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Choi H, Hardy AP, Leissing TM, Chowdhury R, Nakashima Y, Ge W, Markoulides M, Scotti JS, Gerken PA, Thorbjornsrud H, Kang D, Hong S, Lee J, McDonough MA, Park H, Schofield CJ. A human protein hydroxylase that accepts D-residues. Commun Chem 2020; 3:52. [PMID: 36703414 PMCID: PMC9814778 DOI: 10.1038/s42004-020-0290-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/12/2020] [Indexed: 01/29/2023] Open
Abstract
Factor inhibiting hypoxia-inducible factor (FIH) is a 2-oxoglutarate-dependent protein hydroxylase that catalyses C3 hydroxylations of protein residues. We report FIH can accept (D)- and (L)-residues for hydroxylation. The substrate selectivity of FIH differs for (D) and (L) epimers, e.g., (D)- but not (L)-allylglycine, and conversely (L)- but not (D)-aspartate, undergo monohydroxylation, in the tested sequence context. The (L)-Leu-containing substrate undergoes FIH-catalysed monohydroxylation, whereas (D)-Leu unexpectedly undergoes dihydroxylation. Crystallographic, mass spectrometric, and DFT studies provide insights into the selectivity of FIH towards (L)- and (D)-residues. The results of this work expand the potential range of known substrates hydroxylated by isolated FIH and imply that it will be possible to generate FIH variants with altered selectivities.
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Affiliation(s)
- Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK.,Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006, Korea
| | - Adam P Hardy
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Thomas M Leissing
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Yu Nakashima
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Marios Markoulides
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - John S Scotti
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Philip A Gerken
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Helen Thorbjornsrud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Dahye Kang
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006, Korea.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK.
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Dickinson RS, Murphy F, Doherty C, Williams S, Mirchandani A, Willson J, Scotti JS, Preston G, Schofield CJ, Whyte MK, Walmsley SR. Pseudomonas expression of an oxygen sensing prolyl hydroxylase homologue regulates neutrophil host responses in vitro and in vivo. Wellcome Open Res 2017; 2:104. [PMID: 29387803 PMCID: PMC5701443 DOI: 10.12688/wellcomeopenres.12871.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2017] [Indexed: 12/13/2022] Open
Abstract
Background: Pseudomonas species are adapted to evade innate immune responses and can persist at sites of relative tissue hypoxia, including the mucus-plugged airways of patients with cystic fibrosis and bronchiectasis. The ability of these bacteria to directly sense and respond to changes in local oxygen availability is in part consequent upon expression of the 2-oxoglutarate oxygenase, Pseudomonas prolyl hydroxylase (PPHD), which acts on elongation factor Tu (EF-Tu), and is homologous with the human hypoxia inducible factor (HIF) prolyl hydroxylases. We report that PPHD expression regulates the neutrophil response to acute pseudomonal infection. Methods:In vitro co-culture experiments were performed with human neutrophils and PPHD-deficient and wild-type bacteria and supernatants, with viable neutrophil counts determined by flow cytometry. In vivo consequences of infection with PPHD deficient P. aeruginosa were determined in an acute pneumonia mouse model following intra-tracheal challenge. Results: Supernatants of PPHD-deficient bacterial cultures contained higher concentrations of the phenazine exotoxin pyocyanin and induced greater acceleration of neutrophil apoptosis than wild-type PAO1 supernatants in vitro. In vivo infection with PPHD mutants compared to wild-type PAO1 controls resulted in increased levels of neutrophil apoptosis and impaired control of infection, with higher numbers of P. aeruginosa recovered from the lungs of mice infected with the PPHD-deficient strain. This resulted in an overall increase in mortality in mice infected with the PPHD-deficient strain. Conclusions: Our data show that Pseudomonas expression of its prolyl hydroxylase influences the outcome of host-pathogen interactions in vitro and in vivo, demonstrating the importance of considering how both host and pathogen adaptations to hypoxia together define outcomes of infection. Given that inhibitors for the HIF prolyl hydroxylases are in late stage trials for the treatment of anaemia and that the active sites of PPHD and human HIF prolyl hydroxylases are closely related, the results are of current clinical interest.
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Affiliation(s)
- Rebecca S. Dickinson
- MRC/University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Fiona Murphy
- MRC/University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Catherine Doherty
- MRC/University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Sam Williams
- MRC/University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Ananda Mirchandani
- MRC/University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Joseph Willson
- MRC/University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - John S. Scotti
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Gail Preston
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Moira K.B. Whyte
- MRC/University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Sarah R. Walmsley
- MRC/University of Edinburgh Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK
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Horita S, Scotti JS, Thinnes C, Mottaghi-Taromsari YS, Thalhammer A, Ge W, Aik W, Loenarz C, Schofield CJ, McDonough MA. Structure of the ribosomal oxygenase OGFOD1 provides insights into the regio- and stereoselectivity of prolyl hydroxylases. Structure 2015; 23:639-52. [PMID: 25728928 PMCID: PMC4396695 DOI: 10.1016/j.str.2015.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/13/2015] [Accepted: 01/21/2015] [Indexed: 01/24/2023]
Abstract
Post-translational ribosomal protein hydroxylation is catalyzed by 2-oxoglutarate (2OG) and ferrous iron dependent oxygenases, and occurs in prokaryotes and eukaryotes. OGFOD1 catalyzes trans-3 prolyl hydroxylation at Pro62 of the small ribosomal subunit protein uS12 (RPS23) and is conserved from yeasts to humans. We describe crystal structures of the human uS12 prolyl 3-hydroxylase (OGFOD1) and its homolog from Saccharomyces cerevisiae (Tpa1p): OGFOD1 in complex with the broad-spectrum 2OG oxygenase inhibitors; N-oxalylglycine (NOG) and pyridine-2,4-dicarboxylate (2,4-PDCA) to 2.1 and 2.6 Å resolution, respectively; and Tpa1p in complex with NOG, 2,4-PDCA, and 1-chloro-4-hydroxyisoquinoline-3-carbonylglycine (a more selective prolyl hydroxylase inhibitor) to 2.8, 1.9, and 1.9 Å resolution, respectively. Comparison of uS12 hydroxylase structures with those of other prolyl hydroxylases, including the human hypoxia-inducible factor (HIF) prolyl hydroxylases (PHDs), reveals differences between the prolyl 3- and prolyl 4-hydroxylase active sites, which can be exploited for developing selective inhibitors of the different subfamilies.
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Affiliation(s)
- Shoichiro Horita
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK; Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| | - John S Scotti
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Cyrille Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Yousef S Mottaghi-Taromsari
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Armin Thalhammer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - WeiShen Aik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christoph Loenarz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
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Wilkins SE, Flashman E, Scotti JS, Hopkinson RJ, Chowdhury R, Schofield CJ. CHAPTER 6. The Role of 2-Oxoglutarate-Dependent Oxygenases in Hypoxia Sensing. 2-Oxoglutarate-Dependent Oxygenases 2015. [DOI: 10.1039/9781782621959-00169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Aik W, Scotti JS, Choi H, Gong L, Demetriades M, Schofield CJ, McDonough MA. Structure of human RNA N⁶-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. Nucleic Acids Res 2014; 42:4741-54. [PMID: 24489119 PMCID: PMC3985658 DOI: 10.1093/nar/gku085] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
ALKBH5 is a 2-oxoglutarate (2OG) and ferrous iron-dependent nucleic acid oxygenase (NAOX) that catalyzes the demethylation of N6-methyladenine in RNA. ALKBH5 is upregulated under hypoxia and plays a role in spermatogenesis. We describe a crystal structure of human ALKBH5 (residues 66–292) to 2.0 Å resolution. ALKBH566–292 has a double-stranded β-helix core fold as observed in other 2OG and iron-dependent oxygenase family members. The active site metal is octahedrally coordinated by an HXD…H motif (comprising residues His204, Asp206 and His266) and three water molecules. ALKBH5 shares a nucleotide recognition lid and conserved active site residues with other NAOXs. A large loop (βIV–V) in ALKBH5 occupies a similar region as the L1 loop of the fat mass and obesity-associated protein that is proposed to confer single-stranded RNA selectivity. Unexpectedly, a small molecule inhibitor, IOX3, was observed covalently attached to the side chain of Cys200 located outside of the active site. Modelling substrate into the active site based on other NAOX–nucleic acid complexes reveals conserved residues important for recognition and demethylation mechanisms. The structural insights will aid in the development of inhibitors selective for NAOXs, for use as functional probes and for therapeutic benefit.
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Affiliation(s)
- WeiShen Aik
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Liu S, Scotti JS, Kozmin SA. Emulating the logic of monoterpenoid alkaloid biogenesis to access a skeletally diverse chemical library. J Org Chem 2013; 78:8645-54. [PMID: 23937288 DOI: 10.1021/jo401262v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a synthetic strategy that mimics the diversity-generating power of monoterpenoid indole alkaloid biosynthesis. Our general approach goes beyond diversification of a single natural product-like substructure and enables production of a highly diverse collection of small molecules. The reaction sequence begins with rapid and highly modular assembly of the tetracyclic indoloquinolizidine core, which can be chemoselectively processed into several additional skeletally diverse structural frameworks. The general utility of this approach was demonstrated by parallel synthesis of two representative chemical libraries containing 847 compounds with favorable physicochemical properties to enable its subsequent broad pharmacological evaluation.
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Affiliation(s)
- Song Liu
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607, USA
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Yang M, Hardy AP, Chowdhury R, Loik ND, Scotti JS, McCullagh JSO, Claridge TDW, McDonough MA, Ge W, Schofield CJ. Substrate Selectivity Analyses of Factor Inhibiting Hypoxia-Inducible Factor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Yang M, Hardy AP, Chowdhury R, Loik ND, Scotti JS, McCullagh JSO, Claridge TDW, McDonough MA, Ge W, Schofield CJ. Substrate selectivity analyses of factor inhibiting hypoxia-inducible factor. Angew Chem Int Ed Engl 2013; 52:1700-4. [PMID: 23296631 DOI: 10.1002/anie.201208046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Ming Yang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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