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Liu K, Chen X, Zhong Y, Gao C, Hu G, Liu J, Guo L, Song W, Liu L. Rational design of a highly efficient catalytic system for the production of PAPS from ATP and its application in the synthesis of chondroitin sulfate. Biotechnol Bioeng 2021; 118:4503-4515. [PMID: 34406648 DOI: 10.1002/bit.27919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/14/2021] [Indexed: 12/19/2022]
Abstract
The compound 3'-phosphoadenosine-5'-phosphosulfate (PAPS) serves as a sulfate group donor in the production of valuable sulfated compounds. However, elevated costs and low conversion efficiency limit the industrial applicability of PAPS. Here, we designed and constructed an efficient and controllable catalytic system for the conversion of adenosine triphosphate (ATP) (disodium salt) into PAPS without inhibition from by-products. In vitro and in vivo testing in Escherichia coli identified adenosine-5'-phosphosulfate kinase from Penicillium chrysogenum (PcAPSK) as the rate-limiting enzyme. Based on analysis of the catalytic steps and molecular dynamics simulations, a mechanism-guided "ADP expulsion" strategy was developed to generate an improved PcAPSK variant (L7), with a specific activity of 48.94 U·mg-1 and 73.27-fold higher catalytic efficiency (kcat/Km) that of the wild-type enzyme. The improvement was attained chiefly by reducing the ADP-binding affinity of PcAPSK, as well as by changing the enzyme's flexibility and lid structure to a more open conformation. By introducing PcAPSK L7 in an in vivo catalytic system, 73.59 mM (37.32 g·L-1 ) PAPS was produced from 150 mM ATP in 18.5 h using a 3-L bioreactor, and achieved titer is the highest reported to date and corresponds to a 98.13% conversion rate. Then, the PAPS catalytic system was combined with the chondroitin 4-sulfotransferase using a one-pot method. Finally, chondroitin sulfate was transformed from chondroitin at a conversion rate of 98.75%. This strategy has great potential for scale biosynthesis of PAPS and chondroitin sulfate.
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Affiliation(s)
- Kaifang Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yunlu Zhong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Wei Song
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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Schumacher MA, Henderson M, Zeng W. Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2020; 26:69-82. [PMID: 31704716 PMCID: PMC6913127 DOI: 10.1261/rna.072231.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/25/2019] [Indexed: 05/05/2023]
Abstract
Most mitochondrial mRNAs are transcribed as polycistronic precursors that are cleaved by endonucleases to produce mature mRNA transcripts. However, recent studies have shown that mitochondrial transcripts in the kinetoplastid protozoan, Trypanosoma brucei, are transcribed individually. Also unlike most mitochondrial mRNAs, the 5' end of these transcripts harbor a triphosphate that is hydrolyzed. This modification is carried out by a putative Nudix hydrolase called MERS1. The Nudix motif in MERS1 is degenerate, lacking a conserved glutamic acid, thus it is unclear how it may bind its substrates and whether it contains a Nudix fold. To obtain insight into this unusual hydrolase, we determined structures of apo, GTP-bound and RNA-bound T. brucei MERS1 to 2.30 Å, 2.45 Å, and 2.60 Å, respectively. The MERS1 structure has a unique fold that indeed contains a Nudix motif. The nucleotide bound structures combined with binding studies reveal that MERS1 shows preference for RNA sequences with a central guanine repeat which it binds in a single-stranded conformation. The apo MERS1 structure indicates that a significant portion of its nucleotide binding site folds upon substrate binding. Finally, a potential interaction region for a binding partner, MERS2, that activates MERS1 was identified. The MERS2-like peptide inserts a glutamate near the missing Nudix acidic residue in the RNA binding pocket, suggesting how the enzyme may be activated. Thus, the combined studies reveal insight into the structure and enzyme properties of MERS1 and its substrate-binding activities.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Max Henderson
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Wenjie Zeng
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
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3
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Hill SE, Nguyen E, Ukachukwu CU, Freeman DM, Quirk S, Lieberman RL. Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism. PLoS One 2017; 12:e0180241. [PMID: 28742822 PMCID: PMC5526541 DOI: 10.1371/journal.pone.0180241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/12/2017] [Indexed: 01/02/2023] Open
Abstract
Dihydroneopterin triphosphate pyrophosphatase (DHNTPase), a member of the Mg2+ dependent Nudix hydrolase superfamily, is the recently-discovered enzyme that functions in the second step of the pterin branch of the folate biosynthetic pathway in E. coli. DHNTPase is of interest because inhibition of enzymes in bacterial folate biosynthetic pathways is a strategy for antibiotic development. We determined crystal structures of DHNTPase with and without activating, Mg2+-mimicking metals Co2+ and Ni2+. Four metal ions, identified by anomalous scattering, and stoichiometrically confirmed in solution by isothermal titration calorimetry, are held in place by Glu56 and Glu60 within the Nudix sequence motif, Glu117, waters, and a sulfate ion, of which the latter is further stabilized by a salt bridge with Lys7. In silico docking of the DHNTP substrate reveals a binding mode in which the pterin ring moiety is nestled in a largely hydrophobic pocket, the β-phosphate activated for nucleophilic attack overlays with the crystallographic sulfate and is in line with an activated water molecule, and remaining phosphate groups are stabilized by all four identified metal ions. The structures and binding data provide new details regarding DHNTPase metal requirements, mechanism, and suggest a strategy for efficient inhibition.
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Affiliation(s)
- Shannon E. Hill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Elaine Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chiamaka U. Ukachukwu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Dana M. Freeman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stephen Quirk
- Kimberly-Clark Corporation, Roswell, Georgia, United States of America
| | - Raquel L. Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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Oliveira EF, Cerqueira NMFSA, Ramos MJ, Fernandes PA. QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase. Catal Sci Technol 2016. [DOI: 10.1039/c6cy00356g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Detailing with atomistic resolution the reaction mechanism of human HMG-CoA reductase (HMG-CoA-R) might provide valuable insights for the development of new cholesterol-lowering drugs.
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Affiliation(s)
- Eduardo F. Oliveira
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | | | - Maria J. Ramos
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | - Pedro A. Fernandes
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
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de la Peña AH, Suarez A, Duong-ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. PLoS One 2015; 10:e0141716. [PMID: 26524597 PMCID: PMC4629899 DOI: 10.1371/journal.pone.0141716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/12/2015] [Indexed: 11/18/2022] Open
Abstract
Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases.
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Affiliation(s)
- Andres H. de la Peña
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Allison Suarez
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Krisna C. Duong-ly
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew J. Schoeffield
- Biology Department, Loyola University Maryland, Baltimore, Maryland, United States of America
| | - Mario A. Pizarro-Dupuy
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Melissa Zarr
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Silvia A. Pineiro
- Department of Medical and Research Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - L. Mario Amzel
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sandra B. Gabelli
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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