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Hernández-Prieto JH, Martini VP, Iulek J. Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii in complex with an aldonic sugar acid. Biochimie 2024; 218:20-33. [PMID: 37709188 DOI: 10.1016/j.biochi.2023.09.013] [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: 02/19/2023] [Revised: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The pathogen Paracoccidioides lutzii (Pb01) is found in South America countries Colombia, Ecuador, Venezuela and Brazil, especially in the central, west, and north regions of the latter. It belongs to the Ajellomycetaceae family, Onygenales order, and is typically thermodimorphic, presenting yeast cells when it grows in animal tissues, but mycelia when in the environment, where it produces the infectious propagule. This fungus is one of the etiologic agents of Paracoccidioidomycosis (PCM), the most important endemic fungal infection in Latin America. Investigations on its genome have contributed to a better understanding about its metabolism and revealed the complexity of several metabolic glycolytic pathways. Glyceraldehyde-3-Phosphate Dehydrogenase from Paracoccidioides lutzii (PlGAPDH) is considered a moonlighting protein and participates in several biological processes of this pathogen. The enzyme was expressed and purified, as seen in SDS-PAGE gel, crystallized and had its three dimensional structure (3D) determined in complex with NAD+, a sulphate ion and d-galactonic acid, therefore, a type of 'GAA site'. It is the first GAPDH structure to show this chemical type in this site and how this protein can bind an acid derived from oxidation of a linear hexose.
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Affiliation(s)
| | | | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil.
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2
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Son HF, Yu H, Hong J, Lee D, Kim IK, Kim KJ. Structure-Guided Protein Engineering of Glyceraldehyde-3-phosphate Dehydrogenase from Corynebacterium glutamicum for Dual NAD/NADP Cofactor Specificity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17852-17859. [PMID: 37935620 DOI: 10.1021/acs.jafc.3c06176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Since the discovery of l-glutamate-producing Corynebacterium glutamicum, it has evolved to be an industrial workhorse. For biobased chemical production, suppling sufficient amounts of the NADPH cofactor is crucial. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme that converts glyceraldehyde-3-phosphate (G3P) to 1,3-bisphosphoglycerate and produces NADH, is a major prospective solution for the cofactor imbalance issue. In this study, we determined the crystal structure of GAPDH from C. glutamicum ATCC13032 (CgGAPDH). Based on the structural information, we generated six CgGAPDH variants, CgGAPDHL36S, CgGAPDHL36S/T37K, CgGAPDHL36S/T37K/P192S, CgGAPDHL36S/T37K/F100V/P192S, CgGAPDHL36S/T37K/F100L/P192S, and CgGAPDHL36S/T37K/F100I/P192S, that can produce both NADH and NAPDH. The final CgGAPDHL36S/T37K/F100V/P192S variant showed a 212-fold increase in enzyme activity for NADP as well as 200% and 30% increased activity for the G3P substrate under NAD and NADP cofactor conditions, respectively. In addition, crystal structures of CgGAPDH variants in complex with NAD(P) permit the elucidation of differences between wild-type CgGAPDH and variants in relation to cofactor stabilization.
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Affiliation(s)
- Hyeoncheol Francis Son
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Hyeonjeong Yu
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jiyeon Hong
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Donghoon Lee
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Il-Kwon Kim
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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3
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Galbiati A, Bova S, Pacchiana R, Borsari C, Persico M, Zana A, Bruno S, Donadelli M, Fattorusso C, Conti P. Discovery of a spirocyclic 3-bromo-4,5-dihydroisoxazole covalent inhibitor of hGAPDH with antiproliferative activity against pancreatic cancer cells. Eur J Med Chem 2023; 254:115286. [PMID: 37058971 DOI: 10.1016/j.ejmech.2023.115286] [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: 01/17/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/16/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a key glycolytic enzyme, plays a crucial role in the energy metabolism of cancer cells and has been proposed as a valuable target for the development of anticancer agents. Among a series of 5-substituted 3-bromo-4,5-dihydroisoxazole (BDHI) derivatives, we identified the spirocyclic compound 11, which is able to covalently inactivate recombinant human GAPDH (hGAPDH) with a faster reactivity than koningic acid, one of the most potent hGAPDH inhibitors known to date. Computational studies confirmed that conformational rigidification is crucial to stabilize the interaction of the inhibitor with the binding site, thus favoring the subsequent covalent bond formation. Investigation of intrinsic warhead reactivity at different pH disclosed the negligible reactivity of 11 with free thiols, highlighting its ability to selectively react with the activated cysteine of hGAPDH with respect to other sulfhydryl groups. Compound 11 strongly reduced cancer cell growth in four different pancreatic cancer cell lines and its antiproliferative activity correlated well with the intracellular inhibition of hGAPDH. Overall, our results qualify 11 as a potent hGAPDH covalent inhibitor with a moderate drug-like reactivity that could be further exploited to develop anticancer agents.
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Affiliation(s)
- Andrea Galbiati
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy
| | - Stefania Bova
- Department of Medicine and Surgery, University of Parma, 43125, Parma, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, 37134, Verona, Italy
| | - Chiara Borsari
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy; Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Marco Persico
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Aureliano Zana
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy
| | - Stefano Bruno
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, 37134, Verona, Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy.
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4
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Galbiati A, Zana A, Borsari C, Persico M, Bova S, Tkachuk O, Corfu AI, Tamborini L, Basilico N, Fattorusso C, Bruno S, Parapini S, Conti P. Role of Stereochemistry on the Biological Activity of Nature-Inspired 3-Br-Acivicin Isomers and Derivatives. Molecules 2023; 28:molecules28073172. [PMID: 37049935 PMCID: PMC10095986 DOI: 10.3390/molecules28073172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Chiral natural compounds are often biosynthesized in an enantiomerically pure fashion, and stereochemistry plays a pivotal role in biological activity. Herein, we investigated the significance of chirality for nature-inspired 3-Br-acivicin (3-BA) and its derivatives. The three unnatural isomers of 3-BA and its ester and amide derivatives were prepared and characterized for their antimalarial activity. Only the (5S, αS) isomers displayed significant antiplasmodial activity, revealing that their uptake might be mediated by the L-amino acid transport system, which is known to mediate the acivicin membrane’s permeability. In addition, we investigated the inhibitory activity towards Plasmodium falciparum glyceraldehyde 3-phosphate dehydrogenase (PfGAPDH) since it is involved in the multitarget mechanism of action of 3-BA. Molecular modeling has shed light on the structural and stereochemical requirements for an efficient interaction with PfGAPDH, leading to covalent irreversible binding and enzyme inactivation. While stereochemistry affects the target binding only for two subclasses (1a–d and 4a–d), it leads to significant differences in the antimalarial activity for all subclasses, suggesting that a stereoselective uptake might be responsible for the enhanced biological activity of the (5S, αS) isomers.
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Affiliation(s)
- Andrea Galbiati
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Aureliano Zana
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Chiara Borsari
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Marco Persico
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Stefania Bova
- Department of Medicine and Surgery, University of Parma, 43124 Parma, Italy
| | - Oleh Tkachuk
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Alexandra Ioana Corfu
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Lucia Tamborini
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Nicoletta Basilico
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Stefano Bruno
- Food and Drug Department, University of Parma, 43124 Parma, Italy
| | - Silvia Parapini
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
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Nimma R, Kumar A, Gani Z, Gahlawat A, Dilawari R, Rohilla RK, Kumbhar H, Garg P, Chopra S, Raje M, Iyengar Raje C. Characterization of the enzymatic and multifunctional properties of Acinetobacter baumannii erythrose-4-phosphate dehydrogenase (E4PDH). Microb Pathog 2023; 175:105992. [PMID: 36649779 DOI: 10.1016/j.micpath.2023.105992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
Infections due to Acinetobacter baumannii (A. baumannii) are rapidly increasing worldwide and consequently therapeutic options for treatment are limited. The emergence of multi drug resistant (MDR) strains has rendered available antibiotics ineffective, necessitating the urgent discovery of new drugs and drug targets. The vitamin B6 biosynthetic pathway has been considered as a potential antibacterial drug target but it is as yet uncharacterized for A. baumannii. In the current work, we have carried out in silico and biochemical characterization of Erythrose-4-phosphate dehydrogenase (E4PDH) (EC 1.2.1.72). This enzyme catalyzes the first step in the deoxyxylulose-5-phosphate (DXP) dependent Vitamin B6 biosynthetic pathway i.e. the conversion of d-erythrose-4-phosphate (E4P) to 4-Phosphoerythronate. E4PDH also possesses an additional activity whereby it can catalyze the conversion of Glyceraldehyde-3-phosphate (G3P) to 1,3 bisphosphoglycerate (1,3BPG). Our studies have revealed that this enzyme exhibits an alternate moonlighting function as a cell surface receptor for the human iron transport proteins transferrin (Tf) and lactoferrin (Lf). The present work reports the internalization of Tf and consequent iron acquisition as an alternate strategy for iron acquisition. Given its essential role in two crucial pathways i.e. metabolism and iron acquisition, A. baumannii E4PDH may play a vital role in bacterial pathogenesis.
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Affiliation(s)
- Ramesh Nimma
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Ajay Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Zahid Gani
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Anuj Gahlawat
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Rahul Dilawari
- Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Sector 39A, Chandigarh, 160036, India
| | - Rajesh Kumar Rohilla
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Hemangi Kumbhar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Sidharth Chopra
- Council of Scientific and Industrial Research-CSIR (CSIR-CDRI), Sector10, Janakipuram Extension, Sitapur Road, Lucknow, 226031, UP, India
| | - Manoj Raje
- Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Sector 39A, Chandigarh, 160036, India
| | - Chaaya Iyengar Raje
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India.
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Lei J, Yang Y, Lu Z, Pan H, Fang J, Jing B, Chen Y, Yin L. Taming metabolic competition via glycolysis inhibition for safe and potent tumor immunotherapy. Biochem Pharmacol 2022; 202:115153. [PMID: 35750199 DOI: 10.1016/j.bcp.2022.115153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/02/2022]
Abstract
Metabolic competition between tumors and T cells is fierce in the tumor microenvironment (TME). Tumors usually exhaust glucose and accumulate lactic acid in TME. Nutrient deprivation and lactic acid accumulation in TME blunt T cell functions and antitumor immune responses. Here, we reported that glycolysis-related genes were upregulated in melanoma patients with weak immune responses and T cell poorly infiltrated tumors of BRCA and COAD patients. Dimethyl fumarate (DMF), a GAPDH inhibitor, which is FDA proved to treat autoimmune diseases was identified to promote oxidative pentose phosphate pathway through glucose-6-phosphate dehydrogenase (G6PD) but to suppress aerobic glycolysis and oxidative phosphorylation in tumor cells. Additionally, DMF normalized metabolic competition between tumors and T cells, thus potentiate antitumor responses of tumor infiltrating CD8+ T lymphocytes (TILs). Moreover, DMF optimized the efficiency of immune checkpoint therapy and interleukin-2 (IL-2) therapy while eliminating severe toxicity induced by IL-2 therapy. This study indicates a novel clinically feasible therapy strategy aiming shared metabolic pathway of tumors and T cells for effective and less toxic tumor immunotherapy.
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Affiliation(s)
- Jun Lei
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yi Yang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaoliang Lu
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Haiyan Pan
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jialing Fang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Baowei Jing
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongshun Chen
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Zhang L, Liu M, Bao L, Boström KI, Yao Y, Li J, Gu S, Ji C. Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid. Biomolecules 2021; 11:biom11111565. [PMID: 34827563 PMCID: PMC8615399 DOI: 10.3390/biom11111565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a highly conserved enzyme involved in the ubiquitous process of glycolysis and presents a loop (residues 208–215 of Escherichia coli GAPDH) in two alternative conformations (I and II). It is uncertain what triggers this loop rearrangement, as well as which is the precise site from which phosphate attacks the thioacyl intermediate precursor of 1,3-bisphosphoglycerate (BPG). To clarify these uncertainties, we determined the crystal structures of complexes of wild-type GAPDH (WT) with NAD and phosphate or G3P, and of essentially inactive GAPDH mutants (C150S, H177A), trapping crystal structures for the thioacyl intermediate or for ternary complexes with NAD and either phosphate, BPG, or G3P. Analysis of these structures reported here lead us to propose that phosphate is located in the “new Pi site” attacks the thioester bond of the thioacyl intermediate to generate 1,3-bisphosphoglyceric acid (BPG). In the structure of the thioacyl intermediate, the mobile loop is in conformation II in subunits O, P, and R, while both conformations coexist in subunit Q. Moreover, only the Q subunit hosts bound NADH. In the R subunit, only the pyrophosphate part of NADH is well defined, and NADH is totally absent from the O and P subunits. Thus, the change in loop conformation appears to occur after NADH is produced, before NADH is released. In addition, two new D-glyceraldehyde-3-phosphate (G3P) binding forms are observed in WT.NAD.G3P and C150A+H177A.NAD.G3P. In summary, this paper improves our understanding of the GAPDH catalytic mechanism, particularly regarding BPG formation.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Meiruo Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Luyao Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Kristina I. Boström
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1679, USA; (K.I.B.); (Y.Y.)
| | - Yucheng Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1679, USA; (K.I.B.); (Y.Y.)
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Shaohua Gu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
- Correspondence:
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Ayna A, Moody PC. Crystal structures of a dual coenzyme specific glyceraldehyde-3-phosphate dehydrogenase from the enteric pathogen Campylobacter jejuni. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Perez AM, Wolfe JA, Schermerhorn JT, Qian Y, Cela BA, Kalinowski CR, Largoza GE, Fields PA, Brandt GS. Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora. RSC Adv 2021; 11:10364-10374. [PMID: 35423531 PMCID: PMC8695597 DOI: 10.1039/d0ra10119b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
Corals are vulnerable to increasing ocean temperatures. It is known that elevated temperatures lead to the breakdown of an essential mutualistic relationship with photosynthetic algae. The molecular mechanisms of this temperature-dependent loss of symbiosis are less well understood. Here, the thermal stability of a critical metabolic enzyme, glyceraldehyde-3-phosphate dehydrogenase, from the stony coral Acropora millepora was found to increase significantly in the presence of its cofactor NAD+. Determination of the structure of the cofactor-enzyme complex (PDB ID 6PX2) revealed variable NAD+ occupancy across the four monomers of the tetrameric enzyme. The structure of the fully occupied monomers was compared to those with partial cofactor occupancy, identifying regions of difference that may account for the increased thermal stability.
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Affiliation(s)
- Astrid M Perez
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Jacob A Wolfe
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Janse T Schermerhorn
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Yiwen Qian
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Bekim A Cela
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Cody R Kalinowski
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Garrett E Largoza
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Peter A Fields
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Gabriel S Brandt
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
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10
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Koshkarov AA, Makshakova ON. The Influence of Cofactor Binding on the Intramolecular Dynamics of Glyceraldehyde-3-Phosphate Dehydrogenase. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921020111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Abstract
In yeast, many proteins are found in both the cytoplasmic and extracellular compartments, and consequently it can be difficult to distinguish nonconventional secretion from cellular leakage. Therefore, we monitored the extracellular glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity of intact cells as a specific marker for nonconventional secretion. Extracellular GAPDH activity was proportional to the number of cells assayed, increased with incubation time, and was dependent on added substrates. Preincubation of intact cells with 100 μM dithiothreitol increased the reaction rate, consistent with increased access of the enzyme after reduction of cell wall disulfide cross-links. Such treatment did not increase cell permeability to propidium iodide, in contrast to effects of higher concentrations of reducing agents. An amine-specific membrane-impermeant biotinylation reagent specifically inactivated extracellular GAPDH. The enzyme was secreted again after a 30- to 60-min lag following the inactivation, and there was no concomitant increase in propidium iodide staining. There were about 4 × 104 active GAPDH molecules per cell at steady state, and secretion studies showed replenishment to that level 1 h after inactivation. These results establish conditions for specific quantitative assays of cell wall proteins in the absence of cytoplasmic leakage and for subsequent quantification of secretion rates in intact cells.IMPORTANCE Eukaryotic cells secrete many proteins, including many proteins that do not follow the classical secretion pathway. Among these, the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is unexpectedly found in the walls of yeasts and other fungi and in extracellular space in mammalian cell cultures. It is difficult to quantify extracellular GAPDH, because leakage of just a little of the very large amount of cytoplasmic enzyme can invalidate the determinations. We used enzymatic assays of intact cells while also maintaining membrane integrity. The results lead to estimates of the amount of extracellular enzyme and its rate of secretion to the wall in intact cells. Therefore, enzyme assays under controlled conditions can be used to investigate nonconventional secretion more generally.
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Schormann N, Campos J, Motamed R, Hayden KL, Gould JR, Green TJ, Senkovich O, Banerjee S, Ulett GC, Chattopadhyay D. Chlamydia trachomatis glyceraldehyde 3-phosphate dehydrogenase: Enzyme kinetics, high-resolution crystal structure, and plasminogen binding. Protein Sci 2020; 29:2446-2458. [PMID: 33058314 DOI: 10.1002/pro.3975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/27/2022]
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is an evolutionarily conserved essential enzyme in the glycolytic pathway. GAPDH is also involved in a wide spectrum of non-catalytic cellular 'moonlighting' functions. Bacterial surface-associated GAPDHs engage in many host interactions that aid in colonization, pathogenesis, and virulence. We have structurally and functionally characterized the recombinant GAPDH of the obligate intracellular bacteria Chlamydia trachomatis, the leading cause of sexually transmitted bacterial and ocular infections. Contrary to earlier speculations, recent data confirm the presence of glucose-catabolizing enzymes including GAPDH in both stages of the biphasic life cycle of the bacterium. The high-resolution crystal structure described here provides a close-up view of the enzyme's active site and surface topology and reveals two chemically modified cysteine residues. Moreover, we show for the first time that purified C. trachomatis GAPDH binds to human plasminogen and plasmin. Based on the versatility of GAPDH's functions, data presented here emphasize the need for investigating the Chlamydiae GAPDH's involvement in biological functions beyond energy metabolism.
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Affiliation(s)
- Norbert Schormann
- Department of Biochemistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Juan Campos
- Department of Chemistry and Physics, Birmingham-Southern College, Birmingham, Alabama, USA
| | - Rachael Motamed
- Department of Chemistry and Physics, Birmingham-Southern College, Birmingham, Alabama, USA
| | - Katherine L Hayden
- Department of Chemistry and Physics, Birmingham-Southern College, Birmingham, Alabama, USA
| | - Joseph R Gould
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Todd J Green
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olga Senkovich
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, Arizona, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, Illinois, USA
| | - Glen C Ulett
- School of Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Parklands, Australia
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13
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Serna J, Bergwitz C. Importance of Dietary Phosphorus for Bone Metabolism and Healthy Aging. Nutrients 2020; 12:E3001. [PMID: 33007883 PMCID: PMC7599912 DOI: 10.3390/nu12103001] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/13/2022] Open
Abstract
Inorganic phosphate (Pi) plays a critical function in many tissues of the body: for example, as part of the hydroxyapatite in the skeleton and as a substrate for ATP synthesis. Pi is the main source of dietary phosphorus. Reduced bioavailability of Pi or excessive losses in the urine causes rickets and osteomalacia. While critical for health in normal amounts, dietary phosphorus is plentiful in the Western diet and is often added to foods as a preservative. This abundance of phosphorus may reduce longevity due to metabolic changes and tissue calcifications. In this review, we examine how dietary phosphorus is absorbed in the gut, current knowledge about Pi sensing, and endocrine regulation of Pi levels. Moreover, we also examine the roles of Pi in different tissues, the consequences of low and high dietary phosphorus in these tissues, and the implications for healthy aging.
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Affiliation(s)
- Juan Serna
- Yale College, Yale University, New Haven, CT 06511, USA;
| | - Clemens Bergwitz
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06519, USA
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14
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Zhang L, Liu MR, Yao YC, Bostrom IK, Wang YD, Chen AQ, Li JX, Gu SH, Ji CN. Characterization and structure of glyceraldehyde-3-phosphate dehydrogenase type 1 from Escherichia coli. Acta Crystallogr F Struct Biol Commun 2020; 76:406-413. [PMID: 32880588 PMCID: PMC7470045 DOI: 10.1107/s2053230x20010067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/21/2020] [Indexed: 11/10/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme in the glycolytic pathway that catalyzes the conversion of D-glyceraldehyde 3-phosphate to 1,3-diphosphoglycerate. Here, the full-length GAPDH type 1 from Escherichia coli (EcGAPDH1) was cloned and overexpressed, and the protein was purified. Biochemical analyses found that the optimum reaction temperature and pH of EcGAPDH1 were 55°C and 10.0, respectively. The protein has a certain amount of thermostability. Crystals of EcGAPDH1 were obtained using the sitting-drop vapor-diffusion technique and X-ray diffraction data were collected to 1.88 Å resolution. Characterization of the crystals showed that they belonged to space group P41212, with unit-cell parameters a = b = 89.651, c = 341.007 Å, α = β = γ = 90°. The structure of EcGAPDH1 contains four subunits, each of which includes an N-terminal NAD+-binding domain and a C-terminal catalytic domain. Analysis of the NAD+-bound form showed some differences between the structures of EcGAPDH1 and human GAPDH. As EcGAPDH1 shares 100% identity with GAPDH from Shigella sonnei, its structure may help in finding a drug for the treatment of shigellosis.
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Affiliation(s)
- L. Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - M. R. Liu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Y. C. Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1679, USA
| | - I. K. Bostrom
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1679, USA
| | - Y. D. Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - A. Q. Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - J. X. Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - S. H. Gu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - C. N. Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
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15
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Scotti MT, Monteiro AFM, de Oliveira Viana J, Bezerra Mendonça Junior FJ, Ishiki HM, Tchouboun EN, De Araújo RSA, Scotti L. Recent Theoretical Studies Concerning Important Tropical Infections. Curr Med Chem 2020; 27:795-834. [DOI: 10.2174/0929867326666190711121418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/20/2018] [Accepted: 04/12/2019] [Indexed: 01/02/2023]
Abstract
Neglected Tropical Diseases (NTDs) form a group of diseases that are strongly associated
with poverty, flourish in impoverished environments, and thrive best in tropical areas,
where they tend to present overlap. They comprise several diseases, and the symptoms
vary dramatically from disease to disease, often causing from extreme pain, and untold misery
that anchors populations to poverty, permanent disability, and death. They affect more than 1
billion people worldwide; mostly in poor populations living in tropical and subtropical climates.
In this review, several complementary in silico approaches are presented; including
identification of new therapeutic targets, novel mechanisms of activity, high-throughput
screening of small-molecule libraries, as well as in silico quantitative structure-activity relationship
and recent molecular docking studies. Current and active research against Sleeping
Sickness, American trypanosomiasis, Leishmaniasis and Schistosomiasis infections will hopefully
lead to safer, more effective, less costly and more widely available treatments against
these parasitic forms of Neglected Tropical Diseases (NTDs) in the near future.
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Affiliation(s)
- Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Alex France Messias Monteiro
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Jéssika de Oliveira Viana
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | | | - Hamilton M. Ishiki
- University of Western Sao Paulo (Unoeste), Presidente Prudente, SP, Brazil
| | | | - Rodrigo Santos A. De Araújo
- Laboratory of Synthesis and Drug Delivery, Department of Biological Science, State University of Paraiba, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
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16
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Li R, Liang C, Jiang L, Yuan C, Huang M. Structural determination of group A Streptococcal surface dehydrogenase and characterization of its interaction with urokinase-type plasminogen activator receptor. Biochem Biophys Res Commun 2019; 510:539-544. [PMID: 30737033 DOI: 10.1016/j.bbrc.2019.01.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
Streptococcus pyogenes (group A Streptococcus, GAS) has caused a wide variety of human diseases. Its multifunctional surface dehydrogenase (SDH) is crucial for GAS life cycle. Furthermore, GAS infection into human pharyngeal cells has been previously shown to be mediated by the interaction between SDH and host urokinase-type plasminogen activator receptor (uPAR). However, the structural information of SDH remains to be elucidated and there are few detailed studies to characterize its interaction with uPAR. In-depth research on these issues will provide potential targets and strategies for combating GAS. Here, we prepared recombinant SDH tetramer in Escherichia coli BL21 (DE3) cells. After purification and crystallization, we determined its crystal structure at 1.74 Å. The unique characteristics might be potentially explored as drug targets or vaccine immunogen. We subsequently performed gel filtration chromatography, native-polyacrylamide gel electrophoresis (PAGE) and in vitro pull-down analyses. The results showed that their interaction was too weak to form stable complexes and the role of uPAR involved in GAS infection needs further demonstration. Altogether the current work provides the first view of SDH and deepens the knowledge of GAS infection.
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Affiliation(s)
- Rui Li
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
| | - Chenghui Liang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China.
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou, 350116, Fujian, China.
| | - Cai Yuan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China.
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, 350116, Fujian, China.
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17
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Kim YJ. A cryoprotectant induces conformational change in glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2018; 74:277-282. [PMID: 29717994 PMCID: PMC5931139 DOI: 10.1107/s2053230x18004557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/19/2018] [Indexed: 12/28/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme, catalyses the conversion of D-glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. While mammalian and yeast GAPDHs are multifunctional proteins that have additional functions beyond those involved in glycolysis, including reactions related to nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis, Escherichia coli GAPDH (ecGAPDH) has only been reported to function in glycolysis. The S-loop of GAPDH is required for interaction with its cofactor and with other proteins. In this study, the three-dimensional crystal structure of GAPDH treated with trehalose is reported at 2.0 Å resolution. Trehalose was used as a cryoprotectant for the GAPDH crystals. The structure of trehalose-bound ecGAPDH was compared with the structures of both NAD+-free and NAD+-bound ecGAPDH. At the S-loop, the bound trehalose in the GAPDH structure induces a 2.4° rotation compared with the NAD+-free ecGAPDH structure and a 3.1° rotation compared with the NAD+-bound ecGAPDH structure.
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Affiliation(s)
- Yong Ju Kim
- Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea
- Department of Lifestyle, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea
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18
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Dubey R, Staker BL, Foe IT, Bogyo M, Myler PJ, Ngô HM, Gubbels MJ. Membrane skeletal association and post-translational allosteric regulation of Toxoplasma gondii GAPDH1. Mol Microbiol 2017; 103:618-634. [PMID: 27859784 PMCID: PMC5296235 DOI: 10.1111/mmi.13577] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2016] [Indexed: 01/07/2023]
Abstract
When Toxoplasma gondii egresses from the host cell, glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1), which is primary a glycolysis enzyme but actually a quintessential multifunctional protein, translocates to the unique cortical membrane skeleton. Here, we report the 2.25 Å resolution crystal structure of the GAPDH1 holoenzyme in a quaternary complex providing the basis for the molecular dissection of GAPDH1 structure-function relationships Knockdown of GAPDH1 expression and catalytic site disruption validate the essentiality of GAPDH1 in intracellular replication but we confirmed that glycolysis is not strictly essential. We identify, for the first time, S-loop phosphorylation as a novel, critical regulator of enzymatic activity that is consistent with the notion that the S-loop is critical for cofactor binding, allosteric activation and oligomerization. We show that neither enzymatic activity nor phosphorylation state correlate with the ability to translocate to the cortex. However, we demonstrate that association of GAPDH1 with the cortex is mediated by the N-terminus, likely palmitoylation. Overall, glycolysis and cortical translocation are functionally decoupled by post-translational modifications.
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Affiliation(s)
- Rashmi Dubey
- Department of Biology, Boston College, MA 02467, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA 98109, USA,The Center for Infectious Disease Research, Seattle (formerly Seattle BioMed), WA 98109, USA
| | - Ian T. Foe
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 55324, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 55324, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA 98109, USA,The Center for Infectious Disease Research, Seattle (formerly Seattle BioMed), WA 98109, USA,Department of Global Health and Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Disease, Northwestern University, Chicago, IL 60611, USA,BrainMicro LLC, New Haven, CT 06511, USA,Corresponding authors: Huân Ngô and Marc-Jan Gubbels
| | - Marc-Jan Gubbels
- Department of Biology, Boston College, MA 02467, USA,Corresponding authors: Huân Ngô and Marc-Jan Gubbels
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19
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Abstract
Aside from its well-established role in glycolysis, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been shown to possess many key functions in cells. These functions are regulated by protein oligomerization , biomolecular interactions, post-translational modifications , and variations in subcellular localization . Several GAPDH functions and regulatory mechanisms overlap with one another and converge around its role in intermediary metabolism. Several structural determinants of the protein dictate its function and regulation. GAPDH is ubiquitously expressed and is found in all domains of life. GAPDH has been implicated in many diseases, including those of pathogenic, cardiovascular, degenerative, diabetic, and tumorigenic origins. Understanding the mechanisms by which GAPDH can switch between its functions and how these functions are regulated can provide insights into ways the protein can be modulated for therapeutic outcomes.
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20
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Schormann N, Ayres CA, Fry A, Green TJ, Banerjee S, Ulett GC, Chattopadhyay D. Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes. PLoS One 2016; 11:e0165917. [PMID: 27875551 PMCID: PMC5119734 DOI: 10.1371/journal.pone.0165917] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/19/2016] [Indexed: 01/07/2023] Open
Abstract
Glyceraldehyde 3-phosphate dehydrogenase or GAPDH is an evolutionarily conserved glycolytic enzyme. It catalyzes the two step oxidative phosphorylation of D-glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate using inorganic phosphate and NAD+ as cofactor. GAPDH of Group B Streptococcus is a major virulence factor and a potential vaccine candidate. Moreover, since GAPDH activity is essential for bacterial growth it may serve as a possible drug target. Crystal structures of Group B Streptococcus GAPDH in the apo-form, two different binary complexes and the ternary complex are described here. The two binary complexes contained NAD+ bound to 2 (mixed-holo) or 4 (holo) subunits of the tetrameric protein. The structure of the mixed-holo complex reveals the effects of NAD+ binding on the conformation of the protein. In the ternary complex, the phosphate group of the substrate was bound to the new Pi site in all four subunits. Comparison with the structure of human GAPDH showed several differences near the adenosyl binding pocket in Group B Streptococcus GAPDH. The structures also reveal at least three surface-exposed areas that differ in amino acid sequence compared to the corresponding areas of human GAPDH.
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Affiliation(s)
- Norbert Schormann
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Chapelle A. Ayres
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Alexandra Fry
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Todd J. Green
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Surajit Banerjee
- North-Eastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, Illinois 60439, United States of America
| | - Glen C. Ulett
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Parklands 4222, Australia
| | - Debasish Chattopadhyay
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
- * E-mail:
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21
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Mih N, Brunk E, Bordbar A, Palsson BO. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput Biol 2016; 12:e1005039. [PMID: 27467583 PMCID: PMC4965186 DOI: 10.1371/journal.pcbi.1005039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/27/2016] [Indexed: 12/31/2022] Open
Abstract
Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies. Recently, genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include the three-dimensional structure of proteins. The integration of these molecular-level details, such as the physical, structural, and dynamical properties of proteins, notably expands the computational description of biochemical network-level properties and the possibility of understanding and predicting whole cell phenotypes. In this study, we present a multi-scale modeling framework that describes biological processes which range in scale from atomistic details to an entire metabolic network. Using this approach, we can understand how genetic variation, which impacts the structure and reactivity of a protein, influences both native and drug-induced metabolic states. As a proof-of-concept, we study three enzymes (catechol-O-methyltransferase, glucose-6-phosphate dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase) and their respective genetic variants which have clinically relevant associations. Using all-atom molecular dynamic simulations enables the sampling of long timescale conformational dynamics of the proteins (and their mutant variants) in complex with their respective native metabolites or drug molecules. We find that changes in a protein's structure due to a mutation influences protein binding affinity to metabolites and/or drug molecules, and inflicts large-scale changes in metabolism.
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Affiliation(s)
- Nathan Mih
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, United States of America
| | - Elizabeth Brunk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (EB); (BOP)
| | - Aarash Bordbar
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (EB); (BOP)
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22
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Cook WJ, Senkovich O, Hernandez A, Speed H, Chattopadhyay D. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase. Int J Biol Macromol 2014; 74:608-19. [PMID: 25542170 DOI: 10.1016/j.ijbiomac.2014.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis. This paper describes the biochemical characterization of C. parvum lactate dehydrogenase and high resolution crystal structures of the apo-enzyme and four ternary complexes. The ternary complexes capture the enzyme bound to NAD/NADH or its 3-acetylpyridine analog in the cofactor binding pocket, while the substrate binding site is occupied by one of the following ligands: lactate, pyruvate or oxamate. The results reveal distinctive features of the parasitic enzyme. For example, C. parvum lactate dehydrogenase prefers the acetylpyridine analog of NADH as a cofactor. Moreover, it is slightly less sensitive to gossypol inhibition compared with mammalian lactate dehydrogenases and not inhibited by excess pyruvate. The active site loop and the antigenic loop in C. parvum lactate dehydrogenase are considerably different from those in the human counterpart. Structural features and enzymatic properties of C. parvum lactate dehydrogenase are similar to enzymes from related parasites. Structural comparison with malate dehydrogenase supports a common ancestry for the two genes.
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Affiliation(s)
- William J Cook
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Olga Senkovich
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Agustin Hernandez
- Instituto de Bioquímica Vegetal y Fotosintesis (CSIC/U. Sevilla), Avda. Americo Vespucio 49, Seville 41092, Spain
| | - Haley Speed
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Debasish Chattopadhyay
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, United States; Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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23
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Ayres CA, Schormann N, Senkovich O, Fry A, Banerjee S, Ulett GC, Chattopadhyay D. Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface. Acta Crystallogr F Struct Biol Commun 2014; 70:1333-9. [PMID: 25286935 PMCID: PMC4188075 DOI: 10.1107/s2053230x14019517] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 08/28/2014] [Indexed: 11/11/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH from Streptococcus agalactiae in complex with NAD is reported at 2.46 Å resolution. Although the overall structure of GBS GAPDH is very similar to those of other GAPDHs, the crystal structure reveals a significant difference in the area spanning residues 294-307, which appears to be more acidic. The amino-acid sequence of this region of GBS GAPDH is also distinct compared with other GAPDHs. This region therefore may be of interest as an immunogen for vaccine development.
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Affiliation(s)
- Chapelle A. Ayres
- Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Norbert Schormann
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Olga Senkovich
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alexandra Fry
- Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, IL 60439, USA
| | - Glen C. Ulett
- School of Medical Science and Griffith Health Institute, Griffith University, QLD 4222, Australia
| | - Debasish Chattopadhyay
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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24
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Lozano NBH, Oliveira RF, Weber KC, Honorio KM, Guido RVC, Andricopulo AD, de Sousa AG, da Silva ABF. Pattern recognition techniques applied to the study of leishmanial glyceraldehyde-3-phosphate dehydrogenase inhibition. Int J Mol Sci 2014; 15:3186-203. [PMID: 24566143 PMCID: PMC3958905 DOI: 10.3390/ijms15023186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 01/21/2014] [Accepted: 01/24/2014] [Indexed: 11/16/2022] Open
Abstract
Chemometric pattern recognition techniques were employed in order to obtain Structure-Activity Relationship (SAR) models relating the structures of a series of adenosine compounds to the affinity for glyceraldehyde 3-phosphate dehydrogenase of Leishmania mexicana (LmGAPDH). A training set of 49 compounds was used to build the models and the best ones were obtained with one geometrical and four electronic descriptors. Classification models were externally validated by predictions for a test set of 14 compounds not used in the model building process. Results of good quality were obtained, as verified by the correct classifications achieved. Moreover, the results are in good agreement with previous SAR studies on these molecules, to such an extent that we can suggest that these findings may help in further investigations on ligands of LmGAPDH capable of improving treatment of leishmaniasis.
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Affiliation(s)
- Norka B H Lozano
- Instituto de Química de São Carlos, USP, São Carlos (SP), 13566-590, Brazil.
| | - Rafael F Oliveira
- Universidade Federal da Paraíba, João Pessoa (PB), 58051-900, Brazil.
| | - Karen C Weber
- Universidade Federal da Paraíba, João Pessoa (PB), 58051-900, Brazil.
| | - Kathia M Honorio
- Escola de Artes Ciências e Humanidades, USP, São Paulo (SP), 03828-000, Brazil.
| | - Rafael V C Guido
- Instituto de Física de São Carlos, USP, São Carlos (SP), 13566-590, Brazil.
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25
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Lozano NBH, Oliveira RF, Weber KC, Honorio KM, Guido RV, Andricopulo AD, Da Silva ABF. Identification of electronic and structural descriptors of adenosine analogues related to inhibition of leishmanial glyceraldehyde-3-phosphate dehydrogenase. Molecules 2013; 18:5032-50. [PMID: 23629757 PMCID: PMC6269754 DOI: 10.3390/molecules18055032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 04/27/2013] [Accepted: 04/28/2013] [Indexed: 11/24/2022] Open
Abstract
Quantitative structure-activity relationship (QSAR) studies were performed in order to identify molecular features responsible for the antileishmanial activity of 61 adenosine analogues acting as inhibitors of the enzyme glyceraldehyde 3-phosphate dehydrogenase of Leishmania mexicana (LmGAPDH). Density functional theory (DFT) was employed to calculate quantum-chemical descriptors, while several structural descriptors were generated with Dragon 5.4. Variable selection was undertaken with the ordered predictor selection (OPS) algorithm, which provided a set with the most relevant descriptors to perform PLS, PCR and MLR regressions. Reliable and predictive models were obtained, as attested by their high correlation coefficients, as well as the agreement between predicted and experimental values for an external test set. Additional validation procedures were carried out, demonstrating that robust models were developed, providing helpful tools for the optimization of the antileishmanial activity of adenosine compounds.
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Affiliation(s)
- Norka B. H. Lozano
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13566-590, Brazil; E-Mail:
| | - Rafael F. Oliveira
- Departamento de Química, Universidade Federal da Paraiba, João Pessoa, PB 13083-970, Brazil; E-Mails: (R.F.O.); (K.W.C.)
| | - Karen C. Weber
- Departamento de Química, Universidade Federal da Paraiba, João Pessoa, PB 13083-970, Brazil; E-Mails: (R.F.O.); (K.W.C.)
| | - Kathia M. Honorio
- Centro de Ciência Naturais e Humanas, Universidade Federal do ABC, Santo Andre, SP 09210-170, Brazil; E-Mail:
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP 03828-000, Brazil; E-Mail:
| | - Rafael V. Guido
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-590, Brazil; E-Mails: (R.V.G.); (A.D.A.)
| | - Adriano D. Andricopulo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-590, Brazil; E-Mails: (R.V.G.); (A.D.A.)
| | - Albérico B. F. Da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13566-590, Brazil; E-Mail:
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Tien YC, Chuankhayan P, Huang YC, Chen CD, Alikhajeh J, Chang SL, Chen CJ. Crystal structures of rice (Oryza sativa) glyceraldehyde-3-phosphate dehydrogenase complexes with NAD and sulfate suggest involvement of Phe37 in NAD binding for catalysis. PLANT MOLECULAR BIOLOGY 2012; 80:389-403. [PMID: 22903596 DOI: 10.1007/s11103-012-9953-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 08/06/2012] [Indexed: 05/03/2023]
Abstract
Cytosolic Oryza sativa glyceraldehyde-3-phosphate dehydrogenase (OsGAPDH), the enzyme involved in the ubiquitous glycolysis, catalyzes the oxidative phosphorylation of glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate (BPG) using nicotinamide adenine dinucleotide (NAD) as an electron acceptor. We report crystal structures of OsGAPDH in three conditions of NAD-free, NAD-bound and sulfate-soaked forms to discuss the molecular determinants for coenzyme specificity. The structure of OsGAPDH showed a homotetramer form with each monomer comprising three domains-NAD-binding, catalytic and S-loop domains. NAD binds to each OsGAPDH subunits with some residues forming positively charged grooves that attract sulfate anions, as a simulation of phosphate groups in the product BPG. Phe37 not only forms a bottleneck to improve NAD-binding but also combines with Pro193 and Asp35 as key conserved residues for NAD-specificity in OsGAPDH. The binding of NAD alters the side-chain conformation of Phe37 with a 90° rotation related to the adenine moiety of NAD, concomitant with clamping the active site about 0.6 Å from the "open" to "closed" form, producing an increased affinity specific for NAD. Phe37 exists only in higher organisms, whereas it is replaced by other residues (Thr or Leu) with smaller side chains in lower organisms, which makes a greater distance between Leu34 and NAD of E. coli GAPDH than that between Phe37 and NAD of OsGAPDH. We demonstrated that Phe37 plays a crucial role in stabilizing NAD binding or intermediating of apo-holo transition, resulting in a greater NAD-dependent catalytic efficiency using site-directed mutagenesis. Phe37 might be introduced by evolution generating a catalytic advantage in cytosolic GAPDH.
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Affiliation(s)
- Yueh-Chu Tien
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
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27
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Mukherjee S, Dutta D, Saha B, Das AK. Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism. J Mol Biol 2010; 401:949-68. [PMID: 20620151 DOI: 10.1016/j.jmb.2010.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 07/01/2010] [Accepted: 07/02/2010] [Indexed: 11/29/2022]
Abstract
The dreaded pathogen Staphylococcus aureus is one of the causes of morbidity and mortality worldwide. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the key glycolytic enzymes, is irreversibly oxidized under oxidative stress and is responsible for sustenance of the pathogen inside the host. With an aim to elucidate the catalytic mechanism and identification of intermediates involved, we describe in this study different crystal structures of GAPDH1 from methicillin-resistant S. aureus MRSA252 (SaGAPDH1) in apo and holo forms of wild type, thioacyl intermediate, and ternary complexes of active-site mutants with physiological substrate d-glyceraldehyde-3-phosphate (G3P) and coenzyme NAD(+). A new phosphate recognition site, "new P(i)" site, similar to that observed in GAPDH from Thermotoga maritima, is reported here, which is 3.40 A away from the "classical P(i)" site. Ternary complexes discussed are representatives of noncovalent Michaelis complexes in the ground state. d-G3P is bound to all the four subunits of C151S.NAD and C151G.NAD in more reactive hydrate (gem-di-ol) form. However, in C151S+H178N.NAD, the substrate is bound to two chains in aldehyde form and in gem-di-ol form to the other two. This work reports binding of d-G3P to the C151G mutant in an inverted manner for the very first time. The structure of the thiaocyl complex presented here is formed after the hydride transfer. The C3 phosphate of d-G3P is positioned at the "P(s)" site in the ternary complexes but at the "new P(i)" site in the thioacyl complex and C1-O1 bond points opposite to His178 disrupting the alignment between itself and NE2 of His178. A new conformation (Conformation I) of the 209-215 loop has also been identified, where the interaction between phosphate ion at the "new P(i)" site and conserved Gly212 is lost. Altogether, inferences drawn from the kinetic analyses and crystal structures suggest the "flip-flop" model proposed for the enzyme mechanism.
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Affiliation(s)
- Somnath Mukherjee
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, Pin-721302, West Bengal, India
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Fermani S, Sparla F, Marri L, Thumiger A, Pupillo P, Falini G, Trost P. Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform A4) from Arabidopsis thaliana in complex with NAD. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:621-6. [PMID: 20516587 DOI: 10.1107/s1744309110013527] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 04/12/2010] [Indexed: 11/10/2022]
Abstract
The crystal structure of the A(4) isoform of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Arabidopsis thaliana, expressed in recombinant form and complexed with NAD, is reported. The crystals, which were grown in 2.4 M ammonium sulfate and 0.1 M sodium citrate, belonged to space group I222. The asymmetric unit includes ten subunits, i.e. two independent tetramers plus a dimer that generates a third tetramer by a crystallographic symmetry operation. The crystal structure was solved by molecular replacement and refined to an R factor of 23.7% and an R(free) factor of 28.9% at 2.6 A resolution. In the final model, each subunit binds one NAD(+) molecule and two sulfates, which occupy the P(s) and the P(i) anion-binding sites. Detailed knowledge of this structure is instrumental for structural investigation of supramolecular complexes of A(4)-GAPDH, phosphoribulokinase and CP12, which are involved in the regulation of photosynthesis in the model plant A. thaliana.
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Affiliation(s)
- Simona Fermani
- Department of Chemistry, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
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