1
|
Ma S, Chen H, Liu S, Huang X, Mo T, Liu WQ, Zhang W, Ding W, Zhang Q. A gene-encoded aldehyde tag repurposed from RiPP cyclophane-forming pathway. Bioorg Med Chem Lett 2024; 101:129653. [PMID: 38360420 DOI: 10.1016/j.bmcl.2024.129653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/19/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Gene-encoded aldehyde tag technology has been widely utilized in protein bioorthogonal chemistry and biotechnological application. Herein, we report utilization of the promiscuous rSAM cyclophane synthase SjiB involved in triceptide biosynthesis as a dedicated and highly efficient formylglycine synthase. The new aldehyde tag sequence in this system, YQSSI, is biosynthetically orthogonal to the known aldehyde tag (C/S)x(P/A)xR. The potential use of SjiB/YQSSI aldehyde tag system was further validated in fluorescent labelling of model proteins.
Collapse
Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Heng Chen
- Department of Chemistry, Fudan University, Shanghai 200433, China; State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuxun Liu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xuedong Huang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China.
| |
Collapse
|
2
|
Jiang H, Chen H, Wang Y, Qian Y. Novel Molecular Subtyping Scheme Based on In Silico Analysis of Cuproptosis Regulator Gene Patterns Optimizes Survival Prediction and Treatment of Hepatocellular Carcinoma. J Clin Med 2023; 12:5767. [PMID: 37762710 PMCID: PMC10531788 DOI: 10.3390/jcm12185767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/11/2023] [Accepted: 07/20/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The liver plays an important role in maintaining copper homeostasis. Copper ion accumulation was elevated in HCC tissue samples. Copper homeostasis is implicated in cancer cell proliferation and angiogenesis. The potential of copper homeostasis as a new theranostic biomarker for molecular imaging and the targeted therapy of HCC has been demonstrated. Recent studies have reported a novel copper-dependent nonapoptotic form of cell death called cuproptosis, strikingly different from other known forms of cell death. The correlation between cuproptosis and hepatocellular carcinoma (HCC) is not fully understood. MATERIALS AND METHODS The transcriptomic data of patients with HCC were retrieved from the Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) and were used as a discovery cohort to construct the prognosis model. The gene expression data of patients with HCC retrieved from the International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) databases were used as the validation cohort. The Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis was used to construct the prognosis model. A principal component analysis (PCA) was used to evaluate the overall characteristics of cuproptosis regulator genes and obtain the PC1 and PC2 scores. Unsupervised clustering was performed using the ConsensusClusterPlus R package to identify the molecular subtypes of HCC. Cox regression analysis was performed to identify cuproptosis regulator genes that could predict the prognosis of patients with HCC. The receiver operating characteristics curve and Kaplan-Meier survival analysis were used to understand the role of hub genes in predicting the diagnosis and prognosis of patients, as well as the prognosis risk model. A weighted gene co-expression network analysis (WGCNA) was used for screening the cuproptosis subtype-related hub genes. The functional enrichment analysis was performed using Metascape. The 'glmnet' R package was used to perform the LASSO regression analysis, and the randomForest algorithm was performed using the 'randomForest' R package. The 'pRRophetic' R package was used to estimate the anticancer drug sensitivity based on the data retrieved from the Genomics of Drug Sensitivity in Cancer database. The nomogram was constructed using the 'rms' R package. Pearson's correlation analysis was used to analyze the correlations. RESULTS We constructed a six-gene signature prognosis model and a nomogram to predict the prognosis of patients with HCC. The Kaplan-Meier survival analysis revealed that patients with a high-risk score, which was predicted by the six-gene signature model, had poor prognoses (log-rank test p < 0.001; HR = 1.83). The patients with HCC were grouped into three distinct cuproptosis subtypes (Cu-clusters A, B, and C) based on the expression pattern of cuproptosis regulator genes. The patients in Cu-cluster B had poor prognosis (log-rank test p < 0.001), high genomic instability, and were not sensitive to conventional chemotherapeutic treatment compared to the patients in the other subtypes. Cancer cells in Cu-cluster B exhibited a higher degree of the senescence-associated secretory phenotype (SASP), a marker of cellular senescence. Three representative genes, CDCA8, MCM6, and NCAPG2, were identified in patients in Cu-cluster B using WGCNA and the "randomForest" algorithm. A nomogram was constructed to screen patients in the Cu-cluster B subtype based on three genes: CDCA8, MCM6, and NCAPG2. CONCLUSION Publicly available databases and various bioinformatics tools were used to study the heterogeneity of cuproptosis in patients with HCC. Three HCC subtypes were identified, with differences in the survival outcomes, genomic instability, senescence environment, and response to anticancer drugs. Further, three cuproptosis-related genes were identified, which could be used to design personalized therapeutic strategies for HCC.
Collapse
Affiliation(s)
- Heng Jiang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Hao Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Yao Wang
- Department of Digestive Endoscopy, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Yeben Qian
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| |
Collapse
|
3
|
Kerber O, Tran J, Misiaszek A, Chorążewska A, Bal W, Krężel A. Zn(II) to Ag(I) Swap in Rad50 Zinc Hook Domain Leads to Interprotein Complex Disruption through the Formation of Highly Stable Ag x(Cys) y Cores. Inorg Chem 2023; 62:4076-4087. [PMID: 36863010 PMCID: PMC10015552 DOI: 10.1021/acs.inorgchem.2c03767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The widespread application of silver nanoparticles in medicinal and daily life products increases the exposure to Ag(I) of thiol-rich biological environments, which help control the cellular metallome. A displacement of native metal cofactors from their cognate protein sites is a known phenomenon for carcinogenic and otherwise toxic metal ions. Here, we examined the interaction of Ag(I) with the peptide model of the interprotein zinc hook (Hk) domain of Rad50 protein from Pyrococcus furiosus, a key player in DNA double-strand break (DSB) repair. The binding of Ag(I) to 14 and 45 amino acid long peptide models of apo- and Zn(Hk)2 was experimentally investigated by UV-vis spectroscopy, circular dichroism, isothermal titration calorimetry, and mass spectrometry. The Ag(I) binding to the Hk domain was found to disrupt its structure via the replacement of the structural Zn(II) ion by multinuclear Agx(Cys)y complexes. The ITC analysis indicated that the formed Ag(I)-Hk species are at least 5 orders of magnitude stronger than the otherwise extremely stable native Zn(Hk)2 domain. These results show that Ag(I) ions may easily disrupt the interprotein zinc binding sites as an element of silver toxicity at the cellular level.
Collapse
Affiliation(s)
- Olga Kerber
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Józef Tran
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Alicja Misiaszek
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Aleksandra Chorążewska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| |
Collapse
|
4
|
Lu YY, Cao M, Li F, Tian M, Ren H, Chi Q, Huang Q. Atmospheric PM 2.5 induce autophagy and autophagic flux blockage in HUVEC cells via ROS/TXNIP signaling: Important role of metal components. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130623. [PMID: 37056006 DOI: 10.1016/j.jhazmat.2022.130623] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 06/19/2023]
Abstract
Autophagy was involved in vascular endothelial injury caused by PM2.5, which aggravated the pathogenesis of cardiovascular diseases. However, major toxic components and underlying mechanism responsible for PM2.5-induced autophagy remain unclear. In this study, the effects of water-extracted PM2.5 (WE-PM2.5) on autophagy in human umbilical vein endothelial cells (HUVEC) were studied. Our results showed WE-PM2.5 promoted autophagosome initiation and formation, meanwhile, lysosomal function was impaired, which further caused autophagic flux blockage in HUVEC cells. Furthermore, removal of metals alleviated WE-PM2.5-induced autophagic flux blockage, while the artificial metal mixture reproduced the WE-PM2.5 response. Mechanistically, ROS regulated autophagy-related proteins evidenced by BECN1, LC3B and p62 expression reversed by NAC pretreatment in WE-PM2.5-exposed cells. WE-PM2.5 also increased TXNIP expression mediated by ROS; moreover, knockdown of TXNIP in WE-PM2.5-exposed cells decreased BECN1 and LC3B expression, but had little effects on the expression of p62, CTSB, and CTSD, indicating WE-PM2.5-induced TXNIP was involved in autophagosome initiation and formation rather than autophagic degradation. Collectively, WE-PM2.5-induced ROS not only promoted autophagosome initiation and formation, but also inhibited autophagic degradation. However, as the downstream molecule of ROS, TXNIP was only involved in autophagosome initiation and formation. Importantly, WE-PM2.5-bound metals were largely responsible for autophagic flux blockage in HUVEC cells.
Collapse
Affiliation(s)
- Yan-Yang Lu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Meiyi Cao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Environmental and Safety Engineering, Fuzhou University, Fuzhou 10386, China
| | - Fuping Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Meiping Tian
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hongyun Ren
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiaoqiao Chi
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingyu Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| |
Collapse
|
5
|
Wu Y, Zhao C, Su Y, Shaik S, Lai W. Mechanistic Insight into Peptidyl-Cysteine Oxidation by the Copper-Dependent Formylglycine-Generating Enzyme. Angew Chem Int Ed Engl 2023; 62:e202212053. [PMID: 36545867 DOI: 10.1002/anie.202212053] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The copper-dependent formylglycine-generating enzyme (FGE) catalyzes the oxygen-dependent oxidation of specific peptidyl-cysteine residues to formylglycine. Our QM/MM calculations provide a very likely mechanism for this transformation. The reaction starts with dioxygen binding to the tris-thiolate CuI center to form a triplet CuII -superoxide complex. The rate-determining hydrogen atom abstraction involves a triplet-singlet crossing to form a CuII -OOH species that couples with the substrate radical, leading to a CuI -alkylperoxo intermediate. This is accompanied by proton transfer from the hydroperoxide to the S atom of the substrate via a nearby water molecule. The subsequent O-O bond cleavage is coupled with the C-S bond breaking that generates the formylglycine and a CuII -oxyl complex. Moreover, our results suggest that the aldehyde oxygen of the final product originates from O2 , which will be useful for future experimental work.
Collapse
Affiliation(s)
- Yao Wu
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Cong Zhao
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Yanzhuang Su
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Wenzhen Lai
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, Department of Chemistry, Renmin University of China, Beijing, 100872, China
| |
Collapse
|
6
|
Moula G, Bag J, Bose M, Barman S, Pal K. Oxygen Activation by a Copper Complex with Sulfur-Only Coordination Relevant to the Formylglycine Generating Enzyme. Inorg Chem 2022; 61:6660-6671. [PMID: 35446020 DOI: 10.1021/acs.inorgchem.2c00746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthesizing hydrosulfido Cu thiolate complexes is quite challenging. In this report, two new and rare hydrosulfido Cu thiolate complexes, [Et4N]2[(mnt)Cu-SH] (2, mnt = maleonitrile dithiolene = S2C2(CN)2) and [Et4N]3[(mnt)Cu-(μ-SH)-Cu(mnt)] (3), have been synthesized. Coordination sites and O2 activation by complex 2 resemble the formylglycine generating enzyme (FGE), an enzyme recently crystallographically characterized with sulfur-only coordination around Cu (three thiolate ligands). The function of this enzyme (and complex 2) is surprising because vulnerable thiolates should not be well suited for O2 activation rationally. Indeed, activation of oxygen by such an all-sulfur-coordinated Cu complex 2 is lacking in the literature. Aerial O2 (ambient O2 from the air) activation by complex 2 could proceed through a superoxide radical intermediate and a sulfur radical intermediate detected by resonance Raman (rR) spectroscopy and electron paramagnetic resonance (EPR) spectroscopy, respectively. The chemistry of 2 has been examined by its reactivity, crystal structure, and spectroscopic and cyclic voltammetric analyses. In addition, the results have been complemented with density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations.
Collapse
Affiliation(s)
- Golam Moula
- Department of Chemistry, Rajabazar Science College, University of Calcutta, Kolkata 700009, West Bengal, India
| | - Jayanta Bag
- Department of Chemistry, Rajabazar Science College, University of Calcutta, Kolkata 700009, West Bengal, India
| | - Moumita Bose
- Department of Chemistry, Rajabazar Science College, University of Calcutta, Kolkata 700009, West Bengal, India
| | - Souvik Barman
- Department of Chemistry, Rajabazar Science College, University of Calcutta, Kolkata 700009, West Bengal, India
| | - Kuntal Pal
- Department of Chemistry, Rajabazar Science College, University of Calcutta, Kolkata 700009, West Bengal, India
| |
Collapse
|
7
|
Formylglycine-generating enzyme-like proteins constitute a novel family of widespread type VI secretion system immunity proteins. J Bacteriol 2021; 203:e0028121. [PMID: 34398661 DOI: 10.1128/jb.00281-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Competition is a critical aspect of bacterial life, as it enables niche establishment and facilitates the acquisition of essential nutrients. Warfare between Gram-negative bacteria is largely mediated by the type VI secretion system (T6SS), a dynamic nanoweapon that delivers toxic effector proteins from an attacking cell to adjacent bacteria in a contact-dependent manner. Effector-encoding bacteria prevent self-intoxication and kin cell killing by the expression of immunity proteins, which prevent effector toxicity by specifically binding their cognate effector and either occluding its active site or preventing structural rearrangements necessary for effector activation. In this study, we investigate Tsi3, a previously uncharacterized T6SS immunity protein present in multiple strains of the human pathogen Acinetobacter baumannii. We show that Tsi3 is the cognate immunity protein of the antibacterial effector of unknown function Tse3. Our bioinformatic analyses indicate that Tsi3 homologs are widespread among Gram-negative bacteria, often encoded within T6SS effector-immunity modules. Surprisingly, we found that Tsi3 homologs are predicted to possess a characteristic formylglycine-generating enzyme (FGE) domain, which is present in various enzymatic proteins. Our data shows that Tsi3-mediated immunity is dependent on Tse3-Tsi3 protein-protein interactions and that Tsi3 homologs from various bacteria do not provide immunity against non-kin Tse3. Thus, we conclude that Tsi3 homologs are unlikely to be functional enzymes. Collectively, our work identifies FGE domain-containing proteins as important mediators of immunity against T6SS attacks and indicates that the FGE domain can be co-opted as a scaffold in multiple proteins to carry out diverse functions. Importance Despite the wealth of knowledge on the diversity of biochemical activities carried out by T6SS effectors, comparably little is known about the various strategies bacteria employ to prevent susceptibility to T6SS-dependent bacterial killing. Our work establishes a novel family of T6SS immunity proteins with a characteristic FGE domain. This domain is present in enzymatic proteins with various catalytic activities. Our characterization of Tsi3 expands the known functions carried out by FGE-like proteins to include defense during T6SS-mediated bacterial warfare. Moreover, it highlights the evolution of FGE domain-containing proteins to carry out diverse biological functions.
Collapse
|
8
|
Wang D, Li Y, Zheng Y, Hsieh YSY. Recent Advances in Screening Methods for the Functional Investigation of Lytic Polysaccharide Monooxygenases. Front Chem 2021; 9:653754. [PMID: 33912540 PMCID: PMC8072006 DOI: 10.3389/fchem.2021.653754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/12/2021] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenase (LPMO) is a newly discovered and widely studied enzyme in recent years. These enzymes play a key role in the depolymerization of sugar-based biopolymers (including cellulose, hemicellulose, chitin and starch), and have a positive significance for biomass conversion. LPMO is a copper-dependent enzyme that can oxidize and cleave glycosidic bonds in cellulose and other polysaccharides. Their mechanism of action depends on the correct coordination of copper ions in the active site. There are still difficulties in the analysis of LPMO activity, which often requires multiple methods to be used in concert. In this review, we discussed various LPMO activity analysis methods reported so far, including mature mass spectrometry, chromatography, labeling, and indirect measurements, and summarized the advantages, disadvantages and applicability of different methods.
Collapse
Affiliation(s)
- Damao Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Yanping Li
- College of Food Science, Southwest University, Chongqing, China
| | - Yuting Zheng
- College of Food Science, Southwest University, Chongqing, China
| | - Yves S Y Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden.,School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
9
|
ATP7A-Regulated Enzyme Metalation and Trafficking in the Menkes Disease Puzzle. Biomedicines 2021; 9:biomedicines9040391. [PMID: 33917579 PMCID: PMC8067471 DOI: 10.3390/biomedicines9040391] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022] Open
Abstract
Copper is vital for numerous cellular functions affecting all tissues and organ systems in the body. The copper pump, ATP7A is critical for whole-body, cellular, and subcellular copper homeostasis, and dysfunction due to genetic defects results in Menkes disease. ATP7A dysfunction leads to copper deficiency in nervous tissue, liver, and blood but accumulation in other tissues. Site-specific cellular deficiencies of copper lead to loss of function of copper-dependent enzymes in all tissues, and the range of Menkes disease pathologies observed can now be explained in full by lack of specific copper enzymes. New pathways involving copper activated lysosomal and steroid sulfatases link patient symptoms usually related to other inborn errors of metabolism to Menkes disease. Additionally, new roles for lysyl oxidase in activation of molecules necessary for the innate immune system, and novel adapter molecules that play roles in ERGIC trafficking of brain receptors and other proteins, are emerging. We here summarize the current knowledge of the roles of copper enzyme function in Menkes disease, with a focus on ATP7A-mediated enzyme metalation in the secretory pathway. By establishing mechanistic relationships between copper-dependent cellular processes and Menkes disease symptoms in patients will not only increase understanding of copper biology but will also allow for the identification of an expanding range of copper-dependent enzymes and pathways. This will raise awareness of rare patient symptoms, and thus aid in early diagnosis of Menkes disease patients.
Collapse
|
10
|
Leisinger F, Miarzlou DA, Seebeck FP. Non-Coordinative Binding of O 2 at the Active Center of a Copper-Dependent Enzyme. Angew Chem Int Ed Engl 2021; 60:6154-6159. [PMID: 33245183 DOI: 10.1002/anie.202014981] [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: 11/09/2020] [Indexed: 12/28/2022]
Abstract
Molecular oxygen (O2 ) is a sustainable oxidation reagent. O2 is strongly oxidizing but kinetically stable and its final reaction product is water. For these reasons learning how to activate O2 and how to steer its reactivity along desired reaction pathways is a longstanding challenge in chemical research.[1] Activation of ground-state diradical O2 can occur either via conversion to singlet oxygen or by one-electron reduction to superoxide. Many enzymes facilitate activation of O2 by direct fomation of a metal-oxygen coordination complex concomitant with inner sphere electron transfer. The formylglycine generating enzyme (FGE) is an unusual mononuclear copper enzyme that appears to follow a different strategy. Atomic-resolution crystal structures of the precatalytic complex of FGE demonstrate that this enzyme binds O2 juxtaposed, but not coordinated to the catalytic CuI . Isostructural complexes that contain AgI instead of CuI or nitric oxide instead of O2 confirm that formation of the initial oxygenated complex of FGE does not depend on redox activity. A stepwise mechanism that decouples binding and activation of O2 is unprecedented for metal-dependent oxidases, but is reminiscent of flavin-dependent enzymes.
Collapse
Affiliation(s)
- Florian Leisinger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Dzmitry A Miarzlou
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4002, Basel, Switzerland
| |
Collapse
|
11
|
Leisinger F, Miarzlou DA, Seebeck FP. Non‐Coordinative Binding of O
2
at the Active Center of a Copper‐Dependent Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Florian Leisinger
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Dzmitry A. Miarzlou
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| |
Collapse
|
12
|
Betts HD, Whitehead C, Harris HH. Silver in biology and medicine: opportunities for metallomics researchers. Metallomics 2020; 13:6029133. [PMID: 33570135 DOI: 10.1093/mtomcs/mfaa001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022]
Abstract
The antibacterial properties of silver have been known for centuries and the threat of antibiotic-resistant bacteria has led to renewed focus on the noble metal. Silver is now commonly included in a range of household and medical items to imbue them with bactericidal properties. Despite this, the chemical fate of the metal in biological systems is poorly understood. Silver(I) is a soft metal with high affinity for soft donor atoms and displays much similarity to the chemistry of Cu(I). In bacteria, interaction of silver with the cell wall/membrane, DNA, and proteins and enzymes can lead to cell death. Additionally, the intracellular generation of reactive oxygen species by silver is posited to be a significant antimicrobial action. While the antibacterial action of silver is well known, bacteria found in silver mines display resistance against it through use of a protein ensemble thought to have been specifically developed for the metal, highlighting the need for judicious use. In mammals, ∼10-20% of ingested silver is retained by the body and thought to predominantly localize in the liver or kidneys. Chronic exposure can result in argyria, a condition characterized by blue staining of the skin, resulting from subdermal deposition of silver [as Ag(0)/sulfides], but more insidious side effects, such as inclusions in the brain, seizures, liver/kidney damage, and immunosuppression, have also been reported. Here, we hope to highlight the current understanding of the biological chemistry of silver and the necessity for continued study of these systems to fill existing gaps in knowledge.
Collapse
Affiliation(s)
- Harley D Betts
- Department of Chemistry, The University of Adelaide, North Terrace, SA 5005, Australia
| | - Carole Whitehead
- Department of Chemistry, The University of Adelaide, North Terrace, SA 5005, Australia
| | - Hugh H Harris
- Department of Chemistry, The University of Adelaide, North Terrace, SA 5005, Australia
| |
Collapse
|
13
|
Wang H, Yang X, Wang M, Hu M, Xu X, Yan A, Hao Q, Li H, Sun H. Atomic differentiation of silver binding preference in protein targets: Escherichia coli malate dehydrogenase as a paradigm. Chem Sci 2020; 11:11714-11719. [PMID: 34123202 PMCID: PMC8162793 DOI: 10.1039/d0sc04151c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/08/2020] [Indexed: 01/04/2023] Open
Abstract
Understanding how metallodrugs interact with their protein targets is of vital importance for uncovering their molecular mode of actions as well as overall pharmacological/toxicological profiles, which in turn facilitates the development of novel metallodrugs. Silver has been used as an antimicrobial agent since antiquity, yet there is limited knowledge about silver-binding proteins. Given the multiple dispersed cysteine residues and histidine-methionine pairs, Escherichia coli malate dehydrogenase (EcMDH) represents an excellent model to investigate silver coordination chemistry as well as its targeting sites in enzymes. We show by systematic biochemical characterizations that silver ions (Ag+) bind EcMDH at multiple sites including three cysteine-containing sites. By X-ray crystallography, we unravel the binding preference of Ag+ to multiple binding sites in EcMDH, i.e., Cys113 > Cys251 > Cys109 > Met227. Silver exhibits preferences to the donor atoms and residues in the order of S > N > O and Cys > Met > His > Lys > Val, respectively, in EcMDH. For the first time, we report the coordination of silver to a lysine in proteins. Besides, we also observed argentophilic interactions (Ag⋯Ag, 2.7 to 3.3 Å) between two silver ions coordinating to one thiolate. Combined with site-directed mutagenesis and an enzymatic activity test, we unveil that the binding of Ag+ to the site IV (His177-Ag-Met227 site) plays a vital role in Ag+-mediated MDH inactivation. This work stands as the first unusual and explicit study of silver binding preference to multiple binding sites in its authentic protein target at the atomic resolution. These findings enrich our knowledge on the biocoordination chemistry of silver(i), which in turn facilitates the prediction of the unknown silver-binding proteins and extends the pharmaceutical potentials of metal-based drugs.
Collapse
Affiliation(s)
- Haibo Wang
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Xinming Yang
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Minji Wang
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
- School of Chemistry and Molecular Engineering, East China Normal University No. 3663 Zhongshan Road North Shanghai 200062 P. R. China
| | - Menglong Hu
- School of Biomedical Sciences, The University of Hong Kong, Laboratory Block 21 Sassoon Road, Pokfulam Hong Kong P. R. China
| | - Xiaohan Xu
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Quan Hao
- School of Biomedical Sciences, The University of Hong Kong, Laboratory Block 21 Sassoon Road, Pokfulam Hong Kong P. R. China
| | - Hongyan Li
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Hongzhe Sun
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
| |
Collapse
|
14
|
Schlotawa L, Adang LA, Radhakrishnan K, Ahrens-Nicklas RC. Multiple Sulfatase Deficiency: A Disease Comprising Mucopolysaccharidosis, Sphingolipidosis, and More Caused by a Defect in Posttranslational Modification. Int J Mol Sci 2020; 21:E3448. [PMID: 32414121 PMCID: PMC7279497 DOI: 10.3390/ijms21103448] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Multiple sulfatase deficiency (MSD, MIM #272200) is an ultra-rare disease comprising pathophysiology and clinical features of mucopolysaccharidosis, sphingolipidosis and other sulfatase deficiencies. MSD is caused by impaired posttranslational activation of sulfatases through the formylglycine generating enzyme (FGE) encoded by the sulfatase modifying factor 1 (SUMF1) gene, which is mutated in MSD. FGE is a highly conserved, non-redundant ER protein that activates all cellular sulfatases by oxidizing a conserved cysteine in the active site of sulfatases that is necessary for full catalytic activity. SUMF1 mutations result in unstable, degradation-prone FGE that demonstrates reduced or absent catalytic activity, leading to decreased activity of all sulfatases. As the majority of sulfatases are localized to the lysosome, loss of sulfatase activity induces lysosomal storage of glycosaminoglycans and sulfatides and subsequent cellular pathology. MSD patients combine clinical features of all single sulfatase deficiencies in a systemic disease. Disease severity classifications distinguish cases based on age of onset and disease progression. A genotype- phenotype correlation has been proposed, biomarkers like excreted storage material and residual sulfatase activities do not correlate well with disease severity. The diagnosis of MSD is based on reduced sulfatase activities and detection of mutations in SUMF1. No therapy exists for MSD yet. This review summarizes the unique FGE/ sulfatase physiology, pathophysiology and clinical aspects in patients and their care and outlines future perspectives in MSD.
Collapse
Affiliation(s)
- Lars Schlotawa
- Department of Paediatrics and Adolescent Medicine, University Medical Centre Goettingen, 37075 Goettingen, Germany
| | - Laura A. Adang
- Division of Child Neurology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | | | - Rebecca C. Ahrens-Nicklas
- Division of Human Genetics and Metabolism, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| |
Collapse
|
15
|
Naowarojna N, Irani S, Hu W, Cheng R, Zhang L, Li X, Chen J, Zhang YJ, Liu P. Crystal Structure of the Ergothioneine Sulfoxide Synthase from Candidatus Chloracidobacterium thermophilum and Structure-Guided Engineering To Modulate Its Substrate Selectivity. ACS Catal 2019; 9:6955-6961. [PMID: 32257583 DOI: 10.1021/acscatal.9b02054] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ergothioneine is a thiohistidine derivative with potential benefits on many aging-related diseases. The central step of aerobic ergothioneine biosynthesis is the oxidative C-S bond formation reaction catalyzed by mononuclear nonheme iron sulfoxide synthases (EgtB and Egt1). Thus far, only the Mycobacterium thermoresistibile EgtB (EgtB Mth ) crystal structure is available, while the structural information for the more industrially attractive Egt1 enzyme is not. Herein, we reported the crystal structure of the ergothioneine sulfoxide synthase (EgtB Cth ) from Candidatus Chloracidobacterium thermophilum. EgtB Cth has both EgtB- and Egt1-type of activities. Guided by the structural information, we conducted Rosetta Enzyme Design calculations, and we biochemically demonstrated that EgtB Cth can be engineered more toward Egt1-type of activity. This study provides information regarding the factors governing the substrate selectivity in Egt1- and EgtB-catalysis and lays the groundwork for future sulfoxide synthase engineering toward the development of an effective ergothioneine process through a synthetic biology approach.
Collapse
Affiliation(s)
- Nathchar Naowarojna
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Seema Irani
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Weiyao Hu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- School of Chemistry and Chemical Engineering, Shanghai JiaoTong University, Shanghai 200240, China
| | - Ronghai Cheng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Li Zhang
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Xinhao Li
- School of Chemistry and Chemical Engineering, Shanghai JiaoTong University, Shanghai 200240, China
| | - Jiesheng Chen
- School of Chemistry and Chemical Engineering, Shanghai JiaoTong University, Shanghai 200240, China
| | - Yan Jessie Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| |
Collapse
|
16
|
Krüger T, Weiland S, Boschanski M, Sinha PK, Falck G, Müller KM, Dierks T, Sewald N. Conversion of Serine‐Type Aldehyde Tags by the Radical SAM Protein AtsB from
Methanosarcina mazei. Chembiochem 2019; 20:2074-2078. [DOI: 10.1002/cbic.201900322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Tobias Krüger
- Organische und Bioorganische ChemieFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Stefanie Weiland
- Biochemie IFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Mareile Boschanski
- Biochemie IFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Prem Kumar Sinha
- Biochemie IFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Georg Falck
- Zelluläre und Molekulare BiotechnologieTechnische FakultätUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Kristian M. Müller
- Zelluläre und Molekulare BiotechnologieTechnische FakultätUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Thomas Dierks
- Biochemie IFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| | - Norbert Sewald
- Organische und Bioorganische ChemieFakultät für ChemieUniversität Bielefeld Universitätsstrasse 25 33615 Bielefeld Germany
| |
Collapse
|
17
|
Miarzlou DA, Leisinger F, Joss D, Häussinger D, Seebeck FP. Structure of formylglycine-generating enzyme in complex with copper and a substrate reveals an acidic pocket for binding and activation of molecular oxygen. Chem Sci 2019; 10:7049-7058. [PMID: 31588272 PMCID: PMC6676471 DOI: 10.1039/c9sc01723b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/11/2019] [Indexed: 01/25/2023] Open
Abstract
The formylglycine generating enzyme (FGE) catalyzes oxidative conversion of specific peptidyl-cysteine residues to formylglycine. FGE mediates O2-activation and hydrogen-atom abstraction in an active site that contains Cu(i) coordinated to two cysteine residues. Similar coordination geometries are common among copper-sensing transcription factors and copper-chaperone but are unprecedented among copper-dependent oxidases. To examine the mechanism of this unusual catalyst we determined the 1.04 Å structure of FGE from Thermomonospora curvata in complex with copper and a cysteine-containing peptide substrate. This structure unveils a network of four crystallographic waters and two active site residues that form a highly acidic O2-binding pocket juxtaposed to the trigonal planar tris-cysteine coordinated Cu(i) center. Comparison with structures of FGE in complex with Ag(i) and Cd(ii) combined with evidence from NMR spectroscopy and kinetic observations highlight several structural changes that are induced by substrate binding and prime the enzyme for O2-binding and subsequent activation.
Collapse
Affiliation(s)
- Dzmitry A Miarzlou
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| | - Florian Leisinger
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| | - Daniel Joss
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| | - Florian P Seebeck
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| |
Collapse
|
18
|
Zhang L, Zang B, Huang C, Ren J, Jia L. One-step Preparation of a VHH-based Immunoadsorbent for the Extracorporeal Removal of β2-microglobulin. Molecules 2019; 24:E2119. [PMID: 31167508 PMCID: PMC6600539 DOI: 10.3390/molecules24112119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 01/30/2023] Open
Abstract
Dialysis-related amyloidosis (DRA), which has been widely recognized to be associated with the accumulation of β2-microglobulin (β2-m) in blood, is one of the most common complications in patients receiving long-term dialysis treatment. The most significant side-effect of existing hemodialysis sorbents for the removal of β2-m from blood is the loss of vital proteins due to non-specific adsorptions. Although the traditional antibodies have the capability to specifically remove β2-m from blood, high cost limits their applications in clinics. Single domain antibodies derived from the Camelidae species serve as a superior choice in the preparation of immunoadsorbents due to their small size, high stability, amenability, simplicity of expression in microbes, and high affinity to recognize and interact with β2-m. In this study, we modified the anti-β2-m VHH by the formylglycine-generating enzyme (FGE), and then directly immobilized the aldehyde-modified VHH to the amino-activated beads. Notably, the fabrication is cost- and time-effective, since all the preparation steps were performed in the crude cell extract without rigorous purification. The accordingly prepared immunoadsorbent with VHHs as ligands exhibited the high capacity of β2-m (0.75 mg/mL). In conclusion, the VHH antibodies were successfully used as affinity ligands in the preparation of novel immunoadsorbents by the site-specific immobilization, and effectively adsorbed β2-m from blood, therefore opening a new avenue for efficient hemodialysis.
Collapse
Affiliation(s)
- Lijun Zhang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian, Liaoning 116023, China.
| | | | | | | | | |
Collapse
|
19
|
Stampfli AR, Goncharenko KV, Meury M, Dubey BN, Schirmer T, Seebeck FP. An Alternative Active Site Architecture for O 2 Activation in the Ergothioneine Biosynthetic EgtB from Chloracidobacterium thermophilum. J Am Chem Soc 2019; 141:5275-5285. [PMID: 30883103 DOI: 10.1021/jacs.8b13023] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sulfoxide synthases are nonheme iron enzymes that catalyze oxidative carbon-sulfur bond formation between cysteine derivatives and N-α-trimethylhistidine as a key step in the biosynthesis of thiohistidines. The complex catalytic mechanism of this enzyme reaction has emerged as the controversial subject of several biochemical and computational studies. These studies all used the structure of the γ-glutamyl cysteine utilizing sulfoxide synthase, MthEgtB from Mycobacterium thermophilum (EC 1.14.99.50), as a structural basis. To provide an alternative model system, we have solved the crystal structure of CthEgtB from Chloracidobacterium thermophilum (EC 1.14.99.51) that utilizes cysteine as a sulfur donor. This structure reveals a completely different configuration of active site residues that are involved in oxygen binding and activation. Furthermore, comparison of the two EgtB structures enables a classification of all ergothioneine biosynthetic EgtBs into five subtypes, each characterized by unique active-site features. This active site diversity provides an excellent platform to examine the catalytic mechanism of sulfoxide synthases by comparative enzymology, but also raises the question as to why so many different solutions to the same biosynthetic problem have emerged.
Collapse
Affiliation(s)
- Anja R Stampfli
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland.,Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Kristina V Goncharenko
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| | - Marcel Meury
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| | - Badri N Dubey
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , Basel 4056 , Switzerland
| | - Florian P Seebeck
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland
| |
Collapse
|
20
|
Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O 2 activation. Proc Natl Acad Sci U S A 2019; 116:5370-5375. [PMID: 30824597 DOI: 10.1073/pnas.1818274116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The formylglycine-generating enzyme (FGE) is required for the posttranslational activation of type I sulfatases by oxidation of an active-site cysteine to Cα-formylglycine. FGE has emerged as an enabling biotechnology tool due to the robust utility of the aldehyde product as a bioconjugation handle in recombinant proteins. Here, we show that Cu(I)-FGE is functional in O2 activation and reveal a high-resolution X-ray crystal structure of FGE in complex with its catalytic copper cofactor. We establish that the copper atom is coordinated by two active-site cysteine residues in a nearly linear geometry, supporting and extending prior biochemical and structural data. The active cuprous FGE complex was interrogated directly by X-ray absorption spectroscopy. These data unambiguously establish the configuration of the resting enzyme metal center and, importantly, reveal the formation of a three-coordinate tris(thiolate) trigonal planar complex upon substrate binding as furthermore supported by density functional theory (DFT) calculations. Critically, inner-sphere substrate coordination turns on O2 activation at the copper center. These collective results provide a detailed mechanistic framework for understanding why nature chose this structurally unique monocopper active site to catalyze oxidase chemistry for sulfatase activation.
Collapse
|
21
|
Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
Collapse
Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
22
|
Krüger T, Dierks T, Sewald N. Formylglycine-generating enzymes for site-specific bioconjugation. Biol Chem 2018; 400:289-297. [DOI: 10.1515/hsz-2018-0358] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 09/28/2018] [Indexed: 01/01/2023]
Abstract
Abstract
Site-specific bioconjugation strategies offer many possibilities for directed protein modifications. Among the various enzyme-based conjugation protocols, formylglycine-generating enzymes allow to posttranslationally introduce the amino acid Cα-formylglycine (FGly) into recombinant proteins, starting from cysteine or serine residues within distinct consensus motifs. The aldehyde-bearing FGly-residue displays orthogonal reactivity to all other natural amino acids and can, therefore, be used for site-specific labeling reactions on protein scaffolds. In this review, the state of research on catalytic mechanisms and consensus motifs of different formylglycine-generating enzymes, as well as labeling strategies and applications of FGly-based bioconjugations are presented.
Collapse
Affiliation(s)
- Tobias Krüger
- Organic and Bioorganic Chemistry, Faculty of Chemistry , Bielefeld University , Universitätsstraße 25 , D-33615 Bielefeld , Germany
| | - Thomas Dierks
- Biochemistry I, Faculty of Chemistry , Bielefeld University , Universitätsstraße 25 , D-33615 Bielefeld , Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Faculty of Chemistry , Bielefeld University , Universitätsstraße 25 , D-33615 Bielefeld , Germany
| |
Collapse
|
23
|
Mehmood A, Jones SI, Tao P, Janesko BG. An Orbital-Overlap Complement to Ligand and Binding Site Electrostatic Potential Maps. J Chem Inf Model 2018; 58:1836-1846. [DOI: 10.1021/acs.jcim.8b00370] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Arshad Mehmood
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 South University Drive, Fort Worth, Texas 76129, United States
| | - Stephanie I. Jones
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 South University Drive, Fort Worth, Texas 76129, United States
| | - Peng Tao
- Department of Chemistry, Southern Methodist University, P.O. Box 750314, Dallas, Texas 75275, United States
| | - Benjamin G. Janesko
- Department of Chemistry and Biochemistry, Texas Christian University, 2800 South University Drive, Fort Worth, Texas 76129, United States
| |
Collapse
|
24
|
Shen X, Zhang Q, Zhang G, Wang J. Significant and Synergistic Intensification of Aerobic Oxidation of Activated Alcohols in Water at Ambient Condition by Adding Perfluoro‐Surfactant. ChemistrySelect 2018. [DOI: 10.1002/slct.201801836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xianbo Shen
- Zhejiang Province Key Laboratory of BiofuelBiodiesel Laboratory of China Petroleum and Chemical Industry Federation and College of Chemical EngineeringCollege of Chemical Engineering, Zhejiang University of Technology Hangzhou 310014, P.R. China
| | - Qi Zhang
- Zhejiang Province Key Laboratory of BiofuelBiodiesel Laboratory of China Petroleum and Chemical Industry Federation and College of Chemical EngineeringCollege of Chemical Engineering, Zhejiang University of Technology Hangzhou 310014, P.R. China
| | - Guoqi Zhang
- Department of SciencesThe City University of New York New York NY 10019 USA
| | - Jianli Wang
- Zhejiang Province Key Laboratory of BiofuelBiodiesel Laboratory of China Petroleum and Chemical Industry Federation and College of Chemical EngineeringCollege of Chemical Engineering, Zhejiang University of Technology Hangzhou 310014, P.R. China
| |
Collapse
|
25
|
Zhang C, Zhou M, Liu S, Wang B, Mao Z, Xu H, Zhong Y, Zhang L, Xu B, Sui X. Copper-loaded nanocellulose sponge as a sustainable catalyst for regioselective hydroboration of alkynes. Carbohydr Polym 2018; 191:17-24. [DOI: 10.1016/j.carbpol.2018.03.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 12/22/2022]
|
26
|
Krüger T, Weiland S, Falck G, Gerlach M, Boschanski M, Alam S, Müller KM, Dierks T, Sewald N. Zweifach-bioorthogonale Derivatisierung durch verschiedene Formylglycin-generierende Enzyme. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Tobias Krüger
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Stefanie Weiland
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Georg Falck
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Marcus Gerlach
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Mareile Boschanski
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Sarfaraz Alam
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Kristian M. Müller
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Thomas Dierks
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| | - Norbert Sewald
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Deutschland
| |
Collapse
|
27
|
Krüger T, Weiland S, Falck G, Gerlach M, Boschanski M, Alam S, Müller KM, Dierks T, Sewald N. Two-fold Bioorthogonal Derivatization by Different Formylglycine-Generating Enzymes. Angew Chem Int Ed Engl 2018; 57:7245-7249. [DOI: 10.1002/anie.201803183] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Tobias Krüger
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Stefanie Weiland
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Georg Falck
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Marcus Gerlach
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Mareile Boschanski
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Sarfaraz Alam
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Kristian M. Müller
- Zelluläre und Molekulare Biotechnologie, Technische Fakultät; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Thomas Dierks
- Biochemie I; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Norbert Sewald
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| |
Collapse
|
28
|
Mazzei L, Cianci M, Gonzalez Vara A, Ciurli S. The structure of urease inactivated by Ag(i): a new paradigm for enzyme inhibition by heavy metals. Dalton Trans 2018; 47:8240-8247. [DOI: 10.1039/c8dt01190g] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular details of the inactivation of urease, a nickel-dependent virulence factor for human pathogens and negatively affecting the efficiency of soil nitrogen fertilization, are elucidated through the crystal structure of the enzyme complex with Ag(i).
Collapse
Affiliation(s)
- Luca Mazzei
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- I-40127 Bologna
- Italy
| | - Michele Cianci
- Department of Agricultural
- Food and Environmental Sciences
- Marche Polytechnic University
- Ancona
- Italy
| | | | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry
- Department of Pharmacy and Biotechnology
- University of Bologna
- I-40127 Bologna
- Italy
| |
Collapse
|
29
|
Ringel MT, Dräger G, Brüser T. PvdO is required for the oxidation of dihydropyoverdine as the last step of fluorophore formation in Pseudomonas fluorescens. J Biol Chem 2017; 293:2330-2341. [PMID: 29208656 DOI: 10.1074/jbc.ra117.000121] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/30/2017] [Indexed: 02/04/2023] Open
Abstract
Pyoverdines are important siderophores that guarantee iron supply to important pathogenic and non-pathogenic pseudomonads in host habitats. A key characteristic of all pyoverdines is the fluorescent dihydroxyquinoline group that contributes two ligands to the iron complexes. Pyoverdines are derived from the non-ribosomally synthesized peptide ferribactin, and their fluorophore is generated by periplasmic oxidation and cyclization reactions of d-tyrosine and l-diaminobutyric acid. The formation of the fluorophore is known to be driven by the periplasmic tyrosinase PvdP. Here we report that the putative periplasmic oxidoreductase PvdO of Pseudomonas fluorescens A506 is required for the final oxidation of dihydropyoverdine to pyoverdine, which completes the fluorophore. The pvdO deletion mutant accumulates dihydropyoverdine, and this phenotype is fully complemented by recombinant PvdO. The autoxidation of dihydropyoverdine at alkaline pH and the presence of high copper concentrations can mask this phenotype. Mutagenesis of conserved residues with potential catalytic function identified Glu-260 as an essential residue whose mutation abolished function without affecting stability or transport. Glu-260 of PvdO is at the exact position of the active-site cysteine in the structurally related formylglycine-generating enzyme. Evolution thus used the same protein fold for two distinct functionalities. As purified PvdO was inactive, additional factors are required for catalysis.
Collapse
Affiliation(s)
- Michael T Ringel
- From the Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany and
| | - Gerald Dräger
- the Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1 B, 30167 Hannover, Germany
| | - Thomas Brüser
- From the Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany and
| |
Collapse
|