstract
Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of one allylic substrate farnesyl pyrophosphate (FPP) and five homoallylic substrate isopentenyl pyrophosphate (IPP) molecules to form a C40 long-chain product OPP, which serves as a side chain of ubiquinone and menaquinone. OPPs belongs to the trans-prenyltransferase class of proteins. The structures of OPPs from Escherichia coli were solved in the apo-form as well as in complexes with IPP and a FPP thio-analog, FsPP, at resolutions of 2.2-2.6 Å, and revealed the detailed interactions between the ligands and enzyme. At the bottom of the active-site tunnel, M123 and M135 act in concert to form a wall which determines the final chain length. These results represent the first ligand-bound crystal structures of a long-chain trans-prenyltransferase and provide new information on the mechanisms of catalysis and product chain elongation.
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Affiliation(s)
- Xu Han
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chun-Chi Chen
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yingying Zheng
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Zhen Zhu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xinxin Feng
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Ke Wang
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan,Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
| | - Yanhe Ma
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China,Contact information of corresponding authors: Yanhe Ma Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861977, Fax number: +86 22 84861926. Rey-Ting Guo Ph.D., Address: 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China, , Telephone number: +86 22 84861999, Fax number: +86 22 24828701. Po-Huang Liang Ph.D., Address: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, , Telephone number: +886-2-2785-5696 ext. 6070, Fax number:+886-2-2788-9759
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Li X, Han X, Ko TP, Chen CC, Zhu Z, Hua E, Guo RT, Huang CH. Preliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:328-31. [PMID: 23519815 PMCID: PMC3606585 DOI: 10.1107/s1744309113003837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 02/07/2013] [Indexed: 11/10/2022]
Abstract
Octaprenyl pyrophosphate synthase (OPPs), which belongs to the E-type prenyltransferase family, catalyses the successive condensation of farnesyl pyrophosphate with five isopentenyl pyrophosphate molecules to form trans-C40-octaprenyl pyrophosphate (OPP). OPP is essential for the biosynthesis of bacterial ubiquinone or menaquinone side chains, which play an important role in the electron-transport system. Here, Escherichia coli OPPs was expressed, purified and crystallized. The crystals, which belonged to the orthorhombic space group P2₁2₁2, with unit-cell parameters a=117.0, b=128.4, c=46.4 Å, were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.2 Å resolution. Initial phase determination by molecular replacement (MR) clearly indicated that the crystal contained one homodimer per asymmetric unit. Further model building and structural refinement are in progress.
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Affiliation(s)
- Xin Li
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People’s Republic of China
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People’s Republic of China
| | - Xu Han
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People’s Republic of China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Chi Chen
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People’s Republic of China
| | - Zhen Zhu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People’s Republic of China
| | - Erbing Hua
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People’s Republic of China
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People’s Republic of China
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People’s Republic of China
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Tonhosolo R, D'Alexandri F, Genta F, Wunderlich G, Gozzo F, Eberlin M, Peres V, Kimura E, Katzin A. Identification, molecular cloning and functional characterization of an octaprenyl pyrophosphate synthase in intra-erythrocytic stages of Plasmodium falciparum. Biochem J 2006; 392:117-26. [PMID: 15984931 PMCID: PMC1317670 DOI: 10.1042/bj20050441] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Isoprenoids play important roles in all living organisms as components of structural cholesterol, steroid hormones in mammals, carotenoids in plants, and ubiquinones. Significant differences occur in the length of the isoprenic side chains of ubiquinone between different organisms, suggesting that different enzymes are involved in the synthesis of these side chains. Whereas in Plasmodium falciparum the isoprenic side chains of ubiquinone contain 7-9 isoprenic units, 10-unit side chains are found in humans. In a search for the P. falciparum enzyme responsible for the biosynthesis of isoprenic side chains attached to the benzoquinone ring of ubiquinones, we cloned and expressed a putative polyprenyl synthase. Polyclonal antibodies raised against the corresponding recombinant protein confirmed the presence of the native protein in trophozoite and schizont stages of P. falciparum. The recombinant protein, as well as P. falciparum extracts, showed an octaprenyl pyrophosphate synthase activity, with the formation of a polyisoprenoid with eight isoprenic units, as detected by reverse-phase HPLC and reverse-phase TLC, and confirmed by electrospray ionization and tandem MS analysis. The recombinant and native versions of the enzyme had similar Michaelis constants with the substrates isopentenyl pyrophosphate and farnesyl pyrophosphate. The recombinant enzyme could be competitively inhibited in the presence of the terpene nerolidol. This is the first report that directly demonstrates an octaprenyl pyrophosphate synthase activity in parasitic protozoa. Given the rather low similarity of the P. falciparum enzyme to its human counterpart, decaprenyl pyrophosphate synthase, we suggest that the identified enzyme and its recombinant version could be exploited in the screening of novel drugs.
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Affiliation(s)
- Renata Tonhosolo
- *Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, Brazil
| | - Fabio L. D'Alexandri
- *Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, Brazil
| | - Fernando A. Genta
- †Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-900 São Paulo, Brazil
| | - Gerhard Wunderlich
- *Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, Brazil
| | - Fabio C. Gozzo
- ‡Thomson Mass Spectrometry Laboratory, Institute of Chemistry, State University of Campinas, 13083-970 Campinas, Brazil
| | - Marcos N. Eberlin
- ‡Thomson Mass Spectrometry Laboratory, Institute of Chemistry, State University of Campinas, 13083-970 Campinas, Brazil
| | - Valnice J. Peres
- *Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, Brazil
| | - Emilia A. Kimura
- *Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, Brazil
| | - Alejandro M. Katzin
- *Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900 São Paulo, Brazil
- To whom correspondence should be addressed (email )
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Guo RT, Kuo CJ, Ko TP, Chou CC, Liang PH, Wang AHJ. A molecular ruler for chain elongation catalyzed by octaprenyl pyrophosphate synthase and its structure-based engineering to produce unprecedented long chain trans-prenyl products. Biochemistry 2004; 43:7678-86. [PMID: 15196010 DOI: 10.1021/bi036336d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with five molecules of isopentenyl pyrophosphate (IPP) to generate C(40) octaprenyl pyrophosphate (OPP) which constitutes the side chain of menaquinone. We have previously reported the X-ray structure of OPPs from Thermotoga maritima, which is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity [Guo, R. T., Kuo, C. J., Ko, T. P., Chou, C. C., Shr, R. L., Liang, P. H., and Wang, A. H.-J. (2004) J. Biol. Chem. 279, 4903-4912]. A76 and S77 are located on top of the active site close to where FPP is bound. A76Y and A76Y/S77F OPPs mutants produce C(20), indicating that the substituted larger residues interfere with the substrate chain elongation. Surprisingly, the A76Y/S77F mutant synthesizes a larger amount of C(20) than the A76Y mutant. In the crystal structure of the A76Y/S77F mutant, F77 is pushed away by Y76, thereby creating more space between those two large amino acids to accommodate the C(20) product. A large F132 residue at the bottom of the tunnel-shaped active site serves as the "floor" and determines the final product chain length. The substitution of F132 with a small Ala, thereby removing the blockade, led to the synthesis of a C(50) product larger than that produced by the wild-type enzyme. On the basis of the structure, we have sequentially mutated the large amino acids, including F132, L128, I123, and D62, to Ala underneath the tunnel. The products of the F132A/L128A/I123A/D62A mutant reach C(95), beyond the largest chain length generated by all known trans-prenyltransferases. Further modifications of the enzyme reaction conditions, including new IPP derivatives, may allow the preparation of high-molecular weight polyprenyl products resembling the rubber molecule.
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Affiliation(s)
- Rey-Ting Guo
- Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
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Guo RT, Kuo CJ, Chou CC, Ko TP, Shr HL, Liang PH, Wang AHJ. Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima and Mechanism of Product Chain Length Determination. J Biol Chem 2004; 279:4903-12. [PMID: 14617622 DOI: 10.1074/jbc.m310161200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with isopentenyl pyrophosphate (IPP) to generate C40 octaprenyl pyrophosphate (OPP), which constitutes the side chain of bacterial ubiquinone or menaquinone. In this study, the first structure of long chain C40-OPPs from Thermotoga maritima has been determined to 2.28-A resolution. OPPs is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity. An elongated hydrophobic tunnel between D and F alpha-helices contains two DDXXD motifs on the top for substrate binding and is occupied at the bottom with two large residues Phe-52 and Phe-132. The products of the mutant F132A OPPs are predominantly C50, longer than the C40 synthesized by the wild-type and F52A mutant OPPs, suggesting that Phe-132 is the key residue for determining the product chain length. Ala-76 and Ser-77 located close to the FPP binding site and Val-73 positioned further down the tunnel were individually mutated to larger amino acids. A76Y and S77F mainly produce C20 indicating that the mutated large residues in the vicinity of the FPP site limit the substrate chain elongation. Ala-76 is the fifth amino acid upstream from the first DDXXD motif on helix D of OPPs, and its corresponding amino acid in FPPs is Tyr. In contrast, V73Y mutation led to additional accumulation of C30 intermediate. The new structure of the trans-type OPPs, together with the recently determined cis-type UPPs, significantly extends our understanding on the biosynthesis of long chain polyprenyl molecules.
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Affiliation(s)
- Rey-Ting Guo
- Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
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