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Davidson J, Nicholas K, Young J, Conrady DG, Mayclin S, Subramanian S, Staker BL, Myler PJ, Asojo OA. Crystal structure of a putative short-chain dehydrogenase/reductase from Paraburkholderia xenovorans. Acta Crystallogr F Struct Biol Commun 2022; 78:25-30. [PMID: 34981772 PMCID: PMC8725002 DOI: 10.1107/s2053230x21012632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/28/2021] [Indexed: 11/22/2022] Open
Abstract
Paraburkholderia xenovorans degrades organic wastes, including polychlorinated biphenyls. The atomic structure of a putative dehydrogenase/reductase (SDR) from P. xenovorans (PxSDR) was determined in space group P21 at a resolution of 1.45 Å. PxSDR shares less than 37% sequence identity with any known structure and assembles as a prototypical SDR tetramer. As expected, there is some conformational flexibility and difference in the substrate-binding cavity, which explains the substrate specificity. Uniquely, the cofactor-binding cavity of PxSDR is not well conserved and differs from those of other SDRs. PxSDR has an additional seven amino acids that form an additional unique loop within the cofactor-binding cavity. Further studies are required to determine how these differences affect the enzymatic functions of the SDR.
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Affiliation(s)
- Jaysón Davidson
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kyndall Nicholas
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Jeremy Young
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Deborah G. Conrady
- UCB Pharma, Bedford, Massachusetts, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Stephen Mayclin
- UCB Pharma, Bedford, Massachusetts, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Oluwatoyin A. Asojo
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
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2
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Mallipeddi PL, Zhang Y, Li H, Markowitz SD, Posner B. Structural Insights into Novel 15-Prostaglandin Dehydrogenase Inhibitors. Molecules 2021; 26:molecules26195903. [PMID: 34641449 PMCID: PMC8512612 DOI: 10.3390/molecules26195903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
We discovered SW033291 in a high throughput chemical screen aimed at identifying 15-prostaglandin dehydrogenase (15-PGDH) modulators. The compound exhibited inhibitory activity in in vitro biochemical and cell-based assays of 15-PGDH activity. We subsequently demonstrated that this compound, and several analogs thereof, are effective in in vivo mouse models of bone marrow transplant, colitis, and liver regeneration, where increased levels of PGE2 positively potentiate tissue regeneration. To better understand the binding of SW033291, we carried out docking studies for both the substrate, PGE2, and an inhibitor, SW033291, to 15-PGDH. Our models suggest similarities in the ways that PGE2 and SW033291 interact with key residues in the 15-PGDH-NAD+ complex. We carried out molecular dynamics simulations (MD) of SW033291 bound to this complex, in order to understand the dynamics of the binding interactions for this compound. The butyl side chain (including the sulfoxide) of SW033291 participates in crucial binding interactions that are similar to those observed for the C15-OH and the C16-C20 alkyl chain of PGE2. In addition, interactions with residues Ser138, Tyr151, and Gln148 play key roles in orienting and stabilizing SW033291 in the binding site and lead to enantioselectivity for the R-enantiomer. Finally, we compare the binding mode of (R)-S(O)-SW033291 with the binding interactions of published 15-PGDH inhibitors.
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Affiliation(s)
- Prema L. Mallipeddi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Yongyou Zhang
- Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (Y.Z.); (H.L.); (S.D.M.)
| | - Hongyun Li
- Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (Y.Z.); (H.L.); (S.D.M.)
| | - Sanford D. Markowitz
- Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (Y.Z.); (H.L.); (S.D.M.)
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence:
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3
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An J, Nie Y, Xu Y. Structural insights into alcohol dehydrogenases catalyzing asymmetric reductions. Crit Rev Biotechnol 2019; 39:366-379. [DOI: 10.1080/07388551.2019.1566205] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jianhong An
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- School of Ophthalmology and Optometry, and Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Brewing Microbiology, Applied Enzymology at Jiangnan University, Wuxi, China
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Brewing Microbiology, Applied Enzymology at Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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4
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Horita S, Kataoka M, Kitamura N, Miyakawa T, Ohtsuka J, Maejima Y, Shimomura K, Nagata K, Shimizu S, Tanokura M. Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds. Biosci Biotechnol Biochem 2018; 83:456-462. [PMID: 30445889 DOI: 10.1080/09168451.2018.1543014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Old yellow enzymes (OYEs) are potential targets of protein engineering for useful biocatalysts because of their excellent asymmetric reductions of enone compounds. Two OYEs from different yeast strains, Candida macedoniensis AKU4588 OYE (CmOYE) and Pichia sp. AKU4542 OYE (PsOYE), have a sequence identity of 46%, but show different substrate preferences; PsOYE shows 3.4-fold and 39-fold higher catalytic activities than CmOYE toward ketoisophorone and (4S)-phorenol, respectively. To gain insights into structural basis of their different substrate preferences, we have solved a crystal structure of PsOYE, and compared its catalytic site structure with that of CmOYE, revealing the catalytic pocket of PsOYE is wider than that of CmOYE due to different positions of Phe246 (PsOYE)/Phe250 (CmOYE) in static Loop 5. This study shows a significance of 3D structural information to explain the different substrate preferences of yeast OYEs which cannot be understood from their amino acid sequences. Abbreviations: OYE: Old yellow enzymes, CmOYE: Candida macedoniensis AKU4588 OYE, PsOYE: Pichia sp. AKU4542 OYE.
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Affiliation(s)
- Shoichiro Horita
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan.,b Department of Bioregulation and Pharmacological Medicine , Fukushima Medical University School of Medicine , Fukushima , Japan
| | - Michihiko Kataoka
- c Division of Applied Life Sciences , Graduate School of Life and Environmental Sciences, Osaka Prefecture University , Osaka , Japan
| | - Nahoko Kitamura
- d Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Takuya Miyakawa
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan
| | - Jun Ohtsuka
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan
| | - Yuko Maejima
- b Department of Bioregulation and Pharmacological Medicine , Fukushima Medical University School of Medicine , Fukushima , Japan
| | - Kenju Shimomura
- b Department of Bioregulation and Pharmacological Medicine , Fukushima Medical University School of Medicine , Fukushima , Japan
| | - Koji Nagata
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan
| | - Sakayu Shimizu
- d Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Masaru Tanokura
- a Department of Applied Biologic al Chemistry , Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo , Japan
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5
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Abstract
Most mycolic acid-containing actinobacteria and some proteobacteria use steroids as growth substrates, but the catabolism of the last two steroid rings has yet to be elucidated. In Mycobacterium tuberculosis, this pathway includes virulence determinants and has been proposed to be encoded by the KstR2-regulated genes, which include a predicted coenzyme A (CoA) transferase gene (ipdAB) and an acyl-CoA reductase gene (ipdC). In the presence of cholesterol, ΔipdC and ΔipdAB mutants of either M. tuberculosis or Rhodococcus jostii strain RHA1 accumulated previously undescribed metabolites: 3aα-H-4α(carboxyl-CoA)-5-hydroxy-7aβ-methylhexahydro-1-indanone (5-OH HIC-CoA) and (R)-2-(2-carboxyethyl)-3-methyl-6-oxocyclohex-1-ene-1-carboxyl-CoA (COCHEA-CoA), respectively. A ΔfadE32 mutant of Mycobacterium smegmatis accumulated 4-methyl-5-oxo-octanedioic acid (MOODA). Incubation of synthetic 5-OH HIC-CoA with purified IpdF, IpdC, and enoyl-CoA hydratase 20 (EchA20), a crotonase superfamily member, yielded COCHEA-CoA and, upon further incubation with IpdAB and a CoA thiolase, yielded MOODA-CoA. Based on these studies, we propose a pathway for the final steps of steroid catabolism in which the 5-member ring is hydrolyzed by EchA20, followed by hydrolysis of the 6-member ring by IpdAB. Metabolites accumulated by ΔipdF and ΔechA20 mutants support the model. The conservation of these genes in known steroid-degrading bacteria suggests that the pathway is shared. This pathway further predicts that cholesterol catabolism yields four propionyl-CoAs, four acetyl-CoAs, one pyruvate, and one succinyl-CoA. Finally, a ΔipdAB M. tuberculosis mutant did not survive in macrophages and displayed severely depleted CoASH levels that correlated with a cholesterol-dependent toxicity. Our results together with the developed tools provide a basis for further elucidating bacterial steroid catabolism and virulence determinants in M. tuberculosis. Bacteria are the only known steroid degraders, but the pathway responsible for degrading the last two steroid rings has yet to be elucidated. In Mycobacterium tuberculosis, this pathway includes virulence determinants. Using a series of mutants in M. tuberculosis and related bacteria, we identified a number of novel CoA thioesters as pathway intermediates. Analysis of the metabolites combined with enzymological studies establishes how the last two steroid rings are hydrolytically opened by enzymes encoded by the KstR2 regulon. Our results provide experimental evidence for novel ring-degrading enzymes, significantly advance our understanding of bacterial steroid catabolism, and identify a previously uncharacterized cholesterol-dependent toxicity that may facilitate the development of novel tuberculosis therapeutics.
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6
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Lerchner A, Daake M, Jarasch A, Skerra A. Fusion of an alcohol dehydrogenase with an aminotransferase using a PAS linker to improve coupled enzymatic alcohol-to-amine conversion. Protein Eng Des Sel 2016; 29:557-562. [PMID: 27578886 DOI: 10.1093/protein/gzw039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 07/18/2016] [Accepted: 07/18/2016] [Indexed: 11/14/2022] Open
Abstract
To facilitate biocatalytic conversion of the biotechnologically accessible dicyclic dialcohol isosorbide into its industrially relevant diamines, we have designed a fusion protein between two homo-oligomeric enzymes: the levodione reductase (LR) from Leifsonia aquatica and the variant L417M of the ω-aminotransferase from Paracoccus denitrificans (PDωAT(L417M)), mutually connected by a short Pro/Ala/Ser linker sequence. The hybrid protein was produced in Escherichia coli in correctly folded state, comprising a tetrameric LR moiety and presumably two dimers of PDωAT(L417M), as proven by SDS-PAGE and size exclusion chromatography. The bifunctional enzyme revealed beneficial kinetics over the two-component system, in particular at low substrate concentration.
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Affiliation(s)
- Alexandra Lerchner
- Munich Center for integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Marina Daake
- Munich Center for integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Alexander Jarasch
- Munich Center for integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Arne Skerra
- Munich Center for integrated Protein Science (CiPSM) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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7
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Büsing I, Höffken HW, Breuer M, Wöhlbrand L, Hauer B, Rabus R. Molecular Genetic and Crystal Structural Analysis of 1-(4-Hydroxyphenyl)-Ethanol Dehydrogenase from 'Aromatoleum aromaticum' EbN1. J Mol Microbiol Biotechnol 2015; 25:327-39. [PMID: 26488297 DOI: 10.1159/000439113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The dehydrogenation of 1-(4-hydroxyphenyl)-ethanol to 4-hydroxyacetophenone represents the second reaction step during anaerobic degradation of p-ethylphenol in the denitrifying bacterium 'Aromatoleum aromaticum' EbN1. Previous proteogenomic studies identified two different proteins (ChnA and EbA309) as possible candidates for catalyzing this reaction [Wöhlbrand et al: J Bacteriol 2008;190:5699-5709]. Physiological-molecular characterization of newly generated unmarked in-frame deletion and complementation mutants allowed defining ChnA (renamed here as Hped) as the enzyme responsible for 1-(4-hydroxyphenyl)-ethanol oxidation. Hped [1-(4-hydroxyphenyl)-ethanol dehydrogenase] belongs to the 'classical' family within the short-chain alcohol dehydrogenase/reductase (SDR) superfamily. Hped was overproduced in Escherichia coli, purified and crystallized. The X-ray structures of the apo- and NAD(+)-soaked form were resolved at 1.5 and 1.1 Å, respectively, and revealed Hped as a typical homotetrameric SDR. Modeling of the substrate 4-hydroxyacetophenone (reductive direction of Hped) into the active site revealed the structural determinants of the strict (R)-specificity of Hped (Phe(187)), contrasting the (S)-specificity of previously reported 1-phenylethanol dehydrogenase (Ped; Tyr(93)) from strain EbN1 [Höffken et al: Biochemistry 2006;45:82-93].
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Affiliation(s)
- Imke Büsing
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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8
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Horita S, Kataoka M, Kitamura N, Nakagawa T, Miyakawa T, Ohtsuka J, Nagata K, Shimizu S, Tanokura M. An engineered old yellow enzyme that enables efficient synthesis of (4R,6R)-Actinol in a one-pot reduction system. Chembiochem 2015; 16:440-5. [PMID: 25639703 DOI: 10.1002/cbic.201402555] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Indexed: 11/06/2022]
Abstract
(4R,6R)-Actinol can be stereo-selectively synthesized from ketoisophorone by a two-step conversion using a mixture of two enzymes: Candida macedoniensis old yellow enzyme (CmOYE) and Corynebacterium aquaticum (6R)-levodione reductase. However, (4S)-phorenol, an intermediate, accumulates because of the limited substrate range of CmOYE. To address this issue, we solved crystal structures of CmOYE in the presence and absence of a substrate analogue p-HBA, and introduced point mutations into the substrate-recognition loop. The most effective mutant (P295G) showed two- and 12-fold higher catalytic activities toward ketoisophorone and (4S)-phorenol, respectively, than the wild-type, and improved the yield of the two-step conversion from 67.2 to 90.1%. Our results demonstrate that the substrate range of an enzyme can be changed by introducing mutation(s) into a substrate-recognition loop. This method can be applied to the development of other favorable OYEs with different substrate preferences.
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Affiliation(s)
- Shoichiro Horita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan)
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9
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Takeshita D, Kataoka M, Miyakawa T, Miyazono KI, Kumashiro S, Nagai T, Urano N, Uzura A, Nagata K, Shimizu S, Tanokura M. Structural basis of stereospecific reduction by quinuclidinone reductase. AMB Express 2014; 4:6. [PMID: 24507746 PMCID: PMC3922912 DOI: 10.1186/2191-0855-4-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 12/28/2013] [Indexed: 11/10/2022] Open
Abstract
Chiral molecule (R)-3-quinuclidinol, a valuable compound for the production of various pharmaceuticals, is efficiently synthesized from 3-quinuclidinone by using NADPH-dependent 3-quinuclidinone reductase (RrQR) from Rhodotorula rubra. Here, we report the crystal structure of RrQR and the structure-based mutational analysis. The enzyme forms a tetramer, in which the core of each protomer exhibits the α/β Rossmann fold and contains one molecule of NADPH, whereas the characteristic substructures of a small lobe and a variable loop are localized around the substrate-binding site. Modeling and mutation analyses of the catalytic site indicated that the hydrophobicity of two residues, I167 and F212, determines the substrate-binding orientation as well as the substrate-binding affinity. Our results revealed that the characteristic substrate-binding pocket composed of hydrophobic amino acid residues ensures substrate docking for the stereospecific reaction of RrQR in spite of its loose interaction with the substrate.
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Simon RC, Richter N, Busto E, Kroutil W. Recent Developments of Cascade Reactions Involving ω-Transaminases. ACS Catal 2013. [DOI: 10.1021/cs400930v] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert C. Simon
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Nina Richter
- ACIB GmbH, c/o Heinrichstraße
28, 8010 Graz, Austria
| | - Eduardo Busto
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
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Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium spp. Reveal the Molecular Basis for Their Recognition of ‘Bulky–Bulky’ Ketones. Top Catal 2013. [DOI: 10.1007/s11244-013-0191-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Bhowmik S, Jones DH, Chiu HP, Park IH, Chiu HJ, Axelrod HL, Farr CL, Tien HJ, Agarwalla S, Lesley SA. Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe. Proteins 2013; 82:216-29. [PMID: 23836456 DOI: 10.1002/prot.24353] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/07/2013] [Accepted: 06/17/2013] [Indexed: 12/19/2022]
Abstract
Despite significant influence of secondary bile acids on human health and disease, limited structural and biochemical information is available for the key gut microbial enzymes catalyzing its synthesis. Herein, we report apo- and cofactor bound crystal structures of BaiA2, a short chain dehydrogenase/reductase from Clostridium scindens VPI 12708 that represent the first protein structure of this pathway. The structures elucidated the basis of cofactor specificity and mechanism of proton relay. A conformational restriction involving Glu42 located in the cofactor binding site seems crucial in determining cofactor specificity. Limited flexibility of Glu42 results in imminent steric and electrostatic hindrance with 2'-phosphate group of NADP(H). Consistent with crystal structures, steady state kinetic characterization performed with both BaiA2 and BaiA1, a close homolog with 92% sequence identity, revealed specificity constant (kcat /KM ) of NADP(+) at least an order of magnitude lower than NAD(+) . Substitution of Glu42 with Ala improved specificity toward NADP(+) by 10-fold compared to wild type. The cofactor bound structure uncovered a novel nicotinamide-hydroxyl ion (NAD(+) -OH(-) ) adduct contraposing previously reported adducts. The OH(-) of the adduct in BaiA2 is distal to C4 atom of nicotinamide and proximal to 2'-hydroxyl group of the ribose moiety. Moreover, it is located at intermediary distances between terminal functional groups of active site residues Tyr157 (2.7 Å) and Lys161 (4.5 Å). Based on these observations, we propose an involvement of NAD(+) -OH(-) adduct in proton relay instead of hydride transfer as noted for previous adducts.
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Affiliation(s)
- Shiva Bhowmik
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037; Joint Center for Structural Genomics
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13
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Lerchner A, Achatz S, Rausch C, Haas T, Skerra A. Coupled Enzymatic Alcohol-to-Amine Conversion of Isosorbide using Engineered Transaminases and Dehydrogenases. ChemCatChem 2013. [DOI: 10.1002/cctc.201300284] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Lerchner A, Jarasch A, Meining W, Schiefner A, Skerra A. Crystallographic analysis and structure-guided engineering of NADPH-dependent Ralstonia sp. alcohol dehydrogenase toward NADH cosubstrate specificity. Biotechnol Bioeng 2013; 110:2803-14. [PMID: 23686719 DOI: 10.1002/bit.24956] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/21/2013] [Accepted: 04/29/2013] [Indexed: 11/10/2022]
Abstract
The NADP⁺-dependent alcohol dehydrogenase from Ralstonia sp. (RasADH) belongs to the protein superfamily of short-chain dehydrogenases/reductases (SDRs). As an enzyme that accepts different types of substrates--including bulky-bulky as well as small-bulky secondary alcohols or ketones--with high stereoselectivity, it offers potential as a biocatalyst for industrial biotechnology. To understand substrate and cosubstrate specificities of RasADH we determined the crystal structure of the apo-enzyme as well as its NADP⁺-bound state with resolutions down to 2.8 Å. RasADH displays a homotetrameric quaternary structure that can be described as a dimer of homodimers while in each subunit a seven-stranded parallel β-sheet, flanked by three α-helices on each side, forms a Rossmann fold-type dinucleotide binding domain. Docking of the well-known substrate (S)-1-phenylethanol clearly revealed the structural determinants of stereospecificity. To favor practical RasADH application in the context of established cofactor recycling systems, for example, those involving an NADH-dependent amino acid dehydrogenase, we attempted to rationally change its cosubstrate specificity from NADP⁺ to NAD⁺ utilizing the structural information that NADP⁺ specificity is largely governed by the residues Asn15, Gly37, Arg38, and Arg39. Furthermore, an extensive sequence alignment with homologous dehydrogenases that have different cosubstrate specificities revealed a modified general SDR motif ASNG (instead of NNAG) at positions 86-89 of RasADH. Consequently, we constructed mutant enzymes with one (G37D), four (N15G/G37D/R38V/R39S), and six (N15G/G37D/R38V/R39S/A86N/S88A) amino acid exchanges. RasADH (N15G/G37D/R38V/R39S) was better able to accept NAD⁺ while showing much reduced catalytic efficiency with NADP⁺, leading to a change in NADH/NADPH specificity by a factor of ∼3.6 million.
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Affiliation(s)
- Alexandra Lerchner
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350, Freising-Weihenstephan, Germany
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15
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3-oxoacyl-ACP reductase from Schistosoma japonicum: integrated in silico-in vitro strategy for discovering antischistosomal lead compounds. PLoS One 2013; 8:e64984. [PMID: 23762275 PMCID: PMC3676400 DOI: 10.1371/journal.pone.0064984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 04/18/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Schistosomiasis is a disease caused by parasitic worms and more than 200 million people are infected worldwide. The emergence of resistance to the most commonly used drug, praziquantel (PZQ), makes the development of novel drugs an urgent task. 3-oxoacyl-ACP reductase (OAR), a key enzyme involved in the fatty acid synthesis pathway, has been identified as a potential drug target against many pathogenic organisms. However, no research on Schistosoma japonicum OAR (SjOAR) has been reported. The characterization of the SjOAR protein will provide new strategies for screening antischistosomal drugs that target SjOAR. METHODOLOGY/PRINCIPAL FINDINGS After cloning the SjOAR gene, recombinant SjOAR protein was purified and assayed for enzymatic activity. The tertiary structure of SjOAR was obtained by homology modeling and 27 inhibitor candidates were identified from 14,400 compounds through molecular docking based on the structure. All of these compounds were confirmed to be able to bind to the SjOAR protein by BIAcore analysis. Two compounds exhibited strong antischistosomal activity and inhibitory effects on the enzymatic activity of SjOAR. In contrast, these two compounds showed relatively low toxicity towards host cells. CONCLUSIONS/SIGNIFICANCE The work presented here shows the feasibility of isolation of new antischistosomal compounds using a combination of virtual screening and experimental validation. Based on this strategy, we successfully identified 2 compounds that target SjOAR with strong antischistosomal activity but relatively low cytotoxicity to host cells.
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Niesen FH, Schultz L, Jadhav A, Bhatia C, Guo K, Maloney DJ, Pilka ES, Wang M, Oppermann U, Heightman TD, Simeonov A. High-affinity inhibitors of human NAD-dependent 15-hydroxyprostaglandin dehydrogenase: mechanisms of inhibition and structure-activity relationships. PLoS One 2010; 5:e13719. [PMID: 21072165 PMCID: PMC2970562 DOI: 10.1371/journal.pone.0013719] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 10/04/2010] [Indexed: 12/12/2022] Open
Abstract
Background 15-hydroxyprostaglandin dehydrogenase (15-PGDH, EC 1.1.1.141) is the key enzyme for the inactivation of prostaglandins, regulating processes such as inflammation or proliferation. The anabolic pathways of prostaglandins, especially with respect to regulation of the cyclooxygenase (COX) enzymes have been studied in detail; however, little is known about downstream events including functional interaction of prostaglandin-processing and -metabolizing enzymes. High-affinity probes for 15-PGDH will, therefore, represent important tools for further studies. Principal Findings To identify novel high-affinity inhibitors of 15-PGDH we performed a quantitative high-throughput screen (qHTS) by testing >160 thousand compounds in a concentration-response format and identified compounds that act as noncompetitive inhibitors as well as a competitive inhibitor, with nanomolar affinity. Both types of inhibitors caused strong thermal stabilization of the enzyme, with cofactor dependencies correlating with their mechanism of action. We solved the structure of human 15-PGDH and explored the binding modes of the inhibitors to the enzyme in silico. We found binding modes that are consistent with the observed mechanisms of action. Conclusions Low cross-reactivity in screens of over 320 targets, including three other human dehydrogenases/reductases, suggest selectivity of the present inhibitors for 15-PGDH. The high potencies and different mechanisms of action of these chemotypes make them a useful set of complementary chemical probes for functional studies of prostaglandin-signaling pathways. Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S2.
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Affiliation(s)
- Frank H. Niesen
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Lena Schultz
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chitra Bhatia
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Kunde Guo
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - David J. Maloney
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ewa S. Pilka
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Minghua Wang
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Udo Oppermann
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Biomedical Research Unit, Nuffield Department of Orthopedic Surgery, Rheumatology and Musculoskeletal Sciences, Botnar Research Center, University of Oxford, Oxford, United Kingdom
| | - Tom D. Heightman
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Biochemical and structural characterization of a short-chain dehydrogenase/reductase of Thermus thermophilus HB8. Chem Biol Interact 2009; 178:117-26. [DOI: 10.1016/j.cbi.2008.09.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 11/24/2022]
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Ehrensberger AH, Elling RA, Wilson DK. Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity. Structure 2006; 14:567-75. [PMID: 16531240 DOI: 10.1016/j.str.2005.11.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Revised: 10/18/2005] [Accepted: 11/04/2005] [Indexed: 10/24/2022]
Abstract
Xylitol dehydrogenase (XDH) is one of several enzymes responsible for assimilating xylose into eukaryotic metabolism and is useful for fermentation of xylose contained in agricultural byproducts to produce ethanol. For efficient xylose utilization at high flux rates, cosubstrates should be recycled between the NAD+-specific XDH and the NADPH-preferring xylose reductase, another enzyme in the pathway. To understand and alter the cosubstrate specificity of XDH, we determined the crystal structure of the Gluconobacter oxydans holoenzyme to 1.9 angstroms resolution. The structure reveals that NAD+ specificity is largely conferred by Asp38, which interacts with the hydroxyls of the adenosine ribose. Met39 stacked under the purine ring and was also located near the 2' hydroxyl. Based on the location of these residues and on sequence alignments with related enzymes of various cosubstrate specificities, we constructed a double mutant (D38S/M39R) that was able to exclusively use NADP+, with no loss of activity.
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Affiliation(s)
- Andreas H Ehrensberger
- Section of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA
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Cho H, Huang L, Hamza A, Gao D, Zhan CG, Tai HH. Role of glutamine 148 of human 15-hydroxyprostaglandin dehydrogenase in catalytic oxidation of prostaglandin E2. Bioorg Med Chem 2006; 14:6486-91. [PMID: 16828555 DOI: 10.1016/j.bmc.2006.06.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2006] [Revised: 06/03/2006] [Accepted: 06/08/2006] [Indexed: 11/30/2022]
Abstract
NAD+-dependent 15-hydroxyprostaglandin dehydrogenase (15-PGDH), a member of the short-chain dehydrogenase/reductase (SDR) family, catalyzes the first step in the catabolic pathways of prostaglandins and lipoxins. This enzyme oxidizes the C-15 hydroxyl group of prostaglandins and lipoxins to produce 15-keto metabolites which exhibit greatly reduced biological activities. A three-dimensional (3D) structure of 15-PGDH based on the crystal structures of the levodione reductase and tropinone reductase-II was generated and used for docking study with NAD+ coenzyme and PGE2 substrate. Three well-conserved residues among SDR family which correspond to Ser-138, Tyr-151, and Lys-155 of 15-PGDH have been shown to participate in the catalytic reaction. Based on the molecular interactions observed from 3D structure of 15-PGDH, we further propose that Gln-148 in 15-PGDH is important in properly positioning the 15-hydroxyl group of PGE2 by hydrogen bonding with the side-chain oxygen atom of Gln-148. This residue is found to be less conserved and replaceable by glutamyl, histidinyl, and asparaginyl residues in SDR family. Accordingly, site-directed mutagenesis of Gln-148 of 15-PGDH to alanine, glutamic acid, histidine, and asparagine (Q148A, Q148E, Q148H, and Q148N) was carried out. The activity of mutant Q148A was not detectable, whereas those of mutants Q148E, Q148H, and Q148N were comparable to or higher than the wild type. This indicates that the side-chain oxygen or nitrogen atom at position 148 of 15-PGDH plays an important role in anchoring C-15 hydroxyl group of PGE2 through hydrogen bonding for catalytic reaction.
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Affiliation(s)
- Hoon Cho
- Polymer Science Engineering, Chosun University, Gwangju 501-579, Republic of Korea
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Buque-Taboada EM, Straathof AJ, Heijnen JJ, van der Wielen LA. Substrate inhibition and product degradation during the reduction of 4-oxoisophorone by Saccharomyces cerevisiae. Enzyme Microb Technol 2005. [DOI: 10.1016/j.enzmictec.2005.04.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hamza A, Cho H, Tai HH, Zhan CG. Understanding human 15-hydroxyprostaglandin dehydrogenase binding with NAD+ and PGE2 by homology modeling, docking and molecular dynamics simulation. Bioorg Med Chem 2005; 13:4544-51. [PMID: 15908215 DOI: 10.1016/j.bmc.2005.04.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 04/13/2005] [Accepted: 04/13/2005] [Indexed: 11/26/2022]
Abstract
Homology modeling, molecular docking, and molecular dynamics simulation have been performed to determine human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) binding with its NAD+ cofactor and prostaglandin E2 (PGE2) substrate. The computational studies have led to a three-dimensional (3D) model of the entire 15-PGDH-NAD+-PGE2 complex, demonstrating the detailed binding of PGE2 with 15-PGDH for the first time. This 3D model shows specific interactions of the protein with the cofactor and substrate in qualitative agreement with available experimental data. Our model demonstrates the PGE2-binding cavity of the protein for the first time. The model further leads to an interesting prediction that the catalytic activity of 15-PGDH should also significantly be affected by Gln148, in addition to the previously known three catalytic residues (Ser138, Tyr151, and Lys155). The reported 3D model of 15-PGDH-NAD+-PGE2 complex might be valuable for future rational design of novel inhibitors of 15-PGDH.
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Affiliation(s)
- Adel Hamza
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
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