1
|
Sadarangani V, Kalia A, Kausar T, Murarka P, Sau AK. Effect of the Macromolecular Crowding Agents on the Structure and Function of Human Arginase-I, a Therapeutically Important Enzyme. J Phys Chem B 2023; 127:8749-8761. [PMID: 37796726 DOI: 10.1021/acs.jpcb.3c02940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Macromolecular crowding has been known to influence the structure and function of many enzymes through excluded volume effects and/or soft interactions. Here, we employed two synthetic macromolecular crowders, Dextrans and poly(ethylene glycol)s (PEGs) with varying molecular masses, to examine how they affected the structure and function of a therapeutically important enzyme, human arginase-I that catalyzes the conversion of l-arginine to l-ornithine and urea. Except at greater concentrations of Dextran 200, Dextrans were observed to slightly reduce the enzymatic activity, indicating that they exert their influence mainly through the excluded volume effects. Similar outcomes were seen with PEGs, with the exception of PEG 1000, where the activity decreased with increasing PEG concentrations, showing the maximum effect at a 20 g/L concentration. This finding suggests that the enzyme function is reduced by the soft interactions of this macromolecule with the enzyme, supported by the binding measurement. Secondary and local tertiary structures and thermodynamic stability were also affected, suggesting that PEG 1000 has an impact on the protein's structure. Furthermore, molecular dynamics simulation studies suggest that the catalytic pocket is disturbed, presumably by the unwinding of neighboring helix 9. As a result, the positioning of nearby Glu277 is altered, which prevents His141 and Glu277 from making contact. This hampers the proton transfer from the catalytic His141 to the intermediate species to form ornithine, a crucial step for the substrate hydrolysis reaction by this arginase. Overall, the knowledge gained from this study might be helpful for understanding how different enzymes work in a crowded/cellular environment.
Collapse
Affiliation(s)
- Vineet Sadarangani
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anjali Kalia
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tasneem Kausar
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pooja Murarka
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Apurba Kumar Sau
- Protein Engineering Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
2
|
Sarkar D, Sau AK. Illuminating the structure-function landscape of an evolutionary nonconserved motif in the arginases of Helicobacter gastric pathogens. IUBMB Life 2023; 75:782-793. [PMID: 37086465 DOI: 10.1002/iub.2728] [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: 12/08/2022] [Accepted: 04/03/2023] [Indexed: 04/24/2023]
Abstract
The bimetallic enzyme arginase catalyses the conversion of L-arginine to L-ornithine and urea. In Helicobacter pylori (a known human gastric pathogen), this enzyme is an important virulence factor. In spite of the conservation of the catalytic and the metal-binding residues, the H. pylori homolog possesses a 13-residue motif (-153 ESEEKAWQKLCSL165 -) present in the middle of the protein sequence, whose role was recently elucidated. Despite several reviews available on arginases, no report has thoroughly illustrated the underlying basis for the importance of the above motif of the H. pylori enzyme in structure and function. In this review, we systematically describe a mechanistic basis for its importance in structure and function based on the known data. This motif of the H. pylori enzyme is present exclusively in the arginases of other Helicobacter gastric pathogens, where the critical residues are conserved, implying that the nonconserved stretch has been selected during the evolution of the enzyme in these gastric pathogens in a specific manner to perform its role in the structure and function. The combined information can be useful for understanding the function of arginases in other Helicobacter gastric pathogens. Additionally, this knowledge can be utilised to screen and design new small molecule inhibitors, specific to the arginases of these pathogens.
Collapse
Affiliation(s)
- Ditsa Sarkar
- Protein Engineering Laboratory, National Institute of Immunology, New Delhi, Delhi, India
| | - Apurba Kumar Sau
- Protein Engineering Laboratory, National Institute of Immunology, New Delhi, Delhi, India
| |
Collapse
|
3
|
Sarkar D, Vijayan R, Gourinath S, Sau AK. A unique aromatic cluster near the active site of H. pylori CPA is essential for catalytic function. Biophys J 2022; 121:248-262. [PMID: 34932956 PMCID: PMC8790187 DOI: 10.1016/j.bpj.2021.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/16/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
Polyamines are essential for cell growth and proliferation. In plants and many bacteria, including Helicobacter pylori, the parent polyamine putrescine is only produced through the metabolism of N-carbamoylputrescine by N-carbamoylputrescine amidase (CPA). Thus, CPA is a crucial intermediate enzyme. Moreover, the absence of CPA in humans makes its presence in H. pylori a potential target for the development of new therapeutics against this pathogen. Despite this enzyme's presence in plants and bacteria, its function is not completely explored. Using structure-guided biochemical and biophysical studies on H. pylori CPA, we discovered an aromatic cluster containing four conserved tryptophans near the catalytic site and elucidated its role. Mutational studies revealed that they are individually vital to enzyme function. Unlike wild-type, which forms a hexamer, the Trp to Ala mutants only formed dimers. Interestingly, two other conserved residues, Gln155 and Asp278, interact with the tryptophan cluster and perform similar roles. Our results indicate that aromatic-aromatic and H-bonding contacts between the residues (Trp156-Trp273, Trp196-Gln155, and Trp153-Asp278) play a crucial role in stimulating activity through hexamer formation. Additionally, Trp156 is essential to generating a catalytically efficient hexamer. These results suggest dual roles for the tryptophans; in hexamer formation and in generating its functionally active form, thereby providing a mechanistic understanding into the role of the cluster. We also elucidated the catalytic roles of Glu43, Lys115, and Cys152, which are present at the active site. Our findings highlight, for the first time, the importance of a tryptophan cluster in H. pylori CPA that can be exploited to design therapeutic inhibitors.
Collapse
Affiliation(s)
- Ditsa Sarkar
- National Institute of Immunology, New Delhi, India
| | | | | | - Apurba Kumar Sau
- National Institute of Immunology, New Delhi, India,Correspondence:
| |
Collapse
|
4
|
Li M, Qin J, Xiong K, Jiang B, Zhang T. Review of arginase as a promising biocatalyst: characteristics, preparation, applications and future challenges. Crit Rev Biotechnol 2021; 42:651-667. [PMID: 34612104 DOI: 10.1080/07388551.2021.1947962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
As a committed step in the urea cycle, arginase cleaves l-arginine to form l-ornithine and urea. l-Ornithine is essential to: cell proliferation, collagen formation and other physiological functions, while the urea cycle itself converts highly toxic ammonia to urea for excretion. Recently, arginase was exploited as an efficient catalyst for the environmentally friendly synthesis of l-ornithine, an abundant nonprotein amino acid that is widely employed as a food supplement and nutrition product. It was also proposed as an arginine-reducing agent in order to treat arginase deficiency and to be a means of depleting arginine to treat arginine auxotrophic tumors. Targeting arginase inhibitors of the arginase/ornithine pathway offers great promise as a therapy for: cardiovascular, central nervous system diseases and cancers with high arginase expression. In this review, recent advances in the characteristics, structure, catalytic mechanism and preparation of arginase were summarized, with a focus being placed on the biotechnical and medical applications of arginase. In particular, perspectives have been presented on the challenges and opportunities for the environmentally friendly utilization of arginase during l-ornithine production and in therapies.
Collapse
Affiliation(s)
- Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiufu Qin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kai Xiong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| |
Collapse
|
5
|
Hernández VM, Arteaga A, Dunn MF. Diversity, properties and functions of bacterial arginases. FEMS Microbiol Rev 2021; 45:6308370. [PMID: 34160574 DOI: 10.1093/femsre/fuab034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
The metalloenzyme arginase hydrolyzes L-arginine to produce L-ornithine and urea. In bacteria, arginase has important functions in basic nitrogen metabolism and redistribution, production of the key metabolic precursor L-ornithine, stress resistance and pathogenesis. We describe the regulation and specific functions of the arginase pathway as well as summarize key characteristics of related arginine catabolic pathways. The use of arginase-derived ornithine as a precursor molecule is reviewed. We discuss the biochemical and transcriptional regulation of arginine metabolism, including arginase, with the latter topic focusing on the RocR and AhrC transcriptional regulators in the model organism Bacillus subtilis. Finally, we consider similarities and contrasts in the structure and catalytic mechanism of the arginases from Bacillus caldovelox and Helicobacter pylori. The overall aim of this review is to provide a panorama of the diversity of physiological functions, regulation, and biochemical features of arginases in a variety of bacterial species.
Collapse
Affiliation(s)
- Victor M Hernández
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Alejandra Arteaga
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| | - Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas-Universidad Nacional Autonoma de México, Cuernavaca, Morelos, C.P. 62210, Mexico
| |
Collapse
|
6
|
An evolutionary non-conserved motif in Helicobacter pylori arginase mediates positioning of the loop containing the catalytic residue for catalysis. Biochem J 2021; 478:871-894. [PMID: 33480396 DOI: 10.1042/bcj20200978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 01/01/2023]
Abstract
The binuclear metalloenzyme Helicobacter pylori arginase is important for pathogenesis of the bacterium in the human stomach. Despite conservation of the catalytic residues, this single Trp enzyme has an insertion sequence (-153ESEEKAWQKLCSL165-) that is extremely crucial to function. This sequence contains the critical residues, which are conserved in the homolog of other Helicobacter gastric pathogens. However, the underlying basis for the role of this motif in catalytic function is not completely understood. Here, we used biochemical, biophysical and molecular dynamics simulations studies to determine that Glu155 of this stretch interacts with both Lys57 and Ser152. These interactions are essential for positioning of the motif through Trp159, which is located near Glu155 (His122-Trp159-Tyr125 contact is essential to tertiary structural integrity). The individual or double mutation of Lys57 and Ser152 to Ala considerably reduces catalytic activity with Lys57 to Ala being more significant, indicating they are crucial to function. Our data suggest that the Lys57-Glu155-Ser152 interaction influences the positioning of the loop containing the catalytic His133 so that this His can participate in catalysis, thereby providing a mechanistic understanding into the role of this motif in catalytic function. Lys57 was also found only in the arginases of other Helicobacter gastric pathogens. Based on the non-conserved motif, we found a new molecule, which specifically inhibits this enzyme. Thus, the present study not only provides a molecular basis into the role of this motif in function, but also offers an opportunity for the design of inhibitors with greater efficacy.
Collapse
|
7
|
Huang K, Zhang S, Guan X, Liu J, Li S, Song H. Thermostable arginase from Sulfobacillus acidophilus with neutral pH optimum applied for high-efficiency l-ornithine production. Appl Microbiol Biotechnol 2020; 104:6635-6646. [DOI: 10.1007/s00253-020-10721-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 01/31/2023]
|
8
|
Metal-induced change in catalytic loop positioning in Helicobacter pylori arginase alters catalytic function. Biochem J 2019; 476:3595-3614. [DOI: 10.1042/bcj20190545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022]
Abstract
Arginase is a bimetallic enzyme that utilizes mainly Mn2+ or Co2+ for catalytic function. In human homolog, the substitution of Mn2+ with Co2+ significantly reduces the Km value without affecting the kcat. However, in the Helicobacter pylori counterpart (important for pathogenesis), the kcat increases nearly 4-fold with Co2+ ions both in the recombinant holoenzyme and arginase isolated from H. pylori grown with Co2+ or Mn2+. This suggests that the active site of arginase in the two homologs is modulated differently by these two metal ions. To investigate the underlying mechanism for metal-induced difference in catalytic activity in the H. pylori enzyme, we used biochemical, biophysical and microsecond molecular dynamics simulations studies. The study shows that the difference in binding affinity of Co2+ and Mn2+ ions with the protein is linked to a different positioning of a loop (–122HTAYDSDSKHIHG134–) that contains a conserved catalytic His133. Consequently, the proximity of His133 and conserved Glu281 is varied. We found that the Glu281–His133 interaction is crucial for catalytic function and was previously unexplored in other homologs. We suggest that the proximity difference between these two residues in the Co2+- and Mn2+-proteins alters the proportion of protonated His133 via variation in its pKa. This affects the efficiency of proton transfer — an essential step of l-arginine hydrolysis reaction catalyzed by arginase and thus activity. Unlike in human arginase, the flexibility of the above segment observed in H. pylori homolog suggests that this region in the H. pylori enzyme may be explored to design its specific inhibitors.
Collapse
|
9
|
Metal ions-induced stability and function of bimetallic human arginase-I, a therapeutically important enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1153-1164. [DOI: 10.1016/j.bbapap.2018.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/21/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022]
|
10
|
Alam M, Srivastava A, Dutta A, Sau AK. Biochemical and biophysical studies ofHelicobacter pyloriarginine decarboxylase, an enzyme important for acid adaptation in host. IUBMB Life 2018; 70:658-669. [DOI: 10.1002/iub.1754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Mashkoor Alam
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Abhishek Srivastava
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Ankita Dutta
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| | - Apurba Kumar Sau
- National Institute of Immunology, Aruna Asaf Ali Marg; New Delhi Delhi India
| |
Collapse
|
11
|
George G, Kombrabail M, Raninga N, Sau AK. Arginase of Helicobacter Gastric Pathogens Uses a Unique Set of Non-catalytic Residues for Catalysis. Biophys J 2017; 112:1120-1134. [PMID: 28355540 DOI: 10.1016/j.bpj.2017.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/26/2017] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
Helicobacter pylori arginase, a bimetallic enzyme, is crucial for pathogenesis of the bacterium in human stomach. Despite conservation of the signature motifs in all arginases, the H. pylori homolog has a non-conserved motif (153ESEEKAWQKLCSL165), whose role was recently shown to be critical for its stability and function. The sequence analysis also reveals the presence of this motif with critical residues in the homolog of other Helicobacter gastric pathogens. However, the underlying mechanism for its significance in catalytic function is not clearly understood. Using H. pylori arginase, our studies reveal that the interactions of His122 and Tyr125 with Trp159 are indispensable for tertiary structural intactness through optimal positioning of the motif and thus for the catalytic function. The single and double mutants of His122 and Tyr125 not only enhanced the solvent accessibility and conformational flexibility of Trp159 in the holo protein, but also showed complete loss of catalytic activity. An intact bimetallic center and unaltered substrate binding indicate that proper positioning of the motif by aromatic-aromatic contact is vital for the generation of a catalytically active conformation. Additionally, the metal ions provide higher stability to the holo protein. We also identified the presence of these two residues exclusively in arginase of other Helicobacter gastric pathogens, which may have similar function. Therefore, to the best of our knowledge, these findings highlight for the first time that arginase of all Helicobacter gastric pathogens utilizes a unique non-catalytic triad for catalysis, which could be exploited for therapeutics.
Collapse
Affiliation(s)
- Ginto George
- National Institute of Immunology, New Delhi, India
| | - Mamata Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | | | | |
Collapse
|
12
|
Huang K, Zhang T, Jiang B, Mu W, Miao M. Characterization of a thermostable arginase from Rummeliibacillus pycnus SK31.001. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
13
|
Synthesis and Characterization of 4-, 5-, and 6-Coordinate Tris(1-ethyl-4-isopropylimidazolyl-κN)phosphine Cobalt(II) Complexes. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201403203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|