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He Z, Wu M, Tian H, Wang L, Hu Y, Han F, Zhou J, Wang Y, Zhou L. Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun 2024; 15:1628. [PMID: 38388527 PMCID: PMC10884005 DOI: 10.1038/s41467-024-46018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III2 + IV and supercomplex III2 + IV2. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
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Affiliation(s)
- Zhaoxiang He
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengchen Wu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongtao Tian
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Liangdong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yiqi Hu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fangzhu Han
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China.
| | - Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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2
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McLeod MJ, Holyoak T. Biochemical, structural, and kinetic characterization of PP i -dependent phosphoenolpyruvate carboxykinase from Propionibacterium freudenreichii. Proteins 2023; 91:1261-1275. [PMID: 37226637 DOI: 10.1002/prot.26513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023]
Abstract
Phosphoenolpyruvate carboxykinases (PEPCK) are a well-studied family of enzymes responsible for the regulation of TCA cycle flux, where they catalyze the interconversion of oxaloacetic acid (OAA) and phosphoenolpyruvate (PEP) using a phosphoryl donor/acceptor. These enzymes have typically been divided into two nucleotide-dependent classes, those that use ATP and those that use GTP. In the 1960's and early 1970's, a group of papers detailed biochemical properties of an enzyme named phosphoenolpyruvate carboxytransphosphorylase (later identified as a third PEPCK) from Propionibacterium freudenreichii (PPi -PfPEPCK), which instead of using a nucleotide, utilized PPi to catalyze the same interconversion of OAA and PEP. The presented work expands upon the initial biochemical experiments for PPi -PfPEPCK and interprets these data considering both the current understanding of nucleotide-dependent PEPCKs and is supplemented with a new crystal structure of PPi -PfPEPCK in complex with malate at a putative allosteric site. Most interesting, the data are consistent with PPi -PfPEPCK being a Fe2+ activated enzyme in contrast with the Mn2+ activated nucleotide-dependent enzymes which in part results in some unique kinetic properties for the enzyme when compared to the more widely distributed GTP- and ATP-dependent enzymes.
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Affiliation(s)
- Matthew J McLeod
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Physics, Cornell University, Ithaca, New York, USA
| | - Todd Holyoak
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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3
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Torresi F, Rodriguez FM, Gomez-Casati DF, Martín M. Two phosphoenolpyruvate carboxykinases with differing biochemical properties in Chlamydomonas reinhardtii. FEBS Lett 2023; 597:585-597. [PMID: 36708098 DOI: 10.1002/1873-3468.14590] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/29/2023]
Abstract
Phosphoenolpyruvate carboxykinase (PEPCK) catalyses the reversible reaction of decarboxylation and phosphorylation of oxaloacetate (OAA) to generate phosphoenolpyruvate (PEP) and CO2 playing mainly a gluconeogenic role in green algae. We found two PEPCK isoforms in Chlamydomonas reinhardtii and we cloned, purified and characterised both enzymes. ChlrePEPCK1 is more active as decarboxylase than ChlrePEPCK2. ChlrePEPCK1 is hexameric and its activity is affected by citrate, phenylalanine and malate, while ChlrePEPCK2 is monomeric and it is regulated by citrate, phenylalanine and glutamine. We postulate that the two PEPCK isoforms found originate from alternative splicing of the gene or regulated proteolysis of the enzyme. The presence of these two isoforms would be part of a mechanism to finely regulate the biological activity of PEPCKs.
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Affiliation(s)
- Florencia Torresi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Santa Fe, Argentina.,Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Santa Fe, Argentina
| | - Fernanda M Rodriguez
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Santa Fe, Argentina.,Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Santa Fe, Argentina.,Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Santa Fe, Argentina
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Santa Fe, Argentina.,Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Santa Fe, Argentina
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4
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The Trypanosome UDP-Glucose Pyrophosphorylase Is Imported by Piggybacking into Glycosomes, Where Unconventional Sugar Nucleotide Synthesis Takes Place. mBio 2021; 12:e0037521. [PMID: 34044588 PMCID: PMC8262884 DOI: 10.1128/mbio.00375-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Glycosomes are peroxisome-related organelles of trypanosomatid parasites containing metabolic pathways, such as glycolysis and biosynthesis of sugar nucleotides, usually present in the cytosol of other eukaryotes. UDP-glucose pyrophosphorylase (UGP), the enzyme responsible for the synthesis of the sugar nucleotide UDP-glucose, is localized in the cytosol and glycosomes of the bloodstream and procyclic trypanosomes, despite the absence of any known peroxisome-targeting signal (PTS1 and PTS2). The questions that we address here are (i) is the unusual glycosomal biosynthetic pathway of sugar nucleotides functional and (ii) how is the PTS-free UGP imported into glycosomes? We showed that UGP is imported into glycosomes by piggybacking on the glycosomal PTS1-containing phosphoenolpyruvate carboxykinase (PEPCK) and identified the domains involved in the UGP/PEPCK interaction. Proximity ligation assays revealed that this interaction occurs in 3 to 10% of glycosomes, suggesting that these correspond to organelles competent for protein import. We also showed that UGP is essential for the growth of trypanosomes and that both the glycosomal and cytosolic metabolic pathways involving UGP are functional, since the lethality of the knockdown UGP mutant cell line (RNAiUGP, where RNAi indicates RNA interference) was rescued by expressing a recoded UGP (rUGP) in the organelle (RNAiUGP/EXPrUGP-GPDH, where GPDH is glycerol-3-phosphate dehydrogenase). Our conclusion was supported by targeted metabolomic analyses (ion chromatography–high-resolution mass spectrometry [IC-HRMS]) showing that UDP-glucose is no longer detectable in the RNAiUGP mutant, while it is still produced in cells expressing UGP exclusively in the cytosol (PEPCK null mutant) or glycosomes (RNAiUGP/EXPrUGP-GPDH). Trypanosomatids are the only known organisms to have selected functional peroxisomal (glycosomal) sugar nucleotide biosynthetic pathways in addition to the canonical cytosolic ones.
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do Amaral BS, da Silva LRG, Valverde AL, de Sousa LRF, Severino RP, de Souza DHF, Cass QB. Phosphoenolpyruvate carboxykinase from T. cruzi magnetic beads affinity-based screening assays on crude plant extracts from Brazilian Cerrado. J Pharm Biomed Anal 2020; 193:113710. [PMID: 33166842 DOI: 10.1016/j.jpba.2020.113710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 01/05/2023]
Abstract
In T. cruzi, a causative agent of Chagas disease, phosphoenolpyruvate carboxykinase (TcPEPCK) is associated with carbohydrate catabolism. Due to its importance in the metabolism of the parasite, it has become a promising target for the development of new drugs against Chagas disease. Aiming to investigate different approaches for ligands screening, TcPEPCK was immobilized on amine-terminated magnetic beads (TcPEPCK-MB) and kinetically characterized by liquid chromatography tandem mass spectrometry activity assay with a KMapp value of 10 ± 1 μM to oxaloacetate as substrate. Natural products library affords highly diverse molecular frameworks through their secondary metabolites, herein a ligand fishing TcPEPCK-MB assay is described for prospecting ligands in four ethanolic extracts of Brazilian Cerrado plants: Qualea grandiflora (Vochysiaceae), Diospyros burchellii (Ebenaceae), Anadenanthera falcata (Fabaceae) and Byrsonima coccolobifolia (Malpighiaceae). The chemical characterization of eleven identified ligands was carried out by liquid chromatography tandem high-resolution mass spectrometry experiments. Senecic acid, syneilesinolide A, phytosphingosine and vanillic acid 4-glucopyranoside are herein reported for the first time for Q. grandiflora, D. burchellii, A. falcata, respectively. In addition, the specificity of the assay was observed since only catechin was fished out from the ethanolic extract of B. coccolobifolia leaves, despite the presence of epicatechin epimer.
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Affiliation(s)
- Bruno S do Amaral
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, Campus Pirituba, 05110-000, São Paulo, SP, Brazil; Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Larissa R G da Silva
- Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil; Instituto de Química, Programa de Pós-Graduação em Química, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Alessandra L Valverde
- Instituto de Química, Programa de Pós-Graduação em Química, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Lorena R F de Sousa
- Unidade Acadêmica Especial de Química, Universidade Federal de Goiás, Regional Catalão, 75704-020, Catalão, GO, Brazil
| | - Richele P Severino
- Unidade Acadêmica Especial de Química, Universidade Federal de Goiás, Regional Catalão, 75704-020, Catalão, GO, Brazil
| | - Dulce H F de Souza
- Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Quezia B Cass
- Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil.
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6
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Seenappa V, Joshi MB, Satyamoorthy K. Intricate Regulation of Phosphoenolpyruvate Carboxykinase (PEPCK) Isoforms in Normal Physiology and Disease. Curr Mol Med 2020; 19:247-272. [PMID: 30947672 DOI: 10.2174/1566524019666190404155801] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The phosphoenolpyruvate carboxykinase (PEPCK) isoforms are considered as rate-limiting enzymes for gluconeogenesis and glyceroneogenesis pathways. PEPCK exhibits several interesting features such as a) organelle-specific isoforms (cytosolic and a mitochondrial) in vertebrate clade, b) tissue-specific expression of isoforms and c) organism-specific requirement of ATP or GTP as a cofactor. In higher organisms, PEPCK isoforms are intricately regulated and activated through several physiological and pathological stimuli such as corticoids, hormones, nutrient starvation and hypoxia. Isoform-specific transcriptional/translational regulation and their interplay in maintaining glucose homeostasis remain to be fully understood. Mounting evidence indicates the significant involvement of PEPCK isoforms in physiological processes (development and longevity) and in the progression of a variety of diseases (metabolic disorders, cancer, Smith-Magenis syndrome). OBJECTIVE The present systematic review aimed to assimilate existing knowledge of transcriptional and translational regulation of PEPCK isoforms derived from cell, animal and clinical models. CONCLUSION Based on current knowledge and extensive bioinformatics analysis, in this review we have provided a comparative (epi)genetic understanding of PCK1 and PCK2 genes encompassing regulatory elements, disease-associated polymorphisms, copy number variations, regulatory miRNAs and CpG densities. We have also discussed various exogenous and endogenous modulators of PEPCK isoforms and their signaling mechanisms. A comprehensive review of existing knowledge of PEPCK regulation and function may enable identification of the underlying gaps to design new pharmacological strategies and interventions for the diseases associated with gluconeogenesis.
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Affiliation(s)
- Venu Seenappa
- School of Life Sciences, Manipal Academy of Higher Education, Manipal - 576104, India
| | - Manjunath B Joshi
- School of Life Sciences, Manipal Academy of Higher Education, Manipal - 576104, India
| | - Kapaettu Satyamoorthy
- School of Life Sciences, Manipal Academy of Higher Education, Manipal - 576104, India
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7
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Synthesis of new N,S-acetal analogs derived from juglone with cytotoxic activity against Trypanossoma cruzi. J Bioenerg Biomembr 2020; 52:199-213. [PMID: 32418003 DOI: 10.1007/s10863-020-09834-8] [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: 09/06/2019] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
A series of 11 new N,S-acetal juglone derivatives were synthesized and evaluated against T. cruzi epimastigote forms. These compounds were obtained in good to moderate yields using a microwave irradiation protocol. Among all compounds, two N,S-acetal analogs, showed significant trypanocidal activity. Notably, one compound 11g exhibited selectivity index 10-fold higher than the reference drug benznidazole for epimastigote. The compound 11h was more effective for amastigote forms. Both prototypes exhibited S.I. higher than the benznidazole description. Thus, both compounds proving to be useful candidate molecules to further studies in infected animals.
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8
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Chiba Y, Miyakawa T, Shimane Y, Takai K, Tanokura M, Nozaki T. Structural comparisons of phosphoenolpyruvate carboxykinases reveal the evolutionary trajectories of these phosphodiester energy conversion enzymes. J Biol Chem 2019; 294:19269-19278. [PMID: 31662435 DOI: 10.1074/jbc.ra119.010920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/24/2019] [Indexed: 11/06/2022] Open
Abstract
Inorganic pyrophosphate (PPi) consists of two phosphate molecules and can act as an energy and phosphate donor in cellular reactions, similar to ATP. Several kinases use PPi as a substrate, and these kinases have recently been suggested to have evolved from ATP-dependent functional homologs, which have significant amino acid sequence similarity to PPi-utilizing enzymes. In contrast, phosphoenolpyruvate carboxykinase (PEPCK) can be divided into three types according to the phosphate donor (ATP, GTP, or PPi), and the amino acid sequence similarity of these PEPCKs is too low to confirm that they share a common ancestor. Here we solved the crystal structure of a PPi-PEPCK homolog from the bacterium Actinomyces israelii at 2.6 Å resolution and compared it with previously reported structures from ATP- and GTP-specific PEPCKs to assess the degrees of similarities and divergences among these PEPCKs. These comparisons revealed that they share a tertiary structure with significant value and that amino acid residues directly contributing to substrate recognition, except for those that recognize purine moieties, are conserved. Furthermore, the order of secondary structural elements between PPi-, ATP-, and GTP-specific PEPCKs was strictly conserved. The structure-based comparisons of the three PEPCK types provide key insights into the structural basis of PPi specificity and suggest that all of these PEPCKs are derived from a common ancestor.
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Affiliation(s)
- Yoko Chiba
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka-city, Kanagawa, 237-0061, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuhiro Shimane
- Super-Cutting-Edge Grand and Advanced Research Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka-city, Kanagawa, 237-0061, Japan
| | - Ken Takai
- Super-Cutting-Edge Grand and Advanced Research Program, Institute for Extra-Cutting-Edge Science and Technology Avant-Garde, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka-city, Kanagawa, 237-0061, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Lv Z, Qiu L, Wang W, Liu Z, Xue Z, Yu Z, Song X, Chen H, Wang L, Song L. A GTP-dependent Phosphoenolpyruvate Carboxykinase from Crassostrea gigas Involved in Immune Recognition. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:318-329. [PMID: 28888537 DOI: 10.1016/j.dci.2017.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/03/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
Phosphoenolpyruvate carboxykinase (PEPCK) is well known as a key enzyme involved in the metabolic pathway of gluconeogenesis in organisms, but the information about its involvement in immune response is still very limited. In the present study, a novel PEPCK homolog named CgPEPCK was identified from oyster Crassostrea gigas. The deduced amino acid sequence of CgPEPCK shared 52%-74% similarities with those from other known PEPCKs. There were one conserved guanosine triphosphate (GTP) binding site, one substrate binding site, one metal binding site and one active site in CgPEPCK. The mRNA transcripts of CgPEPCK were constitutively expressed in all the tested tissues including hemolymph, mantle, gill, muscle, gonad and hepatopancreas. CgPEPCK proteins were mainly distributed in adductor muscle, gonad, gill and mantle, and rarely detected in hepatopancreas by using immunohistochemical analysis. After the stimulations with lipopolysaccharide (LPS), peptidoglycan (PGN), Vibrio splendidus and V. anguillarum, CgPEPCK transcripts in hemocytes were significantly up-regulated and peaked at 6 h (LPS, 9.62-fold, p < 0.01), 9 h (PGN, 4.25-fold, p < 0.01), 12 h (V. splendidus, 5.72-fold, p < 0.01), 3 h (V. anguillarum, 2.87-fold, p < 0.01), respectively. The recombinant CgPEPCK protein (rCgPEPCK) exhibited Mn2+/Mg2+ dependent GTP binding activity, and the activities to bind LPS and PGN, but not β-1,3-glucan (GLU), lipoteichoic acid (LTA), mannan (MAN) nor polyinosinic-polycytidylic (Poly I: C). It could also bind Escherichia coli, Staphylococcus aureus, Micrococcus luteus and significantly inhibit their growth. All these results collectively suggested that CgPEPCK could not only exert GTP binding activity involved in gluconeogenesis, but also mediate the bacteria recognition and clearance in immune response of oysters.
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Affiliation(s)
- Zhao Lv
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Limei Qiu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Weilin Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoqun Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuang Xue
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Zichao Yu
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Xiaorui Song
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Hao Chen
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingling Wang
- Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China.
| | - Linsheng Song
- Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian 116023, China
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10
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Abstract
Phosphoenolpyruvate carboxykinase (PCK) is the key enzyme to initiate the gluconeogenic pathway in vertebrates, yeast, plants and most bacteria. Nucleotide specificity divided all PCKs into two groups. All the eukaryotic mammalian and most archaeal PCKs are GTP-specific. Bacterial and fungal PCKs can be ATP-or GTP-specific but all plant PCKs are ATP-specific. Amino acid sequence alignment of PCK enzymes shows that the nucleotide binding sites are somewhat conserved within each class with few exceptions that do not have any clear ATP- or GTP-specific binding motif. Although the active site residues are mostly conserved in all PCKs, not much significant sequence homology persists between ATP- and GTP-dependent PCK enzymes. There is only one planctomycetes PCK enzyme (from Cadidatus Kuenenia stuttgartiensis) that shows sequence homology with both ATP-and GTP-dependent PCKs. Phylogenetic studies have been performed to understand the evolutionary relationship of various PCKs from different sources. Based on this study a flowchart of the evolution of PCK has been proposed.
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Affiliation(s)
- Sanjukta Aich
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Louis T.J. Delbaere
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5, Canada
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11
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Shen Z, Dong XM, Gao ZF, Chao Q, Wang BC. Phylogenic and phosphorylation regulation difference of phosphoenolpyruvate carboxykinase of C3 and C4 plants. JOURNAL OF PLANT PHYSIOLOGY 2017; 213:16-22. [PMID: 28285130 DOI: 10.1016/j.jplph.2017.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 05/07/2023]
Abstract
In C4 plants, phosphoenolpyruvate carboxykinase (PEPCK) plays a key role in the C4 cycle. PEPCK is also involved in gluconeogenesis and is conserved in both lower and higher organisms, including in animals and plants. A phylogenic tree constructed from PEPCK sequences from bacteria to higher plants indicates that the C4 Poaceae PEPCKs are conserved and have diverged from the PEPCKs of C3 plants. The maximum enzymatic activities of wild-type and phosphorylation mimic PEPCK proteins indicate that there is a significant difference between C3 and C4 plant PEPCKs. The conserved PEPCK phosphorylation sites are regulated differently in C3 and C4 plants. These results suggest that the functions of PEPCK have been conserved, but that sequences have diverged and regulation of PEPCK is important in C4 plants, but not in herbaceous and, in particular, woody C3 plants.
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Affiliation(s)
- Zhuo Shen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiu-Mei Dong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhi-Fang Gao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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12
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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13
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Mou Z, Li J, Boussoffara T, Kishi H, Hamana H, Ezzati P, Hu C, Yi W, Liu D, Khadem F, Okwor I, Jia P, Shitaoka K, Wang S, Ndao M, Petersen C, Chen J, Rafati S, Louzir H, Muraguchi A, Wilkins JA, Uzonna JE. Identification of broadly conserved cross-species protective Leishmania antigen and its responding CD4+ T cells. Sci Transl Med 2016; 7:310ra167. [PMID: 26491077 DOI: 10.1126/scitranslmed.aac5477] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is currently no clinically effective vaccine against leishmaniasis because of poor understanding of the antigens that elicit dominant T cell immunity. Using proteomics and cellular immunology, we identified a dominant naturally processed peptide (PEPCK335-351) derived from Leishmania glycosomal phosphoenolpyruvate carboxykinase (PEPCK). PEPCK was conserved in all pathogenic Leishmania, expressed in glycosomes of promastigotes and amastigotes, and elicited strong CD4(+) T cell responses in infected mice and humans. I-A(b)-PEPCK335-351 tetramer identified protective Leishmania-specific CD4(+) T cells at a clonal level, which comprised ~20% of all Leishmania-reactive CD4(+) T cells at the peak of infection. PEPCK335-351-specific CD4(+) T cells were oligoclonal in their T cell receptor usage, produced polyfunctional cytokines (interleukin-2, interferon-γ, and tumor necrosis factor), and underwent expansion, effector activities, contraction, and stable maintenance after lesion resolution. Vaccination with PEPCK peptide, DNA expressing full-length PEPCK, or rPEPCK induced strong durable cross-species protection in both resistant and susceptible mice. The effectiveness and durability of protection in vaccinated mice support the development of a broadly cross-species protective vaccine against different forms of leishmaniasis by targeting PEPCK.
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Affiliation(s)
- Zhirong Mou
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Jintao Li
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada. Institute of Tropical Medicine, Third Military Medical University, Chongqing 400038, China
| | - Thouraya Boussoffara
- Laboratory of Transmission, Control and Immunobiology of Infections, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Hiroshi Hamana
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Health Sciences Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Chuanmin Hu
- Department of Clinical Biochemistry, Laboratory Sciences, Third Military Medical University, Chongqing 400038, China
| | - Weijing Yi
- Department of Clinical Biochemistry, Laboratory Sciences, Third Military Medical University, Chongqing 400038, China
| | - Dong Liu
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Forough Khadem
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Ifeoma Okwor
- Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ping Jia
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada
| | - Kiyomi Shitaoka
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Shufeng Wang
- Department of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Momar Ndao
- National Reference Centre for Parasitology, Department of Medicine, Division of Infectious Diseases, McGill University, Montreal, Quebec H3G 1A4, Canada
| | | | - Jianping Chen
- Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610065, China
| | - Sima Rafati
- Molecular Immunology and Vaccine Research Laboratory, Pasteur Institute of Iran, Tehran 13164, Iran
| | - Hechmi Louzir
- Laboratory of Transmission, Control and Immunobiology of Infections, Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - John A Wilkins
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Health Sciences Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Jude E Uzonna
- Department of Immunology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3T 0T5, Canada. Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.
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14
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Sun Z, Chen YF, Du J. Elevated CO2 improves lipid accumulation by increasing carbon metabolism in Chlorella sorokiniana. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:557-66. [PMID: 25973988 DOI: 10.1111/pbi.12398] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/14/2015] [Accepted: 04/16/2015] [Indexed: 05/12/2023]
Abstract
Supplying microalgae with extra CO2 is a promising means for improving lipid production. The molecular mechanisms involved in lipid accumulation under conditions of elevated CO2, however, remain to be fully elucidated. To understand how elevated CO2 improves lipid production, we performed sequencing of Chlorella sorokiniana LS-2 cellular transcripts during growth and compared transcriptional dynamics of genes involved in carbon flow from CO2 to triacylglycerol. These analyses identified the majority genes of carbohydrate metabolism and lipid biosynthesis pathways in C. sorokiniana LS-2. Under high doses of CO2 , despite down-regulation of most de novo fatty acid biosynthesis genes, genes involved in carbohydrate metabolic pathways including carbon fixation, chloroplastic glycolysis, components of the pyruvate dehydrogenase complex (PDHC) and chloroplastic membrane transporters were upexpressed at the prolonged lipid accumulation phase. The data indicate that lipid production is largely independent of de novo fatty acid synthesis. Elevated CO2 might push cells to channel photosynthetic carbon precursors into fatty acid synthesis pathways, resulting in an increase of overall triacylglycerol generation. In support of this notion, genes involved in triacylglycerol biosynthesis were substantially up-regulated. Thus, elevated CO2 may influence regulatory dynamics and result in increased carbon flow to triacylglycerol, thereby providing a feasible approach to increase lipid production in microalgae.
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Affiliation(s)
- Zhilan Sun
- Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yi-Feng Chen
- Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jianchang Du
- Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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15
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Sosa MH, Giordana L, Nowicki C. Exploring biochemical and functional features of Leishmania major phosphoenolpyruvate carboxykinase. Arch Biochem Biophys 2015; 583:120-9. [PMID: 26271440 DOI: 10.1016/j.abb.2015.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 10/23/2022]
Abstract
This work reports the first functional characterization of leishmanial PEPCK. The recombinant Leishmania major enzyme (Lmj_PEPCK) exhibits equivalent kcat values for the phosphoenolpyruvate (PEP) and oxaloacetate (OAA) forming reactions. The apparent Km towards OAA is 10-fold lower than that for PEP, while the Km values for ADP and ATP are equivalent. Mutagenesis studies showed that D241, D242 and H205 of Lmj_PEPCK like the homologous residues of all known PEPCKs are implicated in metal ions binding. In contrast, the replacement of R43 for Q nearly abolishes Lmj_PEPCK activity. Moreover, the Y180F variant exhibits unchanged Km values for PEP, Mn(2+), and [Formula: see text] , being the kcat for PEP- but not that for OAA-forming reaction more notably decreased. Instead, the Y180A mutant displays an increase in the Km value towards Mn(2+). Therefore in Lmj_PEPCK, Y180 seems to exert different functions to those of the analogous residue in ATP- and GTP-dependant enzymes. Besides, the guanidinium group of R43 appears to play an essential but yet unknown role. These findings promote the need for further structural studies to disclose whether Y180 and R43 participate in the catalytic mechanism or/and in the transitions between the open and the catalytically competent (closed) forms of Lmj_PEPCK.
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Affiliation(s)
- Máximo Hernán Sosa
- Instituto de Química y Fisicoquímica Biológica IQUIFIB-CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Lucila Giordana
- Instituto de Química y Fisicoquímica Biológica IQUIFIB-CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Cristina Nowicki
- Instituto de Química y Fisicoquímica Biológica IQUIFIB-CONICET, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina.
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16
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Machová I, Snášel J, Dostál J, Brynda J, Fanfrlík J, Singh M, Tarábek J, Vaněk O, Bednárová L, Pichová I. Structural and functional studies of phosphoenolpyruvate carboxykinase from Mycobacterium tuberculosis. PLoS One 2015; 10:e0120682. [PMID: 25798914 PMCID: PMC4370629 DOI: 10.1371/journal.pone.0120682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/05/2015] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis, the second leading infectious disease killer after HIV, remains a top public health priority. The causative agent of tuberculosis, Mycobacterium tuberculosis (Mtb), which can cause both acute and clinically latent infections, reprograms metabolism in response to the host niche. Phosphoenolpyruvate carboxykinase (Pck) is the enzyme at the center of the phosphoenolpyruvate-pyruvate-oxaloacetate node, which is involved in regulating the carbon flow distribution to catabolism, anabolism, or respiration in different states of Mtb infection. Under standard growth conditions, Mtb Pck is associated with gluconeogenesis and catalyzes the metal-dependent formation of phosphoenolpyruvate. In non-replicating Mtb, Pck can catalyze anaplerotic biosynthesis of oxaloacetate. Here, we present insights into the regulation of Mtb Pck activity by divalent cations. Through analysis of the X-ray structure of Pck-GDP and Pck-GDP-Mn2+ complexes, mutational analysis of the GDP binding site, and quantum mechanical (QM)-based analysis, we explored the structural determinants of efficient Mtb Pck catalysis. We demonstrate that Mtb Pck requires presence of Mn2+ and Mg2+ cations for efficient catalysis of gluconeogenic and anaplerotic reactions. The anaplerotic reaction, which preferably functions in reducing conditions that are characteristic for slowed or stopped Mtb replication, is also effectively activated by Fe2+ in the presence of Mn2+ or Mg2+ cations. In contrast, simultaneous presence of Fe2+ and Mn2+ or Mg2+ inhibits the gluconeogenic reaction. These results suggest that inorganic ions can contribute to regulation of central carbon metabolism by influencing the activity of Pck. Furthermore, the X-ray structure determination, biochemical characterization, and QM analysis of Pck mutants confirmed the important role of the Phe triad for proper binding of the GDP-Mn2+ complex in the nucleotide binding site and efficient catalysis of the anaplerotic reaction.
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Affiliation(s)
- Iva Machová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Snášel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jiří Dostál
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Mahavir Singh
- LIONEX diagnostics & Therapeutics, Braunschweig, Germany
| | - Ján Tarábek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Sciences, Charles University in Prague, Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- * E-mail:
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17
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Menna-Barreto RFS, Perales J. The expected outcome of the Trypanosoma cruzi proteomic map: a review of its potential biological applications for drug target discovery. Subcell Biochem 2014; 74:305-322. [PMID: 24264251 DOI: 10.1007/978-94-007-7305-9_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chagas disease is a neglected tropical illness endemic to Latin America, and its treatment remains unsatisfactory. This disease is caused by the hemoflagellate protozoan Trypanosoma cruzi, which has a complex life cycle involving three evolutive forms in both vertebrate and invertebrate hosts. Targeting metabolic pathways in the parasite for rational drug design represents a promising research field. This research area requires high performance techniques and proteomics become a powerful tool in this context. Here, we review advances in the construction of proteomic maps of the different forms of T. cruzi, emphasizing their biological applications towards the identification of alternative candidates for drug intervention.
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Affiliation(s)
- Rubem F S Menna-Barreto
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
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18
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Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu RY, van der Giezen M, Tielens AGM, Martin WF. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol Mol Biol Rev 2012; 76:444-95. [PMID: 22688819 PMCID: PMC3372258 DOI: 10.1128/mmbr.05024-11] [Citation(s) in RCA: 484] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major insights into the phylogenetic distribution, biochemistry, and evolutionary significance of organelles involved in ATP synthesis (energy metabolism) in eukaryotes that thrive in anaerobic environments for all or part of their life cycles have accrued in recent years. All known eukaryotic groups possess an organelle of mitochondrial origin, mapping the origin of mitochondria to the eukaryotic common ancestor, and genome sequence data are rapidly accumulating for eukaryotes that possess anaerobic mitochondria, hydrogenosomes, or mitosomes. Here we review the available biochemical data on the enzymes and pathways that eukaryotes use in anaerobic energy metabolism and summarize the metabolic end products that they generate in their anaerobic habitats, focusing on the biochemical roles that their mitochondria play in anaerobic ATP synthesis. We present metabolic maps of compartmentalized energy metabolism for 16 well-studied species. There are currently no enzymes of core anaerobic energy metabolism that are specific to any of the six eukaryotic supergroup lineages; genes present in one supergroup are also found in at least one other supergroup. The gene distribution across lineages thus reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style. Some facultative anaerobes have retained both aerobic and anaerobic pathways. Diversified eukaryotic lineages have retained the same enzymes of anaerobic ATP synthesis, in line with geochemical data indicating low environmental oxygen levels while eukaryotes arose and diversified.
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Affiliation(s)
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jaap J. van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Katrin Henze
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Christian Woehle
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Re-Young Yu
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Mark van der Giezen
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aloysius G. M. Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
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Pérez E, Cardemil E. Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase: the relevance of Glu299 and Leu460 for nucleotide binding. Protein J 2010; 29:299-305. [PMID: 20524049 DOI: 10.1007/s10930-010-9252-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A homology model of Saccharomyces cerevisiae phosphoenolpyruvate (PEP) carboxykinase (ATP + oxaloacetate right arrow over left arrow ADP + PEP + CO(2)) in complex with its substrates shows that the isobutyl group of Leu460 is in close proximity to the adenine ring of the nucleotide, while the carboxyl group of Glu299 is within hydrogen-bonding distance of the ribose 2'OH. The Leu460Ala mutation caused three-fold and seven-fold increases in the K (m) for ADPMn(-) and ATPMn(2-), respectively, while the Glu299Ala mutation had no effect. Binding studies showed losses of approximately 2 kcal mol(-1) in the nucleotide binding affinity due to the Leu460Ala mutation and no effect for the Glu299Ala mutation. PEP carboxykinase utilized 2'deoxyADP and 2'deoxyATP as substrates with kinetic and equilibrium dissociation constants very similar to those of ADP and ATP, respectively. These results show that the hydrophobic interaction between Leu460 and the adenine ring of the nucleotide significantly contributed to the nucleotide affinity of the enzyme. The 2'deoxy nucleotide studies and the lack of an effect of the Glu299Ala mutation in nucleotide binding suggest that the possible hydrogen bond contributed by Glu299 and the ribose 2'OH group may not be relevant for nucleotide binding.
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Affiliation(s)
- Estela Pérez
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. B. O'Higgins 3363, Santiago, Chile
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20
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Sepúlveda C, Poch A, Espinoza R, Cardemil E. Electrostatic interactions play a significant role in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn2+. Biochimie 2010; 92:814-9. [PMID: 20211682 DOI: 10.1016/j.biochi.2010.02.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 02/25/2010] [Indexed: 10/19/2022]
Abstract
Phosphoenolpyruvate (PEP) carboxykinases catalyse the reversible formation of oxaloacetate (OAA) and ATP (or GTP) from PEP, ADP (or GDP) and CO(2). They are activated by Mn(2+), a metal ion that coordinates to the protein through the epsilon-amino group of a lysine residue, the N(epsilon-2)-imidazole of a histidine residue, and the carboxylate from an aspartic acid residue. Neutrality in the epsilon-amino group of Lys213 of Saccharomyces cerevisiae PEP carboxykinase is expected to be favoured by the vicinity of ionised Lys212. Glu272 and Glu284, located close to Lys212, should, in turn, electrostatically stabilise its positive charge and hence assist in keeping the epsilon-amino group of Lys213 in a neutral state. The mutations Glu272Gln, Glu284Gln, and Lys212Met increased the activation constant for Mn(2+) in the main reaction of the enzyme up to seven-fold. The control mutation Lys213Gln increased this constant by ten-fold, as opposed to control mutation Lys212Arg, which did not affect the Mn(2+) affinity of the enzyme. These observations indicate a role for Glu272, Glu284, and Lys212 in assisting Lys213 to properly bind Mn(2+). In an unexpected result, the mutations Glu284Gln, Lys212Met and Lys213Gln changed the nucleotide-independent OAA decarboxylase activity of S. cerevisiae PEP carboxykinase into an ADP-requiring activity, implying an effect on the OAA binding characteristics of PEP carboxykinase.
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Affiliation(s)
- Carolina Sepúlveda
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. B. O'Higgins 3363, Santiago 9170022, Chile
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21
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Chapter 14 C4 Decarboxylases: Different Solutions for the Same Biochemical Problem, the Provision of CO2 to Rubisco in the Bundle Sheath Cells. C4 PHOTOSYNTHESIS AND RELATED CO2 CONCENTRATING MECHANISMS 2010. [DOI: 10.1007/978-90-481-9407-0_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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Fischer H, de Oliveira Neto M, Napolitano HB, Polikarpov I, Craievich AF. Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale. J Appl Crystallogr 2009. [DOI: 10.1107/s0021889809043076] [Citation(s) in RCA: 357] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This paper describes a new and simple method to determine the molecular weight of proteins in dilute solution, with an error smaller than ∼10%, by using the experimental data of a single small-angle X-ray scattering (SAXS) curve measured on a relative scale. This procedure does not require the measurement of SAXS intensity on an absolute scale and does not involve a comparison with another SAXS curve determined from a known standard protein. The proposed procedure can be applied to monodisperse systems of proteins in dilute solution, either in monomeric or multimeric state, and it has been successfully tested on SAXS data experimentally determined for proteins with known molecular weights. It is shown here that the molecular weights determined by this procedure deviate from the known values by less than 10% in each case and the average error for the test set of 21 proteins was 5.3%. Importantly, this method allows for an unambiguous determination of the multimeric state of proteins with known molecular weights.
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23
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Alves-Ferreira M, Guimarães ACR, Capriles PVDSZ, Dardenne LE, Degrave WM. A new approach for potential drug target discovery through in silico metabolic pathway analysis using Trypanosoma cruzi genome information. Mem Inst Oswaldo Cruz 2009; 104:1100-10. [DOI: 10.1590/s0074-02762009000800006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 10/28/2009] [Indexed: 11/22/2022] Open
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24
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Carlson GM, Holyoak T. Structural insights into the mechanism of phosphoenolpyruvate carboxykinase catalysis. J Biol Chem 2009; 284:27037-41. [PMID: 19638345 DOI: 10.1074/jbc.r109.040568] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Gerald M Carlson
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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25
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Meesters C, Brack A, Hellmann N, Decker H. Structural characterization of the alpha-hemolysin monomer from Staphylococcus aureus. Proteins 2009; 75:118-26. [PMID: 18798569 DOI: 10.1002/prot.22227] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Alpha-hemolysin from Staphylococcus aureus is secreted as a water-soluble monomer and assembles on membranes to oligomerize into a homo-heptameric, water-filled pore. These pores lead to lysis and cell death. Although the structure of the heptameric pore is solved by means of X-ray crystallography, structures of intermediate states-from the soluble monomer to all potential "pre-pore" structures-are yet unknown. Here, we propose a model of the monomeric alpha-hemolysin in solution based on molecular modeling, verified by small angle X-ray scattering data. This structure reveals details of the monomeric conformation of the alpha-hemolysin, for example inherent flexibility, along with definite differences in comparison to the structures used as templates.
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Molecular and biochemical characterization of phosphoenolpyruvate carboxykinase in the ruminal bacterium Ruminococcus albus. Curr Microbiol 2009; 58:416-20. [PMID: 19194751 DOI: 10.1007/s00284-008-9325-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 10/15/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
Abstract
Molecular properties and transcriptional control of phosphoenolpyruvate carboxykinase (PCK; EC 4.1.1.32) in Ruminococcus albus were examined. The putative 537-amino acid PCK polypeptide has a predicted mass of 59.4 kDa and an isoelectric point of 4.82. RT-PCR and Northern blot analyses of pck mRNA suggest that the transcript is monocistronic and that pck transcription is not affected by changes in sugar sources present in growth medium. PCK enzymatic activity requires either Mg(2+) or Mn(2+) and an optimal pH of 7.0. R. albus PCK phosphorylated ADP more readily than GDP. Apparent K ( m ) values of PCK for PEP and ADP were considerably lower than those for OAA and ATP, suggesting that the reaction from PEP to OAA is favored in R. albus. The enzyme properties of PCK in R. albus appear to be more similar to Selenomonas ruminantium PCK than to Ruminococcus flavefacience, although R. albus and R. flavefacience belong to the same genus. The specific activity of PCK, representing the amount of enzyme per cell, in R. albus was much lower than that in S. ruminantium. The amount of succinate produced in R. albus from one unit of cellobiose was also much lower than the sum of succinate and propionate produced in S. ruminantium. Based on these results, we propose enhancement of PCK activity by stimulating PCK transcription as a method to decrease R. albus H(2) production without suppressing growth.
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Tobar I, González-Nilo FD, Jabalquinto AM, Cardemil E. Relevance of Arg457 for the nucleotide affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase. Int J Biochem Cell Biol 2008; 40:1883-9. [PMID: 18346928 DOI: 10.1016/j.biocel.2008.01.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 12/19/2007] [Accepted: 01/23/2008] [Indexed: 12/16/2022]
Abstract
Phosphoenolpyruvate carboxykinases catalyze one of the first steps in the biosynthesis of glucose and depending on the enzyme origin, preferentially use adenine or guanine nucleotides as substrates. The Saccharomyces cerevisiae enzyme has a marked preference for ADP (or ATP) over other nucleotides. Homology models of the enzyme in complex with ADP or ATP show that the guanidinium group of Arg457 is close to the adenine base, suggesting that this group might be involved in the stabilization of the nucleotide substrate. To evaluate this we have performed the mutation Arg457Met, replacing the positively charged guanidinium group by a neutral residue. The mutated enzyme retained the structural characteristics of the wild-type protein. Fluorescence titration experiments showed that mutation causes a loss of 1.7 kcal mol(-1) in the binding affinity of the enzyme for ADPMn. Similarly, kinetic analyses of the mutated enzyme showed 50-fold increase in K(m) for ADPMn, with minor alterations in the other kinetic parameters. These results show that Arg457 is an important factor for nucleotide binding by S. cerevisiae PEP carboxykinase.
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Affiliation(s)
- Iván Tobar
- Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago 33, Chile
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28
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Yévenes A, González-Nilo FD, Cardemil E. Relevance of phenylalanine 216 in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn(II). Protein J 2006; 26:135-41. [PMID: 17195942 DOI: 10.1007/s10930-006-9054-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Saccharomyces cerevisiae phosphoenolpyruvate (PEP) carboxykinase catalyzes the reversible formation of oxaloacetate and adenosine triphosphate from PEP, adenosine diphosphate and carbon dioxide, and uses Mn(2+) as the activating metal ion. Comparison with the crystalline structure of homologous Escherichia coli PEP carboxykinase [Tari et al. (1997) Nature Struct. Biol. 4, 990-994] shows that Lys(213) is one of the ligands to Mn(2+) at the enzyme active site. Coordination of Mn(2+) to a lysyl residue is not common and suggests a low pK (a) value for the epsilon-NH(2) group of Lys(213). In this work, we evaluate the role of neighboring Phe(216) in contributing to provide a low polarity microenvironment suitable to keep the epsilon-NH(2) of Lys(213) in the unprotonated form. Mutation Phe216Tyr shows that the introduction of a hydroxyl group in the lateral chain of the residue produces a substantial loss in the enzyme affinity for Mn(2+), suggesting an increase of the pK (a) of Lys(213). In agreement with this interpretation, theoretical calculations indicate an alkaline shift of 2.8 pH units in the pK (a) of the epsilon-amino group of Lys(213) upon Phe216Tyr mutation.
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Affiliation(s)
- Alejandro Yévenes
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 33, Chile
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Yévenes A, Espinoza R, Rivas-Pardo JA, Villarreal JM, González-Nilo FD, Cardemil E. Site-directed mutagenesis study of the microenvironment characteristics of Lys213 of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase. Biochimie 2006; 88:663-72. [PMID: 16469427 DOI: 10.1016/j.biochi.2005.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Accepted: 12/19/2005] [Indexed: 10/25/2022]
Abstract
Saccharomyces cerevisiae phosphoenolpyruvate (PEP) carboxykinase catalyzes the reversible formation of oxaloacetate and adenosine triphosphate from PEP, adenosine diphosphate and carbon dioxide, and uses Mn(2+) as the activating metal ion. Comparison with the crystalline structure of homologous Escherichia coli PEP carboxykinase [Tari et al. Nature Struct. Biol. 4 (1997) 990-994] shows that Lys(213) is one of the ligands to Mn(2+) at the enzyme active site. Coordination of Mn(2+) to a lysyl residue is infrequent and suggests a low pK(a) value for the epsilon-NH(2) group of Lys(213). In this work, we evaluate the role of neighboring Phe(416) in contributing to provide a low polarity microenvironment suitable to keep the epsilon-NH(2) of Lys(213) in the unprotonated form. Mutation Phe416Tyr shows that the introduction of a hydroxyl group in the lateral chain of the residue produces a substantial loss in the enzyme affinity for Mn(2+), suggesting an increase of the pK(a) of Lys(213). A study of the effect of pH on K(m) for Mn(2+) indicate that the affinity of recombinant wild type enzyme for the metal ion is dependent on deprotonation of a group with pK(a) of 7.1+/-0.2, compatible with the low pK(a) expected for Lys(213). This pK(a) value increases at least 1.5 pH units upon Phe416Tyr mutation, in agreement with the expected effect of an increase in the polarity of Lys(213) microenvironment. Theoretical calculations of the pK(a) of Lys(213) indicate a value of 6.5+/-0.9, and it increases to 8.2+/-1.6 upon Phe416Tyr mutation. Additionally, mutation Phe416Tyr causes a loss of 1.3 kcal mol(-1) in the affinity of the enzyme for PEP, an effect perhaps related to the close proximity of Phe(416) to Arg(70), a residue previously shown to be important for PEP binding.
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Affiliation(s)
- Alejandro Yévenes
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago 33, Chile
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Cotelesage JJH, Prasad L, Zeikus JG, Laivenieks M, Delbaere LTJ. Crystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop. Int J Biochem Cell Biol 2005; 37:1829-37. [PMID: 15890557 DOI: 10.1016/j.biocel.2005.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 02/17/2005] [Accepted: 03/18/2005] [Indexed: 11/15/2022]
Abstract
The 2.2 Angstroms resolution crystal structure of the enzyme phosphoenolpyruvate carboxykinase (PCK) from the bacterium Anaerobiospirillum succiniciproducens complexed with ATP, Mg(2+), Mn(2+) and the transition state analogue oxalate has been solved. The 2.4 Angstroms resolution native structure of A. succiniciproducens PCK has also been determined. It has been found that upon binding of substrate, PCK undergoes a conformational change. Two domains of the molecule fold towards each other, with the substrates and metal ions held in a cleft formed between the two domains. This domain movement is believed to accelerate the reaction PCK catalyzes by forcing bulk solvent molecules out of the active site. Although the crystal structure of A. succiniciproducens PCK with bound substrate and metal ions is related to the structures of PCK from Escherichia coli and Trypanosoma cruzi, it is the first crystal structure from this class of enzymes that clearly shows an important surface loop (residues 383-397) from the C-terminal domain, hydrogen bonding with the peptide backbone of the active site residue Arg60. The interaction between the surface loop and the active site backbone, which is a parallel beta-sheet, seems to be a feature unique of A. succiniciproducens PCK. The association between the loop and the active site is the third type of interaction found in PCK that is thought to play a part in the domain closure. This loop also appears to help accelerate catalysis by functioning as a 'lid' that shields water molecules from the active site.
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31
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Takahashi-Terada A, Kotera M, Ohshima K, Furumoto T, Matsumura H, Kai Y, Izui K. Maize Phosphoenolpyruvate Carboxylase. J Biol Chem 2005; 280:11798-806. [PMID: 15665330 DOI: 10.1074/jbc.m408768200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphoenolpyruvate carboxylases (PEPC, EC 4.1.1.31) from higher plants are regulated by both allosteric effects and reversible phosphorylation. Previous x-ray crystallographic analysis of Zea mays PEPC has revealed a binding site for sulfate ion, speculated to be the site for an allosteric activator, glucose 6-phosphate (Glc-6-P) (Matsumura, H., Xie, Y., Shirakata, S., Inoue, T., Yoshinaga, T., Ueno, Y., Izui, K., and Kai, Y. (2002) Structure (Lond.) 10, 1721-1730). Because kinetic experiments have also supported this notion, each of the four basic residues (Arg-183, -184, -231, and -372' on the adjacent subunit) located at or near the binding site was replaced by Gln, and the kinetic properties of recombinant mutant enzymes were investigated. Complete desensitization to Glc-6-P was observed for R183Q, R184Q, R183Q/R184Q (double mutant), and R372Q, as was a marked decrease in the sensitivity for R231Q. The heterotropic effect of Glc-6-P on an allosteric inhibitor, l-malate, was also abolished, but sensitivity to Gly, another allosteric activator of monocot PEPC, was essentially not affected, suggesting the distinctness of their binding sites. Considering the kinetic and structural data, Arg-183 and Arg-231 were suggested to be involved directly in the binding with phosphate group of Glc-6-P, and the residues Arg-184 and Arg-372 were thought to be involved in making up the site for Glc-6-P and/or in the transmission of an allosteric regulatory signal. Most unexpectedly, the mutant enzymes had almost lost responsiveness to regulatory phosphorylation at Ser-15. An apparent lack of kinetic competition between the phosphate groups of Glc-6-P and of phospho-Ser at 15 suggested the distinctness of their binding sites. The possible roles of these Arg residues are discussed.
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Affiliation(s)
- Akiko Takahashi-Terada
- Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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Cristina Ravanal M, Flores M, Pérez E, Aroca F, Cardemil E. Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase: relevance of arginine 70 for catalysis. Biochimie 2005; 86:357-62. [PMID: 15358051 DOI: 10.1016/j.biochi.2004.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2003] [Accepted: 06/08/2004] [Indexed: 11/25/2022]
Abstract
Saccharomyces cerevisiae phosphoenolpyruvate (PEP) carboxykinase is a key enzyme of the gluconeogenic pathway and catalyzes the decarboxylation of oxaloacetate and transfer of the gamma-phosphoryl group of ATP to yield PEP, ADP, and CO2 in the presence of a divalent metal ion. Previous experiments indicate that mutation of amino acid residues at metal site 1 decrease the enzyme catalytic efficiency and the affinity of the protein for PEP, evidencing the relevance of hydrogen-bond interactions between PEP and water molecules of the first coordination sphere of the metal ion for catalysis [Biochemistry 41 (2002) 12763]. To further understand the function of amino acid residues located in the PEP binding site, we have now addressed the catalytic importance of Arg70, whose guanidinium group is close to the PEP carboxyl group. Arg70 mutants of PEP carboxykinase were prepared, and almost unaltered kinetic parameters were found for the Arg70Lys PEP carboxykinase, while a decrease in 4-5 orders of magnitude for the catalytic efficiency was detected for the Arg70Gln and Arg70Met altered enzymes. To evaluate the enzyme interaction with PEP, the phosphopyridoxyl-derivatives of wild type, Arg70Lys, Arg70Gln, and Arg70Met S. cerevisiae PEP carboxykinase were prepared, and the change in the fluorescence emission of the probe upon PEP binding was used to obtain the dissociation equilibrium constant of the corresponding derivatized enzyme-PEP-Mn2+ complex. The titration experiments showed that a loss in 2.1 kcal/mol in PEP binding affinity is produced in the Arg70Met and Arg70Gln mutant enzymes. It is proposed that the electrostatic interaction between the guanidinium group of Arg70 and the carboxyl group of PEP is important for PEP binding and for further steps in catalysis.
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Affiliation(s)
- M Cristina Ravanal
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago 33, Chile
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33
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Delbaere LTJ, Sudom AM, Prasad L, Leduc Y, Goldie H. Structure/function studies of phosphoryl transfer by phosphoenolpyruvate carboxykinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1697:271-8. [PMID: 15023367 DOI: 10.1016/j.bbapap.2003.11.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Accepted: 11/12/2003] [Indexed: 11/24/2022]
Abstract
Phosphoenolpyruvate carboxykinase (PCK) catalyzes the conversion of oxaloacetate (OAA) to PEP and carbon dioxide with the subsequent conversion of nucleoside triphosphate to nucleoside diphosphate (NDP). The 1.9 A resolution structure of Escherichia coli PCK consisted of a 275-residue N-terminal domain and a 265-residue C-terminal domain with the active site located in a cleft between these domains. Each domain has an alpha/beta topology and the overall structure represents a new protein fold. Furthermore, PCK has a unique mononucleotide-binding fold. The 1.8 A resolution structure of the complex of ATP/Mg(2+)/oxalate with PCK revealed a 20 degrees hinge-like rotation of the N- and C-terminal domains, which closed the active site cleft. The ATP was found in the unusual syn conformation as a result of binding to the enzyme. Along with the side chain of Lys254, Mg(2+) neutralizes charges on the P beta and P gamma oxygen atoms of ATP and stabilizes an extended, eclipsed conformation of the P beta and P gamma phosphoryl groups. The sterically strained high-energy conformation likely lowers the free energy of activation for phosphoryl transfer. Additionally, the gamma-phosphoryl group becomes oriented in-line with the appropriate enolate oxygen atom, which strongly supports a direct S(N)2-type displacement of this gamma-phosphoryl group by the enolate anion. In the 2.0 A resolution structure of the complex of PCK/ADP/Mg(2+)/AlF(3), the AlF(3) moiety represents the phosphoryl group being transferred during catalysis. There are three positively charged groups that interact with the fluorine atoms, which are complementary to the three negative charges that would occur for an associative transition state.
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Affiliation(s)
- Louis T J Delbaere
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5.
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34
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Bueno C, González-Nilo FD, Victoria Encinas M, Cardemil E. Substrate binding to fluorescent labeled wild type, Lys213Arg, and His233Gln Saccharomyces cerevisiae phosphoenolpyruvate carboxykinases. Int J Biochem Cell Biol 2004; 36:861-9. [PMID: 15006638 DOI: 10.1016/j.biocel.2003.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2003] [Revised: 09/09/2003] [Accepted: 09/29/2003] [Indexed: 11/18/2022]
Abstract
Saccharomyces cerevisiae phosphoenolpyruvate (PEP) carboxykinase is a key enzyme of the gluconeogenic pathway and catalyzes the decarboxylation of oxaloacetate and transfer of the gamma-phosphoryl group of ATP to yield PEP, ADP, and CO(2) in the presence of a divalent metal ion. Previous experiments have shown that mutation of amino acid residues at metal site 1 decrease the steady-state affinity of the enzyme for PEP, suggesting interaction of PEP with the metal ion [Biochemistry 41 (2002) 12763]. To more completely understand this enzyme interactions with substrate ligands, we have prepared the phosphopyridoxyl (P-pyridoxyl)-derivatives of wild type, Lys213Arg, and His233Gln S. cerevisiae PEP carboxykinase and used the changes in the fluorescence probe to determine the dissociation equilibrium constants of PEP, ATPMn(2-), and ADPMn(1-) from the corresponding derivatized enzyme-Mn(2+) complexes. Homology modeling of P-pyridoxyl-PEP carboxykinase and P-pyridoxyl-PEP carboxykinase-substrate complexes agree with experimental evidence indicating that the P-pyridoxyl group does not interfere with substrate binding. ATPMn(2-) binding is 0.8kcalmol(-1) more favorable than ADPMn(1-) binding to wild type P-pyridoxyl-enzyme. The thermodynamic data obtained in this work indicate that PEP binding is 2.3kcalmol(-1) and 3.2kcalmol(-1) less favorable for the Lys213Arg and His233Gln mutant P-pyridoxyl-PEP carboxykinases than for the wild type P-pyridoxyl-enzyme, respectively. The possible relevance of N and O ligands for Mn(2+) in relation to PEP binding and catalysis is discussed.
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Affiliation(s)
- Claudia Bueno
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago 33, Chile
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35
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Jabalquinto AM, González-Nilo FD, Laivenieks M, Cabezas M, Zeikus JG, Cardemil E. Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase. Mutagenesis at metal site 1. Biochimie 2004; 86:47-51. [PMID: 14987800 DOI: 10.1016/j.biochi.2003.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2003] [Revised: 10/02/2003] [Accepted: 10/22/2003] [Indexed: 11/25/2022]
Abstract
Anaerobiospirillum succiniciproducens phosphoenolpyruvate (PEP) carboxykinase catalyses the reversible metal-dependent formation of oxaloacetate (OAA) and ATP from PEP, ADP and CO(2). Mutations of PEP carboxykinase have been constructed where the residues His(225) and Asp(263), two residues of the enzyme's putative Mn(2+) binding site, were altered. Kinetic studies of the His225Glu, and Asp263Glu PEP carboxykinases show 600- and 16,800-fold reductions in V(max) relative to the wild-type enzyme, respectively, with minor alterations in K(m) for Mn(2+). Molecular modeling of wild-type and mutant enzymes suggests that the lower catalytic efficiency of the Asp263Glu enzyme could be explained by a movement of the lateral chain of Lys(248), a critical catalytic residue, away from the reaction center. The effect on catalysis of introducing a negatively charged oxygen atom in place of N(epsilon-2) at position 225 is discussed in terms of altered binding energy of the intermediate enolpyruvate.
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Affiliation(s)
- A M Jabalquinto
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago 33, Chile.
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36
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Jabalquinto AM, Laivenieks M, González-Nilo FD, Encinas MV, Zeikus G, Cardemil E. Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase: mutagenesis at metal site 2. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:515-9. [PMID: 14703984 DOI: 10.1023/b:jopc.0000005500.67125.71] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Phosphoenolpyruvate (PEP) carboxykinases harbor two divalent metal-binding sites. One cation interacts with the enzyme (metal binding site 1) to elicit activation, while a second cation (metal binding site 2) interacts with the nucleotide to serve as the metal nucleotide substrate. Mutants of Anaerobiospirillum succiniciproducens PEP carboxykinase have been constructed where Thr249 and Asp262, two residues of metal binding site 2 of the enzyme, were altered. Binding of the 3'(2')-O-(N-methylantraniloyl) derivative of ADP provides a test of the structural integrity of these mutants. The conservative mutation (Asp262Glu) retains a significant proportion of the wild type enzymatic activity. Meanwhile, removal of the OH group of Thr249 in the Thr249Ala mutant causes a decrease in V(max) by a factor of 1.1 x 10(4). Molecular modeling of wild type and mutant enzymes suggests that the lower catalytic efficiency of the Thr249Ala enzyme could be explained by a movement of the lateral chain of Lys248, a critical catalytic residue, away from the reaction center.
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Affiliation(s)
- Ana María Jabalquinto
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
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37
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Abstract
Phosphoenolpyruvate carboxykinase (PCK) is probably ubiquitous in flowering plants, but is confined to certain cells or tissues. It is regulated by phosphorylation, which renders it less active by altering both its substrate affinities and its sensitivity to regulation by adenylates. In the leaves of some C4 plants, such as Panicum maximum, dephosphorylation increases its activity in the light. In other tissues such regulation probably avoids futile cycling between phosphoenolpyruvate and oxaloacetate. Although PCK generally acts as a decarboxylase in plants, its affinity for CO2 measured at physiological concentrations of metal ions is high and would allow it to be freely reversible in vivo. While its function in gluconeogenesis in seeds postgermination and in leaves of C4 and crassulacean acid metabolism plants is clearly established, the possible functions of PCK in other plant cells are discussed, drawing parallels with those in animals, including its integrated function in cataplerosis, nitrogen metabolism, pH regulation, and gluconeogenesis.
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38
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Ravanal MC, Goldie H, Cardemil E. Thermal stability of phosphoenolpyruvate carboxykinases from Escherichia coli, Trypanosoma brucei, and Saccharomyces cerevisiae. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:311-5. [PMID: 13678294 DOI: 10.1023/a:1025306105105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The quaternary structure of ATP-dependent phosphoenolpyruvate (PEP) carboxykinases is variable. Thus, the carboxykinases from Escherichia coli, Trypanosoma brucei, and Saccharomyces cerevisiae are monomer, homodimer, and homotetramer, respectively. In this work, we studied the effect of temperature on the stability of the enzyme activity of these three carboxykinases, and have found that it follows the order monomer > dimer > tetramer. The inactivation processes are first order with respect to active enzyme. The presence of substrates leads to an increase in the thermal stability of all three PEP carboxykinases. The protection effect of the substrates on the thermal inactivation of these enzymes suggests similarities in the substrate-bound form of these proteins. We propose that the higher structural complexity of some PEP carboxykinases could be related to the acquisition of properties of relevance in vivo.
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Affiliation(s)
- M Cristina Ravanal
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago, Chile
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39
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Krautwurst H, Roschzttardtz H, Bazaes S, González-Nilo FD, Nowak T, Cardemil E. Lysine 213 and histidine 233 participate in Mn(II) binding and catalysis in Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase. Biochemistry 2002; 41:12763-70. [PMID: 12379119 DOI: 10.1021/bi026241w] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Saccharomyces cerevisiae phosphoenolpyruvate (PEP) carboxykinase catalyses the reversible metal-dependent formation of oxaloacetate and ATP from PEP, ADP, and CO2 and plays a key role in gluconeogenesis. This enzyme also has oxaloacetate decarboxylase and pyruvate kinase-like activities. Mutations of PEP carboxykinase have been constructed where the residues Lys213 and His233, two residues of the putative Mn2+ binding site of the enzyme, were altered. Replacement of these residues by Arg and by Gln, respectively, generated enzymes with 1.9 and 2.8 kcal/mol lower Mn2+ binding affinity. Lower PEP binding affinity was inferred for the mutated enzymes from the protection effect of PEP against urea denaturation. Kinetic studies of the altered enzymes show at least a 5000-fold reduction in V(max) for the primary reaction relative to that for the wild-type enzyme. V(max) values for the oxaloacetate decarboxylase and pyruvate kinase-like activities of PEP carboxykinase were affected to a much lesser extent in the mutated enzymes. The mutated enzymes show a decreased steady-state affinity for Mn2+ and PEP. The results are consistent with Lys213 and His233 being at the Mn2+ binding site of S. cerevisiae PEP carboxykinase and the Mn2+ affecting the PEP interaction. The different effects of mutations in V(max) for the main reaction and the secondary activities suggest different rate-limiting steps for these reactions.
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Affiliation(s)
- Hans Krautwurst
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago 33, Chile
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40
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Encinas MV, González-Nilo FD, Goldie H, Cardemil E. Ligand interactions and protein conformational changes of phosphopyridoxyl-labeled Escherichia coli phosphoenolpyruvate carboxykinase determined by fluorescence spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:4960-8. [PMID: 12383254 DOI: 10.1046/j.1432-1033.2002.03196.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Escherichia coli phosphoenolpyruvate (PEP) carboxykinase catalyzes the decarboxylation of oxaloacetate and transfer of the gamma-phosphoryl group of ATP to yield PEP, ADP, and CO2. The interaction of the enzyme with the substrates originates important domain movements in the protein. In this work, the interaction of several substrates and ligands with E. coli PEP carboxykinase has been studied in the phosphopyridoxyl (P-pyridoxyl)-enzyme adduct. The derivatized enzyme retained the substrate-binding characteristics of the native protein, allowing the determination of several protein-ligand dissociation constants, as well as the role of Mg2+ and Mn2+ in substrate binding. The binding affinity of PEP to the enzyme-Mn2+ complex was -8.9 kcal.mol-1, which is 3.2 kcal.mol-1 more favorable than in the complex with Mg2+. For the substrate nucleotide-metal complexes, similar binding affinities (-6.0 to -6.2 kcal.mol-1) were found for either metal ion. The fluorescence decay of the P-pyridoxyl group fitted to two lifetimes of 5.15 ns (34%) and 1.2 ns. These lifetimes were markedly altered in the derivatized enzyme-PEP-Mn complexes, and smaller changes were obtained in the presence of other substrates. Molecular models of the P-pyridoxyl-E. coli PEP carboxykinase showed different degrees of solvent-exposed surfaces for the P-pyridoxyl group in the open (substrate-free) and closed (substrate-bound) forms, which are consistent with acrylamide quenching experiments, and suggest that the fluorescence changes reflect the domain movements of the protein in solution.
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Affiliation(s)
- María Victoria Encinas
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile.
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41
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González-Nilo FD, Krautwurst H, Yévenes A, Cardemil E, Cachau R. Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase: theoretical and experimental study of the effect of glutamic acid 284 on the protonation state of lysine 213. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1599:65-71. [PMID: 12479406 DOI: 10.1016/s1570-9639(02)00400-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The crystal structure of Escherichia coli phosphoenolpyruvate (PEP) carboxykinase shows Lys213 is one of the ligands of enzyme-bound Mn2+ [Nat. Struct. Biol. 4 (1997) 990]. The direct coordination of Mn2+ by N(epsilon) of Lys213 is only consistent with a neutral (uncharged) Lys213, suggesting a low pKa for this residue. This work shows, through theoretical calculations and experimental analyses on homologous Saccharomyces cerevisiae PEP carboxykinase, how the microenvironment affects Mn2+ binding and the protonation state of Lys213. We show that Glu284, a residue close to Lys212, is required for correct protonation states of Lys212 and Lys213, and for Mn2+ binding. deltaG and deltaH values for the proton reorganization processes were calculated to analyze the energetic stability of the two different protonation states of Lys212 and Lys213 in wild-type and Glu284Gln S. cerevisiae PEP carboxykinase. Calculations were done using two modeling approaches, ab-initio density functional calculations and free energy perturbation (FEP) calculations. Both methods suggest that Lys212 must be protonated and Lys213 neutral in the wild-type enzyme. On the other hand, the calculations on the Glu284Gln mutant suggest a more stable neutral Lys212 and protonated Lys213. Experimental measurements showed 3 orders of magnitude lower activity and a threefold increase in Km for Mn2+ for Glu284Gln S. cerevisiae PEP carboxykinase when compared to wild type. The data here presented suggest that Glu284 is required for Mn2+ binding by S. cerevisiae PEP carboxykinase. We propose that Glu284 modulates the pKa value of Lys213 through electrostatic effects mediated by
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Affiliation(s)
- Fernando D González-Nilo
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago 33, Chile
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Jabalquinto AM, Laivenieks M, González-Nilo FD, Yévenes A, Encinas MV, Zeikus JG, Cardemil E. Evaluation by site-directed mutagenesis of active site amino acid residues of Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase. JOURNAL OF PROTEIN CHEMISTRY 2002; 21:393-400. [PMID: 12492149 DOI: 10.1023/a:1021178432158] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Anaerobiospirillum succiniciproducens phosphoenolpyruvate (PEP) carboxykinase catalyzes the reversible formation of oxaloacetate and adenosine triphosphate from PEP, adenosine diphosphate, and carbon dioxide, and uses Mn2+ as the activating metal ion. The enzyme is a monomer and presents 68% identity with Escherichia coli PEP carboxykinase. Comparison with the crystalline structure of homologous E. coli PEP carboxykinase [Tari, L. W., Matte, A., Goldie, H., and Delbaere, L. T. J. (1997). Nature Struct. Biol. 4, 990-994] suggests that His225, Asp262, Asp263, and Thr249 are located in the active site of the protein, interacting with manganese ions. In this work, these residues were individually changed to Gln (His225) or Asn. The mutated enzymes present 3-6 orders of magnitude lower values of Vmax/Km, indicating high catalytic relevance for these residues. The His225Gln mutant showed increased Km values for Mn2+ and PEP as compared with wild-type enzyme, suggesting a role of His225 in Mn2+ and PEP binding. From 1.5-1.6 Kcal/mol lower affinity for the 3'(2')-O-(N-methylantraniloyl) derivative of adenosine diphosphate was observed for the His225Gln and Asp263Asn mutant A. succiniciproducens PEP carboxykinases, implying a role of His225 and Asp263 in nucleotide binding.
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Affiliation(s)
- Ana María Jabalquinto
- Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Santiago 33, Chile
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