1
|
Bigiotti C, Bianconi E, Ruta L, Grottelli S, Coletti A, Dindo M, Carotti A, Cellini B, Macchiarulo A. Molecular Dynamics-Ensemble Docking and Biophysical Studies for Structure-Based Identification of Non-Amino Acidic Ligands of DDAH-1. J Chem Inf Model 2024; 64:6866-6879. [PMID: 39177258 DOI: 10.1021/acs.jcim.4c01150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Dimethylarginine dimethylaminohydrolase-1 (DDAH-1) accounts for the catabolism of the endogenous inhibitors of nitric oxide (NO) synthases, namely, ADMA (Nω,Nω-dimethyl-l-arginine) and NMMA (Nω-monomethyl-l-arginine). Inhibition of DDAH-1 may prove a therapeutic benefit in diseases associated with elevated nitric oxide (NO) levels by providing a tissue-specific increase of ADMA and NMMA. In this work, we have used molecular dynamics to generate a pool of DDAH-1 conformations in the apo and holo forms. Ensemble docking has been instrumental in screening an in-house fragment-based library of 824 compounds. Resulting virtual hits have been validated for their binding activity to recombinant human DDAH-1 using microscale thermophoresis (MST). As a key result, three non-amino acidic ligands of DDAH-1 (VIS212, VIS268, VIS726) are identified with higher binding efficiency index than ADMA. Amid these compounds, purpurogallin (VIS726) proves a potent ligand of DDAH-1, showing a mixed behavior of enzymatic inhibition in a biochemical assay. This finding widens the panel of known molecular targets of purpurogallin and provides clues into the molecular mechanisms of its cellular NO inhibition activity as well as its anti-inflammatory and neuroprotective effects.
Collapse
Affiliation(s)
- Carlo Bigiotti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Elisa Bianconi
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Luana Ruta
- Department of Experimental Medicine and Surgery, University of Perugia, P.le Gambuli, 06132 Perugia, Italy
| | - Silvia Grottelli
- Department of Experimental Medicine and Surgery, University of Perugia, P.le Gambuli, 06132 Perugia, Italy
| | - Alice Coletti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Mirco Dindo
- Department of Experimental Medicine and Surgery, University of Perugia, P.le Gambuli, 06132 Perugia, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Barbara Cellini
- Department of Experimental Medicine and Surgery, University of Perugia, P.le Gambuli, 06132 Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| |
Collapse
|
2
|
Tsikas D. Determination of equilibria constants of arginine:glycine amidinotransferase (AGAT)-catalyzed reactions using concentrations of circulating amino acids. Amino Acids 2023; 55:203-213. [PMID: 36477890 PMCID: PMC9950171 DOI: 10.1007/s00726-022-03218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022]
Abstract
Arginine:glycine amidinotransferase (AGAT) catalyzes mainly two reactions that generate 1) L-homoarginine (hArg) from L-arginine and L-lysine (Kharg) and 2) guanidinoacetate (GAA) and L-ornithine from L-arginine and glycine (Kgaa). Previously, we found that pharmacological treatment of Becker muscular dystrophy (BMD) patients with metformin or L-citrulline resulted in antidromic effects on serum hArg and GAA concentrations, seemingly acting as an inhibitor and effector of AGAT activity, respectively. Here, we used data of this study as a model to determine Kharg and Kgaa values by using the concentrations of the participating amino acids measured in serum samples of the BMD patients. The study aimed to prove the general utility of this approach to investigate effects of amino acids and drugs on AGAT-catalyzed reactions in vivo in humans.
Collapse
Affiliation(s)
- Dimitrios Tsikas
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.
| |
Collapse
|
3
|
Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
Collapse
Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| |
Collapse
|
4
|
Short-Term Supplementation of Sodium Nitrate vs. Sodium Chloride Increases Homoarginine Synthesis in Young Men Independent of Exercise. Int J Mol Sci 2022; 23:ijms231810649. [PMID: 36142560 PMCID: PMC9504822 DOI: 10.3390/ijms231810649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 02/07/2023] Open
Abstract
The aim of the study was to investigate the effects of short-term oral administration of inorganic nitrate (NaNO3; n = 8) or placebo (NaCl; n = 9) (each 0.1 mmol/kg body weight/d for 9 days) on plasma amino acids, creatinine, and oxidative stress in healthy young men. At baseline, the plasma concentrations of amino acids did not differ between the groups. At the end of the study, the plasma concentrations of homoarginine (hArg; by 24%, p = 0.0001), citrulline and ornithine (Cit/Orn; by 16%, p = 0.015), and glutamine/glutamate (Gln/Glu; by 6%, p = 0.0003) were higher in the NaNO3 group compared to the NaCl group. The plasma concentrations of sarcosine (Sarc; by 28%, p < 0.0001), tyrosine (by 14%, p = 0.0051), phenylalanine (by 8%, p = 0.0026), and tryptophan (by 8%, p = 0.0047) were lower in the NaNO3 group compared to the NaCl group. These results suggest that nitrate administration affects amino-acid metabolism. The arginine/glycine amidinotransferase (AGAT) catalyzes two reactions: (1) the formation of l-homoarginine (hArg) and l-ornithine (Orn) from l-arginine (Arg) and l-lysine (Lys): Arg + Lys <−> hArg + Orn, with equilibrium constant Kharg; (2) the formation of guanidinoacetate (GAA) and Orn from Arg and glycine (Gly): Arg + Gly <−> GAA + Orn, with equilibrium constant Kgaa. The plasma Kgaa/KhArg ratio was lower in the NaNO3 group compared to the NaCl group (1.57 vs. 2.02, p = 0.0034). Our study suggests that supplementation of inorganic nitrate increases the AGAT-catalyzed synthesis of hArg and decreases the N-methyltransferase-catalyzed synthesis of GAA, the precursor of creatine. To our knowledge, this is the first study to demonstrate elevation of hArg synthesis by inorganic nitrate supplementation. Remarkably, an increase of 24% corresponds to the synthesis capacity of one kidney in healthy humans. Differences in the association between plasma concentrations of amino acids in the NaNO3 and NaCl groups suggest changes in amino-acid homeostasis. Plasma concentrations of the oxidative stress marker malondialdehyde (MDA) did not change after supplementation of NaNO3 or NaCl over the whole exercise time range. Plasma nitrite concentration turned out to be a more discriminant marker of NaNO3 ingestion than plasma nitrate (area under the receiver operating characteristic curve: 0.951 vs. 0.866, p < 0.0001 each).
Collapse
|
5
|
(De)Activation (Ir)Reversibly or Degradation: Dynamics of Post-Translational Protein Modifications in Plants. Life (Basel) 2022; 12:life12020324. [PMID: 35207610 PMCID: PMC8874572 DOI: 10.3390/life12020324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
The increasing dynamic functions of post-translational modifications (PTMs) within protein molecules present outstanding challenges for plant biology even at this present day. Protein PTMs are among the first and fastest plant responses to changes in the environment, indicating that the mechanisms and dynamics of PTMs are an essential area of plant biology. Besides being key players in signaling, PTMs play vital roles in gene expression, gene, and protein localization, protein stability and interactions, as well as enzyme kinetics. In this review, we take a broader but concise approach to capture the current state of events in the field of plant PTMs. We discuss protein modifications including citrullination, glycosylation, phosphorylation, oxidation and disulfide bridges, N-terminal, SUMOylation, and ubiquitination. Further, we outline the complexity of studying PTMs in relation to compartmentalization and function. We conclude by challenging the proteomics community to engage in holistic approaches towards identification and characterizing multiple PTMs on the same protein, their interaction, and mechanism of regulation to bring a deeper understanding of protein function and regulation in plants.
Collapse
|
6
|
Cummings TFM, Gori K, Sanchez-Pulido L, Gavriilidis G, Moi D, Wilson AR, Murchison E, Dessimoz C, Ponting CP, Christophorou MA. Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria. Mol Biol Evol 2021; 39:6420225. [PMID: 34730808 PMCID: PMC8826395 DOI: 10.1093/molbev/msab317] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Protein posttranslational modifications add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms, and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologs. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than 1 billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared with products of likely endosymbiont gene transfer, mitochondrial proteins, and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.
Collapse
Affiliation(s)
- Thomas F M Cummings
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom,Corresponding authors: E-mails: ;
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Gavriil Gavriilidis
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - David Moi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail R Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Elizabeth Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, Cambridge, United Kingdom
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland,Department of Genetics Evolution and Environment, University College London, London, United Kingdom,Department of Computer Science, University College London, London, United Kingdom
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Maria A Christophorou
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom,Epigenetics Department, The Babraham Institute, Cambridge, United Kingdom,Corresponding authors: E-mails: ;
| |
Collapse
|
7
|
Liu C, Hashimoto J, Kudo K, Shin-Ya K, Kakeya H. An Atypical Arginine Dihydrolase Involved in the Biosynthesis of Cyclic Hexapeptide Longicatenamides. Chem Asian J 2021; 16:1382-1387. [PMID: 33886165 DOI: 10.1002/asia.202100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/02/2021] [Indexed: 11/07/2022]
Abstract
The incorporation of non-proteinogenic amino acids (NPAAs) enriches the structural diversity of nonribosomal peptides. Recently, four NPAA-containing cyclic hexapeptides, longicatenamides A-D, were isolated using a combined-culture strategy. Based on in silico analysis, we discovered their putative biosynthetic gene cluster (lon) and proposed a possible biosynthetic mechanism. Surprisingly, the lon22 gene encodes an atypical arginine dihydrolase, which can also catalyze the hydrolysis of citrulline to ornithine. Phylogenetic analysis showed that Lon22-like proteins form a novel clade that is separated from other guanidine-modifying enzymes. After rational design, the catalytic efficiencies of a Lon22 Y80F mutant for arginine and citrulline substrates were 2.31- and 4.70-fold that of the wild-type (WT), respectively. In addition, characterization of the Lon20-A4 adenylation domain suggested that it can incorporate both ornithine and lysine into the final products.
Collapse
Affiliation(s)
- Chao Liu
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kei Kudo
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku, Kyoto, 606-8501, Japan
| |
Collapse
|
8
|
Marondedze C, Elia G, Thomas L, Wong A, Gehring C. Citrullination of Proteins as a Specific Response Mechanism in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:638392. [PMID: 33897727 PMCID: PMC8060559 DOI: 10.3389/fpls.2021.638392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/17/2021] [Indexed: 05/19/2023]
Abstract
Arginine deimination, also referred to as citrullination of proteins by L-arginine deiminases, is a post-translational modification affecting histone modifications, epigenetic transcriptional regulation, and proteolysis in animals but has not been reported in higher plants. Here we report, firstly, that Arabidopsis thaliana proteome contains proteins with a specific citrullination signature and that many of the citrullinated proteins have nucleotide-binding regulatory functions. Secondly, we show that changes in the citrullinome occur in response to cold stress, and thirdly, we identify an A. thaliana protein with peptidyl arginine deiminase activity that was shown to be calcium-dependent for many peptide substrates. Taken together, these findings establish this post-translational modification as a hitherto neglected component of cellular reprogramming during stress responses.
Collapse
Affiliation(s)
- Claudius Marondedze
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Rijk Zwaan, De Lier, Netherlands
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Gweru, Zimbabwe
- Claudius Marondedze,
| | - Giuliano Elia
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Ludivine Thomas
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center of Wenzhou-Kean University, Wenzhou, China
| | - Chris Gehring
- Division of Biological and Chemical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
- *Correspondence: Chris Gehring,
| |
Collapse
|
9
|
Harris LA, Saint-Vincent PMB, Guo X, Hudson GA, DiCaprio AJ, Zhu L, Mitchell DA. Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases. ACS Chem Biol 2020; 15:3167-3175. [PMID: 33249828 DOI: 10.1021/acschembio.0c00685] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products defined by a genetically encoded precursor peptide that is processed by associated biosynthetic enzymes to form the mature product. Lasso peptides are a class of RiPP defined by an isopeptide linkage between the N-terminal amine and an internal Asp/Glu residue with the C-terminal sequence threaded through the macrocycle. This unique lariat topology, which typically provides considerable stability toward heat and proteases, has stimulated interest in lasso peptides as potential therapeutics. Post-translational modifications beyond the class-defining, threaded macrolactam have been reported, including one example of Arg deimination to yield citrulline (Cit). Although a Cit-containing lasso peptide (i.e., citrulassin) was serendipitously discovered during a genome-guided campaign, the gene(s) responsible for Arg deimination has remained unknown. Herein, we describe the use of reactivity-based screening to discriminate bacterial strains that produce Arg- versus Cit-bearing citrulassins, yielding 13 new lasso peptide variants. Partial phylogenetic profiling identified a distally encoded peptidyl arginine deiminase (PAD) gene ubiquitous to the Cit-containing variants. Absence of this gene correlated strongly with lasso peptide variants only containing Arg (i.e., des-citrulassin). Heterologous expression of the PAD gene in a des-citrulassin producer resulted in the production of the deiminated analog, confirming PAD involvement in Arg deimination. The PADs were then bioinformatically surveyed to provide a deeper understanding of their taxonomic distribution and genomic contexts and to facilitate future studies that will evaluate any additional biochemical roles for the superfamily.
Collapse
|
10
|
Lee H, Rhee S. Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacterium Anabaena. J Biol Chem 2020; 295:5751-5760. [PMID: 32198136 PMCID: PMC7186175 DOI: 10.1074/jbc.ra120.012768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/17/2020] [Indexed: 01/07/2023] Open
Abstract
In cyanobacteria, metabolic pathways that use the nitrogen-rich amino acid arginine play a pivotal role in nitrogen storage and mobilization. The N-terminal domains of two recently identified bacterial enzymes: ArgZ from Synechocystis and AgrE from Anabaena, have been found to contain an arginine dihydrolase. This enzyme provides catabolic activity that converts arginine to ornithine, resulting in concomitant release of CO2 and ammonia. In Synechocystis, the ArgZ-mediated ornithine-ammonia cycle plays a central role in nitrogen storage and remobilization. The C-terminal domain of AgrE contains an ornithine cyclodeaminase responsible for the formation of proline from ornithine and ammonia production, indicating that AgrE is a bifunctional enzyme catalyzing two sequential reactions in arginine catabolism. Here, the crystal structures of AgrE in three different ligation states revealed that it has a tetrameric conformation, possesses a binding site for the arginine dihydrolase substrate l-arginine and product l-ornithine, and contains a binding site for the coenzyme NAD(H) required for ornithine cyclodeaminase activity. Structure-function analyses indicated that the structure and catalytic mechanism of arginine dihydrolase in AgrE are highly homologous with those of a known bacterial arginine hydrolase. We found that in addition to other active-site residues, Asn-71 is essential for AgrE's dihydrolase activity. Further analysis suggested the presence of a passage for substrate channeling between the two distinct AgrE active sites, which are situated ∼45 Å apart. These results provide structural and functional insights into the bifunctional arginine dihydrolase-ornithine cyclodeaminase enzyme AgrE required for arginine catabolism in Anabaena.
Collapse
Affiliation(s)
- Haehee Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
| |
Collapse
|
11
|
Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism. J Biol Chem 2020; 295:2113-2124. [PMID: 31914412 PMCID: PMC7029115 DOI: 10.1074/jbc.ra119.011752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/24/2019] [Indexed: 01/07/2023] Open
Abstract
A recently discovered ornithine-ammonia cycle (OAC) serves as a conduit in the nitrogen storage and remobilization machinery in cyanobacteria. The OAC involves an arginine catabolic reaction catalyzed by the arginine dihydrolase ArgZ whose catalytic mechanism is unknown. Here we determined the crystal structures at 1.2-3.0 Å of unliganded ArgZ from the cyanobacterium Synechocystis sp. PCC6803 and of ArgZ complexed with its substrate arginine, a covalently linked reaction intermediate, or the reaction product ornithine. The structures reveal that a key residue, Asn71, in the ArgZ active center functions as the determinant distinguishing ArgZ from other members of the guanidino group-modifying enzyme superfamily. The structures, along with biochemical evidence from enzymatic assays coupled with electrospray ionization MS techniques, further suggest that ArgZ-catalyzed conversion of arginine to ornithine, ammonia, and carbon dioxide consists of two successive cycles of amine hydrolysis. Finally, we show that arginine dihydrolases are broadly distributed among bacteria and metazoans, suggesting that the OAC may be frequently used for redistribution of nitrogen from arginine catabolism or nitrogen fixation.
Collapse
|
12
|
Lassak J, Koller F, Krafczyk R, Volkwein W. Exceptionally versatile – arginine in bacterial post-translational protein modifications. Biol Chem 2019; 400:1397-1427. [DOI: 10.1515/hsz-2019-0182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/01/2019] [Indexed: 12/24/2022]
Abstract
Abstract
Post-translational modifications (PTM) are the evolutionary solution to challenge and extend the boundaries of genetically predetermined proteomic diversity. As PTMs are highly dynamic, they also hold an enormous regulatory potential. It is therefore not surprising that out of the 20 proteinogenic amino acids, 15 can be post-translationally modified. Even the relatively inert guanidino group of arginine is subject to a multitude of mostly enzyme mediated chemical changes. The resulting alterations can have a major influence on protein function. In this review, we will discuss how bacteria control their cellular processes and develop pathogenicity based on post-translational protein-arginine modifications.
Collapse
Affiliation(s)
- Jürgen Lassak
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Franziska Koller
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| | - Wolfram Volkwein
- Center for Integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology , Ludwig-Maximilians-Universität München , Grosshaderner Strasse 2-4 , D-82152 Planegg , Germany
| |
Collapse
|
13
|
Sekula B, Dauter Z. Structural Study of Agmatine Iminohydrolase From Medicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:320. [PMID: 30984210 PMCID: PMC6447857 DOI: 10.3389/fpls.2019.00320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/27/2019] [Indexed: 05/27/2023]
Abstract
Plants are unique eukaryotes that can produce putrescine (PUT), a basic diamine, from arginine via a three-step pathway. This process starts with arginine decarboxylase that converts arginine to agmatine. Then, the consecutive action of two hydrolytic enzymes, agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase, ultimately produces PUT. An alternative route of PUT biosynthesis requires ornithine decarboxylase that catalyzes direct putrescine biosynthesis. However, some plant species lack this enzyme and rely only on agmatine pathway. The scope of this manuscript concerns the structural characterization of AIH from the model legume plant, Medicago truncatula. MtAIH is a homodimer built of two subunits with a characteristic propeller fold, where five αββαβ repeated units are arranged around the fivefold pseudosymmetry axis. Dimeric assembly of this plant AIH, formed by interactions of conserved structural elements from one repeat, is drastically different from that observed in dimeric bacterial AIHs. Additionally, the structural snapshot of MtAIH in complex with 6-aminohexanamide, the reaction product analog, presents the conformation of the enzyme during catalysis. Our structural results show that MtAIH undergoes significant structural rearrangements of the long loop, which closes a tunnel-shaped active site over the course of the catalytic event. This conformational change is also observed in AIH from Arabidopsis thaliana, indicating the importance of the closed conformation of the gate-keeping loop for the catalysis of plant AIHs.
Collapse
Affiliation(s)
- Bartosz Sekula
- Synchrotron Radiation Research Section of Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL, United States
| | | |
Collapse
|
14
|
El-Sayed ASA, Shindia AA, AbouZaid AA, Yassin AM, Ali GS, Sitohy MZ. Biochemical characterization of peptidylarginine deiminase-like orthologs from thermotolerant Emericella dentata and Aspergillus nidulans. Enzyme Microb Technol 2019; 124:41-53. [PMID: 30797478 DOI: 10.1016/j.enzmictec.2019.02.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
Abstract
Peptidylarginine deiminases (PADs) are a group of hydrolases, mediating the deimination of peptidylarginine residues into peptidyl-citrulline. Equivocal protein citrullination by PADs of fungal pathogens has a strong relation to the progression of multiple human diseases, however, the biochemical properties of fungal PADs remain ambiguous. Thus, this is the first report exploring the molecular properties of PAD from thermotolerant fungi, to imitate the human temperature. The teleomorph Emericella dentata and anamorph Aspergillus nidulans have been morphologically and molecularly identified, with observed robust growth at 37-40 °C, and strong PAD productivity. The physiological profiles of E. dentata and A. nidulans for PADs production in response to carbon, nitrogen sources, initial medium pH and incubation temperature were relatively identical, emphasizing the taxonomical proximity of these fungal isolates. PADs were purified from E. dentata and A. nidulans with apparent molecular masses 41 and 48 kDa, respectively. The peptide fingerprints of PADs from E. dentata and A. nidulans have been analyzed by MALDI-TOF/MS, displaying a higher sequence similarity to human PAD4 by 18% and 31%, respectively. The conserved peptide sequences of E. dentata and A. nidulans PADs displayed a higher similarity to human PAD than A. fumigatus PADs clade. PADs from both fungal isolates have an optimum pH and pH stability at 7.0-8.0, with putative pI 5.0-5.5, higher structural denaturation at pH 4.0-5.5 and 9.5-12 as revealed from absorbance at λ280nm. E. dentata PAD had a higher conformationally thermal stability than A. nidulans PAD as revealed from its lower Kr value. From the proteolytic mapping, the orientation of trypsinolytic recognition sites on the PADs surface from both fungal isolates was very similar. PADs from both isolates are calcium dependent, with participation of serine and cysteine residues on their catalytic sites. PADs displayed a higher affinity to deiminate the peptidylarginine residues with a feeble affinity to work as ADI. So, PADs from E. dentata and A. nidulans had a relatively similar conformational and kinetic properties. Further molecular modeling analysis are ongoing to explore the role of PADs in citrullination of human proteins in Aspergillosis, that will open a new avenue for unraveling the vague of protein-protein interaction of human A. nidulans pathogen.
Collapse
Affiliation(s)
- Ashraf S A El-Sayed
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
| | - Ahmed A Shindia
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Azza A AbouZaid
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Amany M Yassin
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Gul Shad Ali
- MREC, Department of Plant Pathology, University of Florida, Florida, 32703, USA
| | - Mahmoud Z Sitohy
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| |
Collapse
|
15
|
Ying TC, Ibrahim Z, Rahman MBA, Tejo BA. Structure-Based Design of Peptide Inhibitors for Protein Arginine Deiminase Type IV (PAD4). ENCYCLOPEDIA OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2019:729-740. [DOI: 10.1016/b978-0-12-809633-8.20156-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
16
|
Schardon CL, Tuley A, Er JAV, Swartzel JC, Fast W. Selective Covalent Protein Modification by 4-Halopyridines through Catalysis. Chembiochem 2017; 18:1551-1556. [PMID: 28470883 DOI: 10.1002/cbic.201700104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Indexed: 12/12/2022]
Abstract
We have investigated 4-halopyridines as selective, tunable, and switchable covalent protein modifiers for use in the development of chemical probes. Nonenzymatic reactivity of 4-chloropyridine with amino acids and thiols was ranked with respect to common covalent protein-modifying reagents and found to have reactivity similar to that of acrylamide, but could be switched to a reactivity similar to that of iodoacetamide upon stabilization of the positively charged pyridinium. Diverse, fragment-sized 4-halopyridines inactivated human dimethylarginine dimethylaminohydrolase-1 (DDAH1) through covalent modification of the active site cysteine, acting as quiescent affinity labels that required off-pathway catalysis through stabilization of the protonated pyridinium by a neighboring aspartate residue. A series of 2-fluoromethyl-substituted 4-chloropyridines demonstrated that the pKa and kinact /KI values could be predictably varied over several orders of magnitude. Covalent labeling of proteins in an Escherichia coli lysate was shown to require folded proteins, indicating that alternative proteins can be targeted, and modification is likely to be catalysisdependent. 4-Halopyridines, and quiescent affinity labels in general, represent an attractive strategy to develop reagents with switchable electrophilicity as selective covalent protein modifiers.
Collapse
Affiliation(s)
| | - Alfred Tuley
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX, 78712, USA
| | - Joyce A V Er
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX, 78712, USA
| | - Jake C Swartzel
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX, 78712, USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX, 78712, USA.,LaMontagne Center for Infectious Disease, The University of Texas, Austin, TX, 78712, USA
| |
Collapse
|
17
|
Abstract
The post-translational modification of arginine residues represents a key mechanism for the epigenetic control of gene expression. Aberrant levels of histone arginine modifications have been linked to the development of several diseases including cancer. In recent years, great progress has been made in understanding the physiological role of individual arginine modifications and their effects on chromatin function. The present review aims to summarize the structural and functional aspects of histone arginine modifying enzymes and their impact on gene transcription. We will discuss the potential for targeting these proteins with small molecules in a variety of disease states.
Collapse
Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Paul R. Thompson
- Department
of Biochemistry and Molecular Pharmacology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
- Program
in Chemical Biology, UMass Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, United States
| |
Collapse
|
18
|
Fuhrmann J, Clancy K, Thompson PR. Chemical biology of protein arginine modifications in epigenetic regulation. Chem Rev 2015; 115:5413-61. [PMID: 25970731 PMCID: PMC4463550 DOI: 10.1021/acs.chemrev.5b00003] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Kathleen
W. Clancy
- Department of Biochemistry and Molecular Pharmacology and Program in Chemical
Biology, University of Massachusetts Medical
School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| | - Paul R. Thompson
- Department of Biochemistry and Molecular Pharmacology and Program in Chemical
Biology, University of Massachusetts Medical
School, 364 Plantation
Street, Worcester, Massachusetts 01605, United States
| |
Collapse
|
19
|
Lewis HD, Liddle J, Coote JE, Atkinson SJ, Barker MD, Bax BD, Bicker KL, Bingham RP, Campbell M, Chen YH, Chung CW, Craggs PD, Davis RP, Eberhard D, Joberty G, Lind KE, Locke K, Maller C, Martinod K, Patten C, Polyakova O, Rise CE, Rüdiger M, Sheppard RJ, Slade DJ, Thomas P, Thorpe J, Yao G, Drewes G, Wagner DD, Thompson PR, Prinjha RK, Wilson DM. Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation. Nat Chem Biol 2015; 11:189-91. [PMID: 25622091 PMCID: PMC4397581 DOI: 10.1038/nchembio.1735] [Citation(s) in RCA: 458] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 12/01/2014] [Indexed: 01/13/2023]
Abstract
PAD4 has been strongly implicated in the pathogenesis of autoimmune, cardiovascular and oncological diseases, through clinical genetics and gene disruption in mice. Novel, selective PAD4 inhibitors binding to a calcium-deficient form of the PAD4 enzyme have, for the first time, validated the critical enzymatic role of human and mouse PAD4 in both histone citrullination and neutrophil extracellular trap formation. The therapeutic potential of PAD4 inhibitors can now be explored.
Collapse
Affiliation(s)
- Huw D Lewis
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - John Liddle
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Jim E Coote
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Stephen J Atkinson
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Michael D Barker
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Benjamin D Bax
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Kevin L Bicker
- Department of Chemistry, Scripps Florida, The Scripps Research Institute, Jupiter, Florida, USA
| | - Ryan P Bingham
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Matthew Campbell
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Yu Hua Chen
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Chun-Wa Chung
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Peter D Craggs
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Rob P Davis
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | | | | | - Kenneth E Lind
- ELT Boston, Platform Technology and Science, GlaxoSmithKline, Waltham, Massachusetts, USA
| | - Kelly Locke
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Claire Maller
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Kimberly Martinod
- 1] Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA. [2] Immunology Graduate Program, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Chris Patten
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Oxana Polyakova
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Cecil E Rise
- ELT Boston, Platform Technology and Science, GlaxoSmithKline, Waltham, Massachusetts, USA
| | - Martin Rüdiger
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Robert J Sheppard
- 1] EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK. [2] AstraZeneca, Oncology iMed, Cambridge Science Park, Cambridge, UK (R.J.S. and D.M.W.); Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA (D.J.S.); University of Massachussetts Medical School, Worcester, Massachusetts, USA (P.R.T.)
| | - Daniel J Slade
- 1] Department of Chemistry, Scripps Florida, The Scripps Research Institute, Jupiter, Florida, USA. [2] AstraZeneca, Oncology iMed, Cambridge Science Park, Cambridge, UK (R.J.S. and D.M.W.); Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA (D.J.S.); University of Massachussetts Medical School, Worcester, Massachusetts, USA (P.R.T.)
| | - Pamela Thomas
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Jim Thorpe
- Molecular Discovery Research, GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - Gang Yao
- ELT Boston, Platform Technology and Science, GlaxoSmithKline, Waltham, Massachusetts, USA
| | | | - Denisa D Wagner
- 1] Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul R Thompson
- 1] Department of Chemistry, Scripps Florida, The Scripps Research Institute, Jupiter, Florida, USA. [2] AstraZeneca, Oncology iMed, Cambridge Science Park, Cambridge, UK (R.J.S. and D.M.W.); Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA (D.J.S.); University of Massachussetts Medical School, Worcester, Massachusetts, USA (P.R.T.)
| | - Rab K Prinjha
- EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK
| | - David M Wilson
- 1] EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK. [2] AstraZeneca, Oncology iMed, Cambridge Science Park, Cambridge, UK (R.J.S. and D.M.W.); Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA (D.J.S.); University of Massachussetts Medical School, Worcester, Massachusetts, USA (P.R.T.)
| |
Collapse
|
20
|
Dreyton CJ, Knuckley B, Jones JE, Lewallen DM, Thompson PR. Mechanistic studies of protein arginine deiminase 2: evidence for a substrate-assisted mechanism. Biochemistry 2014; 53:4426-33. [PMID: 24989433 PMCID: PMC4100781 DOI: 10.1021/bi500554b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Citrullination, which is catalyzed
by protein arginine deiminases
(PADs 1–4 and 6), is a post-translational modification (PTM)
that effectively neutralizes the positive charge of a guanidinium
group by its replacement with a neutral urea. Given the sequence similarity
of PAD2 across mammalian species and the genomic organization of the
PAD2 gene, PAD2 is predicted to be the ancestral homologue of the
PADs. Although PAD2 has long been known to play a role in myelination,
it has only recently been linked to other cellular processes, including
gene transcription and macrophage extracellular trap formation. For
example, PAD2 deiminates histone H3 at R26, and this PTM leads to
the increased transcription of more than 200 genes under the control
of the estrogen receptor. Given that our understanding of PAD2 biology
remains incomplete, we initiated mechanistic studies on this enzyme
to aid the development of PAD2-specific inhibitors. Herein, we report
that the substrate specificity and calcium dependence of PAD2 are
similar to those of PADs 1, 3, and 4. However, unlike those isozymes,
PAD2 appears to use a substrate-assisted mechanism of catalysis in
which the positively charged substrate guanidinium depresses the pKa of the nucleophilic cysteine. By contrast,
PADs 1, 3, and 4 use a reverse-protonation mechanism. These mechanistic
differences will aid the development of isozyme-specific inhibitors.
Collapse
Affiliation(s)
- Christina J Dreyton
- Department of Chemistry and The Kellogg School of Graduate Studies, The Scripps Research Institute-Florida , 130 Scripps Way, Jupiter, Florida 33458, United States
| | | | | | | | | |
Collapse
|
21
|
Ammerman ML, Tomasello DL, Faktorová D, Kafková L, Hashimi H, Lukeš J, Read LK. A core MRB1 complex component is indispensable for RNA editing in insect and human infective stages of Trypanosoma brucei. PLoS One 2013; 8:e78015. [PMID: 24250748 PMCID: PMC3820961 DOI: 10.1371/journal.pone.0078015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/11/2013] [Indexed: 11/18/2022] Open
Abstract
Uridine insertion/deletion RNA editing is a unique and vital process in kinetoplastids, required for creation of translatable open reading frames in most mitochondrially-encoded RNAs. Emerging as a key player in this process is the mitochondrial RNA binding 1 (MRB1) complex. MRB1 comprises an RNA-independent core complex of at least six proteins, including the GAP1/2 guide RNA (gRNA) binding proteins. The core interacts in an RNA-enhanced or -dependent manner with imprecisely defined TbRGG2 subcomplexes, Armadillo protein MRB10130, and additional factors that comprise the dynamic MRB1 complex. Towards understanding MRB1 complex function in RNA editing, we present here functional characterization of the pentein domain-containing MRB1 core protein, MRB11870. Inducible RNAi studies demonstrate that MRB11870 is essential for proliferation of both insect vector and human infective stage T. brucei. MRB11870 ablation causes a massive defect in RNA editing, affecting both pan-edited and minimally edited mRNAs, but does not substantially affect mitochondrial RNA stability or processing of precursor transcripts. The editing defect in MRB1-depleted cells occurs at the initiation stage of editing, as pre-edited mRNAs accumulate. However, the gRNAs that direct editing remain abundant in the knockdown cells. To examine the contribution of MRB11870 to MRB1 macromolecular interactions, we tagged core complexes and analyzed their composition and associated proteins in the presence and absence of MRB11870. These studies demonstrated that MRB11870 is essential for association of GAP1/2 with the core, as well as for interaction of the core with other proteins and subcomplexes. Together, these data support a model in which the MRB1 core mediates functional interaction of gRNAs with the editing machinery, having GAP1/2 as its gRNA binding constituents. MRB11870 is a critical component of the core, essential for its structure and function.
Collapse
Affiliation(s)
- Michelle L. Ammerman
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Danielle L. Tomasello
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Center, Czech Academy of Sciences and Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Lucie Kafková
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
| | - Hassan Hashimi
- Institute of Parasitology, Biology Center, Czech Academy of Sciences and Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences and Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Laurie K. Read
- Department of Microbiology and Immunology, University at Buffalo School of Medicine, Buffalo, New York, United States of America
- * E-mail:
| |
Collapse
|
22
|
Semimicroscopic investigation of active site pK a values in peptidylarginine deiminase 4. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1293-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
23
|
Johnson CM, Monzingo AF, Ke Z, Yoon DW, Linsky TW, Guo H, Robertus JD, Fast W. On the mechanism of dimethylarginine dimethylaminohydrolase inactivation by 4-halopyridines. J Am Chem Soc 2011; 133:10951-9. [PMID: 21630706 PMCID: PMC3135753 DOI: 10.1021/ja2033684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules capable of selective covalent protein modification are of significant interest for the development of biological probes and therapeutics. We recently reported that 2-methyl-4-bromopyridine is a quiescent affinity label for the nitric oxide controlling enzyme dimethylarginine dimethylaminohydrolase (DDAH) (Johnson, C. M.; Linsky, T. W.; Yoon, D. W.; Person, M. D.; Fast, W. J. Am. Chem. Soc. 2011, 133, 1553-1562). Discovery of this novel protein modifier raised the possibility that the 4-halopyridine motif may be suitable for wider application. Therefore, the inactivation mechanism of the related compound 2-hydroxymethyl-4-chloropyridine is probed here in more detail. Solution studies support an inactivation mechanism in which the active site Asp66 residue stabilizes the pyridinium form of the inactivator, which has enhanced reactivity toward the active site Cys, resulting in covalent bond formation, loss of the halide, and irreversible inactivation. A 2.18 Å resolution X-ray crystal structure of the inactivated complex elucidates the orientation of the inactivator and its covalent attachment to the active site Cys, but the structural model does not show an interaction between the inactivator and Asp66. Molecular modeling is used to investigate inactivator binding, reaction, and also a final pyridinium deprotonation step that accounts for the apparent differences between the solution-based and structural studies with respect to the role of Asp66. This work integrates multiple approaches to elucidate the inactivation mechanism of a novel 4-halopyridine "warhead," emphasizing the strategy of using pyridinium formation as a "switch" to enhance reactivity when bound to the target protein.
Collapse
Affiliation(s)
| | | | | | | | | | - Hua Guo
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| | - Jon D. Robertus
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| | - Walter Fast
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| |
Collapse
|
24
|
Guo Q, Bedford MT, Fast W. Discovery of peptidylarginine deiminase-4 substrates by protein array: antagonistic citrullination and methylation of human ribosomal protein S2. MOLECULAR BIOSYSTEMS 2011; 7:2286-95. [PMID: 21584310 PMCID: PMC3251905 DOI: 10.1039/c1mb05089c] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Peptidylarginine deiminase (PAD) catalyzes the posttranslational citrullination of selected proteins in a calcium dependent manner. The PAD4 isoform has been implicated in multiple sclerosis, rheumatoid arthritis, some types of cancer, and plays a role in gene regulation. However, the substrate selectivity of PAD4 is not well defined, nor is the impact of citrullination on many other pathways. Here, a high-density protein array is used as a primary screen to identify 40 previously unreported PAD4 substrates, 10 of which are selected and verified in a cell lysate-based secondary assay. One of the most prominent hits, human 40S ribosomal protein S2 (RPS2), is characterized in detail. PAD4 citrullinates the Arg-Gly repeat region of RPS2, which is also an established site for Arg methylation by protein arginine methyltransferase 3 (PRMT3). As in other systems, crosstalk is observed; citrullination and methylation modifications are found to be antagonistic to each other, suggesting a conserved posttranslational regulatory strategy. Both PAD4 and PRMT3 are found to co-sediment with the free 40S ribosomal subunit fraction from cell extracts. These findings are consistent with participation of citrullination in the regulation of RPS2 and ribosome assembly. This application of protein arrays to reveal new PAD4 substrates suggests a role for citrullination in a number of different cellular pathways.
Collapse
Affiliation(s)
- Qin Guo
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Mark T. Bedford
- Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Walter Fast
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| |
Collapse
|
25
|
Almonacid DE, Babbitt PC. Toward mechanistic classification of enzyme functions. Curr Opin Chem Biol 2011; 15:435-42. [PMID: 21489855 DOI: 10.1016/j.cbpa.2011.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 11/15/2022]
Abstract
Classification of enzyme function should be quantitative, computationally accessible, and informed by sequences and structures to enable use of genomic information for functional inference and other applications. Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often converge to similar mechanisms too, suggesting that reaction mechanisms could be used to develop finer-grained functional descriptions than provided by the Enzyme Commission (EC) system currently in use. Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic similarities. Together, these provide a foundation for new classifications of enzyme function.
Collapse
Affiliation(s)
- Daniel E Almonacid
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, CA 94158, USA
| | | |
Collapse
|
26
|
Ke Z, Guo H. Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophile. J Phys Chem B 2011; 115:3725-33. [PMID: 21395290 PMCID: PMC3070061 DOI: 10.1021/jp200843s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first step of the hydrolytic deimination of L-arginine catalyzed by arginine deiminase is examined using ab initio quantum mechanical/molecular mechanical molecular dynamics simulations. Two possible protonation states of the nucleophilic Cys406 residue were investigated, and the corresponding activation free energies were obtained via umbrella sampling. Our calculations indicated a reaction free-energy barrier of 21.3 kcal/mol for the neutral cysteine, which is in reasonably good agreement with the experimental k(cat) value of 6.3 s(-1), i.e., a barrier of 16.7 kcal/mol. On the other hand, the deprotonated Cys nucleophile yields a free-energy barrier of 6.7 kcal/mol, much lower than the experimental result. The reaction free-energy barriers along with other data suggest that the Cys nucleophile is dominated by its protonated state in the Michaelis complex, and the reaction barrier corresponds largely to its deprotonation.
Collapse
Affiliation(s)
- Zhihong Ke
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, 87131
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, 87131
| |
Collapse
|
27
|
Johnson CM, Linsky TW, Yoon DW, Person MD, Fast W. Discovery of halopyridines as quiescent affinity labels: inactivation of dimethylarginine dimethylaminohydrolase. J Am Chem Soc 2011; 133:1553-62. [PMID: 21222447 DOI: 10.1021/ja109207m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an effort to develop novel covalent modifiers of dimethylarginine dimethylaminohydrolase (DDAH) that are useful for biological applications, a set of "fragment"-sized inhibitors that were identified using a high-throughput screen are tested for time-dependent inhibition. One structural class of inactivators, 4-halopyridines, show time- and concentration-dependent inactivation of DDAH, and the inactivation mechanism of one example, 4-bromo-2-methylpyridine (1), is characterized in detail. The neutral form of halopyridines is not very reactive with excess glutathione. However, 1 readily reacts, with loss of its halide, in a selective, covalent, and irreversible manner with the active-site Cys249 of DDAH. This active-site Cys is not particularly reactive (pK(a) ca. 8.8), and 1 does not inactivate papain (Cys pK(a) ca. ≤4), suggesting that, unlike many reagents, Cys nucleophilicity is not a predominating factor in selectivity. Rather, binding and stabilization of the more reactive pyridinium form of the inactivator by a second moiety, Asp66, is required for facile reaction. This constraint imparts a unique selectivity profile to these inactivators. To our knowledge, halopyridines have not previously been reported as protein modifiers, and therefore they represent a first-in-class example of a novel type of quiescent affinity label.
Collapse
Affiliation(s)
- Corey M Johnson
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | | | | | | | | |
Collapse
|
28
|
Jones JE, Dreyton CJ, Flick H, Causey CP, Thompson PR. Mechanistic studies of agmatine deiminase from multiple bacterial species. Biochemistry 2010; 49:9413-23. [PMID: 20939536 DOI: 10.1021/bi101405y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
One subfamily of guanidino group-modifying enzymes (GMEs) consists of the agmatine deiminases (AgDs). These enzymes catalyze the conversion of agmatine (decarboxylated arginine) to N-carbamoyl putrescine and ammonia. In plants, viruses, and bacteria, these enzymes are thought to be involved in energy production, biosynthesis of polyamines, and biofilm formation. In particular, we are interested in the role that this enzyme plays in pathogenic bacteria. Previously, we reported the initial kinetic characterization of the agmatine deiminase from Helicobacter pylori and described the synthesis and characterization the two most potent AgD inactivators. Herein, we have expanded our initial efforts to characterize the catalytic mechanisms of AgD from H. pylori as well as Streptococcus mutans and Porphyromonas gingivalis. Through the use of pH rate profiles, pK(a) measurements of the active site cysteine, solvent isotope effects, and solvent viscosity effects, we have determined that the AgDs, like PADs 1 and 4, utilize a reverse protonation mechanism.
Collapse
Affiliation(s)
- Justin E Jones
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 120 Scripps Way, Jupiter, FL 33458, USA
| | | | | | | | | |
Collapse
|