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Crystal structure of the collagen prolyl 4-hydroxylase (C-P4H) catalytic domain complexed with PDI: Toward a model of the C-P4H α 2β 2 tetramer. J Biol Chem 2022; 298:102614. [PMID: 36265586 PMCID: PMC9676403 DOI: 10.1016/j.jbc.2022.102614] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Collagen prolyl 4-hydroxylases (C-P4H) are α2β2 tetramers, which catalyze the prolyl 4-hydroxylation of procollagen, allowing for the formation of the stable triple-helical collagen structure in the endoplasmic reticulum. The C-P4H α-subunit provides the N-terminal dimerization domain, the middle peptide-substrate-binding (PSB) domain, and the C-terminal catalytic (CAT) domain, whereas the β-subunit is identical to the enzyme protein disulfide isomerase (PDI). The structure of the N-terminal part of the α-subunit (N-terminal region and PSB domain) is known, but the structures of the PSB-CAT linker region and the CAT domain as well as its mode of assembly with the β/PDI subunit, are unknown. Here, we report the crystal structure of the CAT domain of human C-P4H-II complexed with the intact β/PDI subunit, at 3.8 Å resolution. The CAT domain interacts with the a, b', and a' domains of the β/PDI subunit, such that the CAT active site is facing bulk solvent. The structure also shows that the C-P4H-II CAT domain has a unique N-terminal extension, consisting of α-helices and a β-strand, which is the edge strand of its major antiparallel β-sheet. This extra region of the CAT domain interacts tightly with the β/PDI subunit, showing that the CAT-PDI interface includes an intersubunit disulfide bridge with the a' domain and tight hydrophobic interactions with the b' domain. Using this new information, the structure of the mature C-P4H-II α2β2 tetramer is predicted. The model suggests that the CAT active-site properties are modulated by α-helices of the N-terminal dimerization domains of both subunits of the α2-dimer.
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Liu S, Li Y, Wang M, Ma Y, Wang J. Efficient co-expression of recombinant human fusion collagen with prolyl 4-hydroxylase from Bacillus anthracis in Escherichia coli. Biotechnol Appl Biochem 2022; 70:761-772. [PMID: 35959739 DOI: 10.1002/bab.2396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/31/2022] [Indexed: 11/09/2022]
Abstract
Collagen family members, the most abundant proteins in the human body, are widely used in biomedical fields and tissue engineering industries. However, the applications of collagen remain mostly relying on material derived from native tissues due to its extremely complex post-translational modifications like proline hydroxylation, which hinder the large-scale exogenous production of collagen. In the current study, we propose a novel prolyl hydroxylated recombinant human fusion collagen containing multiple native cell-interaction sites derived from human type Ⅰ and Ⅲ collagen with good biocompatibility and thermal stability. To obtain prolyl hydroxylated collagen, prolyl 4-hydroxylases from Bacillus anthracis, Arabidopsis thaliana, and Dactylosporangium sp. RH1 were co-expressed with collagen in Escherichia coli (E. coli), respectively. Among of which, prolyl 4-hydroxylase (P4H) from Bacillus anthracis showed the highest hydroxyl rate with 63.6%. Furthermore, a yield of hydroxylated collagen at 0.8 g/L was achieved by fed-batch fermentation in a 5 L fermenter with the productivity of 0.0267 g·L-1 ·h-1 . Compared with non-hydroxylated recombinant collagen, hydroxylated recombinant collagen showed significant improvements in thermal stability and biocompatibility. Taken this together, our studies provide a promising method for further development of collagen application in biomaterials engineering. A novel recombinant human fusion collagen with multiple motifs derived from both human type I and Ⅲ collagen exhibits good biocompatibility and thermal stability as higher molecular weight of ∼120kDa. By co-expression recombinant collagen and P4H genes in Escherichia coli, the maximum hyp in the recombinant collagen reached 63.6%, and a yield of hydroxylated collagen at 0.8 g/L was achieved by fed-batch fermentation in a 5 L fermenter. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Su Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yanmei Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Meng Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.,Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.,Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
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Meier AA, Moon HJ, Toth R, Folta-Stogniew E, Kuczera K, Middaugh CR, Mure M. Oligomeric States and Hydrodynamic Properties of Lysyl Oxidase-Like 2. Biomolecules 2021; 11:biom11121846. [PMID: 34944490 PMCID: PMC8699698 DOI: 10.3390/biom11121846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 11/16/2022] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) has emerged as a promising therapeutic target against metastatic/invasive tumors and organ and tissue fibrosis. LOXL2 catalyzes the oxidative deamination of lysine and hydroxylysine residues in extracellular matrix (ECM) proteins to promote crosslinking of these proteins, and thereby plays a major role in ECM remodeling. LOXL2 secretes as 100-kDa full-length protein (fl-LOXL2) and then undergoes proteolytic cleavage of the first two scavenger receptor cysteine-rich (SRCR) domains to yield 60-kDa protein (Δ1-2SRCR-LOXL2). This processing does not affect the amine oxidase activity of LOXL2 in vitro. However, the physiological importance of this cleavage still remains elusive. In this study, we focused on characterization of biophysical properties of fl- and Δ1-2SRCR-LOXL2s (e.g., oligomeric states, molecular weights, and hydrodynamic radii in solution) to gain insight into the structural role of the first two SRCR domains. Our study reveals that fl-LOXL2 exists predominantly as monomer but also dimer to the lesser extent when its concentration is <~1 mM. The hydrodynamic radius (Rh) determined by multi-angle light scattering coupled with size exclusion chromatography (SEC-MALS) indicates that fl-LOXL2 is a moderately asymmetric protein. In contrast, Δ1-2SRCR-LOXL2 exists solely as monomer and its Rh is in good agreement with the predicted value. The Rh values calculated from a 3D modeled structure of fl-LOXL2 and the crystal structure of the precursor Δ1-2SRCR-LOXL2 are within a reasonable margin of error of the values determined by SEC-MALS for fl- and Δ1-2SRCR-LOXL2s in mature forms in this study. Based on superimposition of the 3D model and the crystal structure of Δ1-2SRCR-LOXL2 (PDB:5ZE3), we propose a configuration of fl-LOXL2 that explains the difference observed in Rh between fl- and Δ1-2SRCR-LOXL2s in solution.
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Affiliation(s)
- Alex A. Meier
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; (A.A.M.); (H.-J.M.); (K.K.)
| | - Hee-Jung Moon
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; (A.A.M.); (H.-J.M.); (K.K.)
| | - Ronald Toth
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA; (R.T.IV); (C.R.M.)
| | - Ewa Folta-Stogniew
- W.M. Keck Biotechnology Resource Laboratory, Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06511, USA;
| | - Krzysztof Kuczera
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; (A.A.M.); (H.-J.M.); (K.K.)
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - C. Russell Middaugh
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA; (R.T.IV); (C.R.M.)
| | - Minae Mure
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA; (A.A.M.); (H.-J.M.); (K.K.)
- Correspondence:
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Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:97-125. [PMID: 32951817 PMCID: PMC7320668 DOI: 10.1016/bs.apcsb.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein composition is restricted by the genetic code to a relatively small number of natural amino acids. Similarly, the known three-dimensional structures adopt a limited number of protein folds. However, proteins exert a large variety of functions and show a remarkable ability for regulation and immediate response to intracellular and extracellular stimuli. To some degree, the wide variability of protein function can be attributed to the post-translational modifications. Post-translational modifications have been observed in all kingdoms of life and give to proteins a significant degree of chemical and consequently functional and structural diversity. Their importance is partly reflected in the large number of genes dedicated to their regulation. So far, hundreds of post-translational modifications have been observed while it is believed that many more are to be discovered along with the technological advances in sequencing, proteomics, mass spectrometry and structural biology. Indeed, the number of studies which report novel post translational modifications is getting larger supporting the notion that their space is still largely unexplored. In this review we explore the impact of post-translational modifications on protein structure and function with emphasis on catalytic activity regulation. We present examples of proteins and protein families whose catalytic activity is substantially affected by the presence of post translational modifications and we describe the molecular basis which underlies the regulation of the protein function through these modifications. When available, we also summarize the current state of knowledge on the mechanisms which introduce these modifications to protein sites.
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Vijayasarathy M, Balaram P. Cone snail prolyl-4-hydroxylase α-subunit sequences derived from transcriptomic data and mass spectrometric analysis of variable proline hydroxylation in C. amadis venom. J Proteomics 2019; 194:37-48. [DOI: 10.1016/j.jprot.2018.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 10/27/2022]
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6
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Gorges J, Panter F, Kjaerulff L, Hoffmann T, Kazmaier U, Müller R. Structure, Total Synthesis, and Biosynthesis of Chloromyxamides: Myxobacterial Tetrapeptides Featuring an Uncommon 6-Chloromethyl-5-methoxypipecolic Acid Building Block. Angew Chem Int Ed Engl 2018; 57:14270-14275. [PMID: 30088846 DOI: 10.1002/anie.201808028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Indexed: 11/08/2022]
Abstract
Soil-living microbes are an important resource for the discovery of new natural products featuring great structural diversity that are reflective of the underlying biosynthetic pathways as well as incorporating a wide range of intriguing small-molecule building blocks. We report here the full structural elucidation, total synthesis, and biosynthesis of chloromyxamides, a new class of tetrapeptides that display an unprecedented 6-chloromethyl-5-methoxypipecolic acid (CMPA) substructure. Chemical synthesis-including an approach to access the CMPA unit-was pursued to confirm the structure of the chloromyxamides and enabled determination of the absolute configuration in the CMPA ring. A model for the nonribosomal assembly of chloromyxamides was devised on the basis of the combined evaluation of the biosynthetic gene cluster sequence and the feeding of stable isotope-labeled precursors. This provided insight into the formation of the various chloromyxamide derivatives and the biogenesis of the CMPA unit.
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Affiliation(s)
- Jan Gorges
- Institute for Organic Chemistry, Saarland University, P.O. Box 151150, 66123, Saarbrücken, Germany
| | - Fabian Panter
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partner Site Hannover-Braunschweig) and Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Louise Kjaerulff
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partner Site Hannover-Braunschweig) and Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Thomas Hoffmann
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partner Site Hannover-Braunschweig) and Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Uli Kazmaier
- Institute for Organic Chemistry, Saarland University, P.O. Box 151150, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), German Center for Infection Research (DZIF, Partner Site Hannover-Braunschweig) and Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
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7
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Gorges J, Panter F, Kjaerulff L, Hoffmann T, Kazmaier U, Müller R. Struktur, Totalsynthese und Biosynthese der Chloromyxamide: Myxobakterielle Tetrapeptide mit einem ungewöhnlichen 6-Chloromethyl-5-methoxypipecolinsäure-Baustein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jan Gorges
- Institut für organische Chemie; Universität des Saarlandes; P.O. Box 151150 66123 Saarbrücken Deutschland
| | - Fabian Panter
- Abteilung Mikrobielle Naturstoffe; Helmholtz Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz Center für Infektionsforschung (HZI); Deutsches Zentrum für Infektionsforschung (DZIF, Partner Site Hannover-Braunschweig); Fachrichtung Pharmazie; Universität des Saarlandes; Campus E8.1 66123 Saarbrücken Deutschland
| | - Louise Kjaerulff
- Abteilung Mikrobielle Naturstoffe; Helmholtz Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz Center für Infektionsforschung (HZI); Deutsches Zentrum für Infektionsforschung (DZIF, Partner Site Hannover-Braunschweig); Fachrichtung Pharmazie; Universität des Saarlandes; Campus E8.1 66123 Saarbrücken Deutschland
| | - Thomas Hoffmann
- Abteilung Mikrobielle Naturstoffe; Helmholtz Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz Center für Infektionsforschung (HZI); Deutsches Zentrum für Infektionsforschung (DZIF, Partner Site Hannover-Braunschweig); Fachrichtung Pharmazie; Universität des Saarlandes; Campus E8.1 66123 Saarbrücken Deutschland
| | - Uli Kazmaier
- Institut für organische Chemie; Universität des Saarlandes; P.O. Box 151150 66123 Saarbrücken Deutschland
| | - Rolf Müller
- Abteilung Mikrobielle Naturstoffe; Helmholtz Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz Center für Infektionsforschung (HZI); Deutsches Zentrum für Infektionsforschung (DZIF, Partner Site Hannover-Braunschweig); Fachrichtung Pharmazie; Universität des Saarlandes; Campus E8.1 66123 Saarbrücken Deutschland
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8
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Characterization of CyrI, the hydroxylase involved in the last step of cylindrospermopsin biosynthesis: Binding studies, site-directed mutagenesis and stereoselectivity. Arch Biochem Biophys 2018; 647:1-9. [DOI: 10.1016/j.abb.2018.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 11/21/2022]
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9
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Schnicker NJ, Razzaghi M, Guha Thakurta S, Chakravarthy S, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu. Biochemistry 2017; 56:5771-5785. [PMID: 28981257 DOI: 10.1021/acs.biochem.7b00601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl hydroxylation is a very common post-translational modification and plays many roles in eukaryotes such as collagen stabilization, hypoxia sensing, and controlling protein transcription and translation. There is a growing body of evidence that suggests that prokaryotes contain prolyl 4-hydroxylases (P4Hs) homologous to the hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD) enzymes that act on elongation factor Tu (EFTu) and are likely involved in the regulation of bacterial translation. Recent biochemical and structural studies with a PHD from Pseudomonas putida (PPHD) determined that it forms a complex with EFTu and hydroxylates a prolyl residue of EFTu. Moreover, while animal, plant, and viral P4Hs act on peptidyl proline, most prokaryotic P4Hs have been known to target free l-proline; the exceptions include PPHD and a P4H from Bacillus anthracis (BaP4H) that modifies collagen-like proline-rich peptides. Here we use biophysical and mass spectrometric methods to demonstrate that BaP4H recognizes full-length BaEFTu and a BaEFTu 9-mer peptide for site-specific proline hydroxylation. Using size-exclusion chromatography coupled small-angle X-ray scattering (SEC-SAXS) and binding studies, we determined that BaP4H forms a 1:1 heterodimeric complex with BaEFTu. The SEC-SAXS studies reveal dissociation of BaP4H dimeric subunits upon interaction with BaEFTu. While BaP4H is unusual within bacteria in that it is structurally and functionally similar to the animal PHDs and collagen P4Hs, respectively, this work provides further evidence of its promiscuous substrate recognition. It is possible that the enzyme might have evolved to hydroxylate a universally conserved protein in prokaryotes, similar to the PHDs, and implies a functional role in B. anthracis.
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Affiliation(s)
- Nicholas J Schnicker
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mortezaali Razzaghi
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Sanjukta Guha Thakurta
- Department of Cell Biology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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10
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Fadouloglou VE, Balomenou S, Aivaliotis M, Kotsifaki D, Arnaouteli S, Tomatsidou A, Efstathiou G, Kountourakis N, Miliara S, Griniezaki M, Tsalafouta A, Pergantis SA, Boneca IG, Glykos NM, Bouriotis V, Kokkinidis M. Unusual α-Carbon Hydroxylation of Proline Promotes Active-Site Maturation. J Am Chem Soc 2017; 139:5330-5337. [DOI: 10.1021/jacs.6b12209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Stavroula Balomenou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Arnaouteli
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Anastasia Tomatsidou
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Giorgos Efstathiou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Miliara
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Marianna Griniezaki
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Aleka Tsalafouta
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Spiros A. Pergantis
- Department
of Chemistry, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Ivo G. Boneca
- Biology
and Genetics of the Bacterial Cell Wall Unit, Institut Pasteur, 75015 Paris, France
- INSERM, Equipe Avenir, Paris, France
| | - Nicholas M. Glykos
- Department
of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
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11
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Assembly of the elongated collagen prolyl 4-hydroxylase α2β2 heterotetramer around a central α2 dimer. Biochem J 2017; 474:751-769. [DOI: 10.1042/bcj20161000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/05/2017] [Accepted: 01/16/2017] [Indexed: 11/17/2022]
Abstract
Collagen prolyl 4-hydroxylase (C-P4H), an α2β2 heterotetramer, is a crucial enzyme for collagen synthesis. The α-subunit consists of an N-terminal dimerization domain, a central peptide substrate-binding (PSB) domain, and a C-terminal catalytic (CAT) domain. The β-subunit [also known as protein disulfide isomerase (PDI)] acts as a chaperone, stabilizing the functional conformation of C-P4H. C-P4H has been studied for decades, but its structure has remained elusive. Here, we present a three-dimensional small-angle X-ray scattering model of the entire human C-P4H-I heterotetramer. C-P4H is an elongated, bilobal, symmetric molecule with a length of 290 Å. The dimerization domains from the two α-subunits form a protein–protein dimer interface, assembled around the central antiparallel coiled-coil interface of their N-terminal α-helices. This region forms a thin waist in the bilobal tetramer. The two PSB/CAT units, each complexed with a PDI/β-subunit, form two bulky lobes pointing outward from this waist region, such that the PDI/β-subunits locate at the far ends of the βααβ complex. The PDI/β-subunit interacts extensively with the CAT domain. The asymmetric shape of two truncated C-P4H-I variants, also characterized in the present study, agrees with this assembly. Furthermore, data from these truncated variants show that dimerization between the α-subunits has an important role in achieving the correct PSB–CAT assembly competent for catalytic activity. Kinetic assays with various proline-rich peptide substrates and inhibitors suggest that, in the competent assembly, the PSB domain binds to the procollagen substrate downstream from the CAT domain.
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Schnicker NJ, Dey M. Structural analysis of cofactor binding for a prolyl 4-hydroxylase from the pathogenic bacteriumBacillus anthracis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:675-81. [DOI: 10.1107/s2059798316004198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/11/2016] [Indexed: 11/11/2022]
Abstract
The prolyl 4-hydroxylases (P4Hs) are mononuclear nonheme iron enzymes that catalyze the formation of 4R-hydroxyproline from many different substrates, with various biological implications. P4H is a key player in collagen accumulation, which has implications in fibrotic disorders. The stabilization of collagen triple-helical structureviaprolyl hydroxylation is the rate-limiting step in collagen biosynthesis, and therefore P4H has been extensively investigated as a potential therapeutic target of fibrotic disease. Understanding how these enzymes recognize cofactors and substrates is important and will aid in the future design of inhibitors of P4H. In this article, X-ray crystal structures of a metallocofactor- and α-ketoglutarate (αKG)-bound form of P4H fromBacillus anthracis(BaP4H) are reported. Structures of BaP4H were solved at 1.63 and 2.35 Å resolution and contained a cadmium ion and αKG bound in the active site. The αKG–Cd–BaP4H ternary complex reveals conformational changes of conserved residues upon the binding of metal ion and αKG, resulting in a closed active-site configuration required for dioxygen, substrate binding and catalysis.
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13
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Schnicker NJ, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Modifies Collagen-like Substrates in Asymmetric Patterns. J Biol Chem 2016; 291:13360-74. [PMID: 27129244 DOI: 10.1074/jbc.m116.725432] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 11/06/2022] Open
Abstract
Proline hydroxylation is the most prevalent post-translational modification in collagen. The resulting product trans-4-hydroxyproline (Hyp) is of critical importance for the stability and thus function of collagen, with defects leading to several diseases. Prolyl 4-hydroxylases (P4Hs) are mononuclear non-heme iron α-ketoglutarate (αKG)-dependent dioxygenases that catalyze Hyp formation. Although animal and plant P4Hs target peptidyl proline, prokaryotes have been known to use free l-proline as a precursor to form Hyp. The P4H from Bacillus anthracis (BaP4H) has been postulated to act on peptidyl proline in collagen peptides, making it unusual within the bacterial clade, but its true physiological substrate remains enigmatic. Here we use mass spectrometry, fluorescence binding, x-ray crystallography, and docking experiments to confirm that BaP4H recognizes and acts on peptidyl substrates but not free l-proline, using elements characteristic of an Fe(II)/αKG-dependent dioxygenases. We further show that BaP4H can hydroxylate unique peptidyl proline sites in collagen-derived peptides with asymmetric hydroxylation patterns. The cofactor-bound crystal structures of BaP4H reveal active site conformational changes that define open and closed forms and mimic "ready" and "product-released" states of the enzyme in the catalytic cycle. These results help to clarify the role of BaP4H as well as provide broader insights into human collagen P4H and proteins with poly-l-proline type II helices.
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Affiliation(s)
- Nicholas J Schnicker
- From the Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727
| | - Mishtu Dey
- From the Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727
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Longbotham JE, Levy C, Johannissen LO, Tarhonskaya H, Jiang S, Loenarz C, Flashman E, Hay S, Schofield CJ, Scrutton NS. Structure and Mechanism of a Viral Collagen Prolyl Hydroxylase. Biochemistry 2015; 54:6093-105. [PMID: 26368022 PMCID: PMC4613865 DOI: 10.1021/acs.biochem.5b00789] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The
Fe(II)- and 2-oxoglutarate (2-OG)-dependent dioxygenases comprise
a large and diverse enzyme superfamily the members of which have multiple
physiological roles. Despite this diversity, these enzymes share a
common chemical mechanism and a core structural fold, a double-stranded
β-helix (DSBH), as well as conserved active site residues. The
prolyl hydroxylases are members of this large superfamily. Prolyl
hydroxylases are involved in collagen biosynthesis and oxygen sensing
in mammalian cells. Structural–mechanistic studies with prolyl
hydroxylases have broader implications for understanding mechanisms
in the Fe(II)- and 2-OG-dependent dioxygenase superfamily. Here, we
describe crystal structures of an N-terminally truncated viral collagen
prolyl hydroxylase (vCPH). The crystal structure shows that vCPH contains
the conserved DSBH motif and iron binding active site residues of
2-OG oxygenases. Molecular dynamics simulations are used to delineate
structural changes in vCPH upon binding its substrate. Kinetic investigations
are used to report on reaction cycle intermediates and compare them
to the closest homologues of vCPH. The study highlights the utility
of vCPH as a model enzyme for broader mechanistic analysis of Fe(II)-
and 2-OG-dependent dioxygenases, including those of biomedical interest.
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Affiliation(s)
- James E Longbotham
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Colin Levy
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Linus O Johannissen
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Shuo Jiang
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christoph Loenarz
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sam Hay
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Nigel S Scrutton
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester , Manchester M1 7DN, United Kingdom
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15
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Yu Z, An B, Ramshaw JA, Brodsky B. Bacterial collagen-like proteins that form triple-helical structures. J Struct Biol 2014; 186:451-61. [DOI: 10.1016/j.jsb.2014.01.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/09/2014] [Accepted: 01/09/2014] [Indexed: 02/06/2023]
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16
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Characterization of BcaA, a putative classical autotransporter protein in Burkholderia pseudomallei. Infect Immun 2013; 81:1121-8. [PMID: 23340315 DOI: 10.1128/iai.01453-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Burkholderia pseudomallei is a tier 1 select agent, and the causative agent of melioidosis, a disease with effects ranging from chronic abscesses to fulminant pneumonia and septic shock, which can be rapidly fatal. Autotransporters (ATs) are outer membrane proteins belonging to the type V secretion system family, and many have been shown to play crucial roles in pathogenesis. The open reading frame Bp1026b_II1054 (bcaA) in B. pseudomallei strain 1026b is predicted to encode a classical autotransporter protein with an approximately 80-kDa passenger domain that contains a subtilisin-related domain. Immediately 3' to bcaA is Bp11026_II1055 (bcaB), which encodes a putative prolyl 4-hydroxylase. To investigate the role of these genes in pathogenesis, large in-frame deletion mutations of bcaA and bcaB were constructed in strain Bp340, an efflux pump mutant derivative of the melioidosis clinical isolate 1026b. Comparison of Bp340ΔbcaA and Bp340ΔbcaB mutants to wild-type B. pseudomallei in vitro demonstrated similar levels of adherence to A549 lung epithelial cells, but the mutant strains were defective in their ability to invade these cells and to form plaques. In a BALB/c mouse model of intranasal infection, similar bacterial burdens were observed after 48 h in the lungs and liver of mice infected with Bp340ΔbcaA, Bp340ΔbcaB, and wild-type bacteria. However, significantly fewer bacteria were recovered from the spleen of Bp340ΔbcaA-infected mice, supporting the idea of a role for this AT in dissemination or in survival in the passage from the site of infection to the spleen.
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17
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Mello LV, Rigden DJ. A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods. FEBS Lett 2012; 586:3908-13. [DOI: 10.1016/j.febslet.2012.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022]
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18
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Kundu S. Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases. BMC Res Notes 2012; 5:410. [PMID: 22862831 PMCID: PMC3475032 DOI: 10.1186/1756-0500-5-410] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/29/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The 2-oxoglutarate dependent superfamily is a diverse group of non-haem dioxygenases, and is present in prokaryotes, eukaryotes, and archaea. The enzymes differ in substrate preference and reaction chemistry, a factor that precludes their classification by homology studies and electronic annotation schemes alone. In this work, I propose and explore the rationale of using substrates to classify structurally similar alpha-ketoglutarate dependent enzymes. FINDINGS Differential catalysis in phylogenetic clades of 2-OG dependent enzymes, is determined by the interactions of a subset of active-site amino acids. Identifying these with existing computational methods is challenging and not feasible for all proteins. A clustering protocol based on validated mechanisms of catalysis of known molecules, in tandem with group specific hidden markov model profiles is able to differentiate and sequester these enzymes. Access to this repository is by a web server that compares user defined unknown sequences to these pre-defined profiles and outputs a list of predicted catalytic domains. The server is free and is accessible at the following URL (http://comp-biol.theacms.in/H2OGpred.html). CONCLUSIONS The proposed stratification is a novel attempt at classifying and predicting 2-oxoglutarate dependent function. In addition, the server will provide researchers with a tool to compare their data to a comprehensive list of HMM profiles of catalytic domains. This work, will aid efforts by investigators to screen and characterize putative 2-OG dependent sequences. The profile database will be updated at regular intervals.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Army College of Medical Sciences, Delhi Cantt., New Delhi 110010, India.
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19
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Xu Y, Brown KM, Wang ZA, van der Wel H, Teygong C, Zhang D, Blader IJ, West CM. The Skp1 protein from Toxoplasma is modified by a cytoplasmic prolyl 4-hydroxylase associated with oxygen sensing in the social amoeba Dictyostelium. J Biol Chem 2012; 287:25098-110. [PMID: 22648409 DOI: 10.1074/jbc.m112.355446] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In diverse types of organisms, cellular hypoxic responses are mediated by prolyl 4-hydroxylases that use O(2) and α-ketoglutarate as substrates to hydroxylate conserved proline residues in target proteins. Whereas in metazoans these enzymes control the stability of the HIFα family of transcription factor subunits, the Dictyostelium enzyme (DdPhyA) contributes to O(2) regulation of development by a divergent mechanism involving hydroxylation and subsequent glycosylation of DdSkp1, an adaptor subunit in E3(SCF) ubiquitin ligases. Sequences related to DdPhyA, DdSkp1, and the glycosyltransferases that cap Skp1 hydroxyproline occur also in the genomes of Toxoplasma and other protists, suggesting that this O(2) sensing mechanism may be widespread. Here we show by disruption of the TgphyA locus that this enzyme is required for Skp1 glycosylation in Toxoplasma and that disrupted parasites grow slowly at physiological O(2) levels. Conservation of cellular function was tested by expression of TgPhyA in DdphyA-null cells. Simple gene replacement did not rescue Skp1 glycosylation, whereas overexpression not only corrected Skp1 modification but also restored the O(2) requirement to a level comparable to that of overexpressed DdPhyA. Bacterially expressed TgPhyA protein can prolyl hydroxylate both Toxoplasma and Dictyostelium Skp1s. Kinetic analyses showed that TgPhyA has similar properties to DdPhyA, including a superimposable dependence on the concentration of its co-substrate α-ketoglutarate. Remarkably, however, TgPhyA had a significantly higher apparent affinity for O(2). The findings suggest that Skp1 hydroxylation by PhyA is a conserved process among protists and that this biochemical pathway may indirectly sense O(2) by detecting the levels of O(2)-regulated metabolites such as α-ketoglutarate.
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Affiliation(s)
- Yuechi Xu
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
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Mazmouz R, Chapuis-Hugon F, Pichon V, Méjean A, Ploux O. The Last Step of the Biosynthesis of the Cyanotoxins Cylindrospermopsin and 7-epi-Cylindrospermopsin is Catalysed by CyrI, a 2-Oxoglutarate-Dependent Iron Oxygenase. Chembiochem 2011; 12:858-62. [DOI: 10.1002/cbic.201000726] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Indexed: 11/11/2022]
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21
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Karamzadeh B, Kumar D, Sastry GN, de Visser SP. Steric Factors Override Thermodynamic Driving Force in Regioselectivity of Proline Hydroxylation by Prolyl-4-hydroxylase Enzymes. J Phys Chem A 2010; 114:13234-43. [DOI: 10.1021/jp1089855] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Baharan Karamzadeh
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India
| | - Devesh Kumar
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India
| | - G. Narahari Sastry
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India
| | - Sam P. de Visser
- The Manchester Interdisciplinary Biocenter and the School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom, and Molecular Modelling Group, Indian Institute of Chemical Technology, Hyderabad 500-607, India
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Abstract
Posttranslational modifications can cause profound changes in protein function. Typically, these modifications are reversible, and thus provide a biochemical on-off switch. In contrast, proline residues are the substrates for an irreversible reaction that is the most common posttranslational modification in humans. This reaction, which is catalyzed by prolyl 4-hydroxylase (P4H), yields (2S,4R)-4-hydroxyproline (Hyp). The protein substrates for P4Hs are diverse. Likewise, the biological consequences of prolyl hydroxylation vary widely, and include altering protein conformation and protein-protein interactions, and enabling further modification. The best known role for Hyp is in stabilizing the collagen triple helix. Hyp is also found in proteins with collagen-like domains, as well as elastin, conotoxins, and argonaute 2. A prolyl hydroxylase domain protein acts on the hypoxia inducible factor alpha, which plays a key role in sensing molecular oxygen, and could act on inhibitory kappaB kinase and RNA polymerase II. P4Hs are not unique to animals, being found in plants and microbes as well. Here, we review the enzymic catalysts of prolyl hydroxylation, along with the chemical and biochemical consequences of this subtle but abundant posttranslational modification.
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Affiliation(s)
- Kelly L Gorres
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
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