1
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De Vitto H, Belfon KKJ, Sharma N, Toay S, Abendroth J, Dranow DM, Lukacs CM, Choi R, Udell HS, Willis S, Barrera G, Beyer O, Li TD, Hicks KA, Torelli AT, French JB. Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate. Biochemistry 2024. [PMID: 38306231 DOI: 10.1021/acs.biochem.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Thiamin and its phosphate derivatives are ubiquitous molecules involved as essential cofactors in many cellular processes. The de novo biosynthesis of thiamin employs the parallel synthesis of 4-methyl-5-(2-hydroxyethyl)thiazole (THZ-P) and 4-amino-2-methyl-5(diphosphooxymethyl) pyrimidine (HMP) pyrophosphate (HMP-PP), which are coupled to generate thiamin phosphate. Most organisms that can biosynthesize thiamin employ a kinase (HMPK or ThiD) to generate HMP-PP. In nearly all cases, this enzyme is bifunctional and can also salvage free HMP, producing HMP-P, the monophosphate precursor of HMP-PP. Here we present high-resolution crystal structures of an HMPK from Acinetobacter baumannii (AbHMPK), both unliganded and with pyridoxal 5-phosphate (PLP) noncovalently bound. Despite the similarity between HMPK and pyridoxal kinase enzymes, our kinetics analysis indicates that AbHMPK accepts HMP exclusively as a substrate and cannot turn over pyridoxal, pyridoxamine, or pyridoxine nor does it display phosphatase activity. PLP does, however, act as a weak inhibitor of AbHMPK with an IC50 of 768 μM. Surprisingly, unlike other HMPKs, AbHMPK catalyzes only the phosphorylation of HMP and does not generate the diphosphate HMP-PP. This suggests that an additional kinase is present in A. baumannii, or an alternative mechanism is in operation to complete the biosynthesis of thiamin.
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Affiliation(s)
- Humberto De Vitto
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kafi K J Belfon
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Nandini Sharma
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Sarah Toay
- Department of Biological Chemistry, Grinnell College, Grinnell, Iowa 50112, United States
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - David M Dranow
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Christine M Lukacs
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Hannah S Udell
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Sydney Willis
- Department of Chemistry, Rollins College, Winter Park, Florida 32789, United States
| | - George Barrera
- Department of Chemistry and Biochemistry, Weber State University, Ogden, Utah 84408, United States
| | - Olive Beyer
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Teng Da Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Katherine A Hicks
- Chemistry Department, State University of New York at Cortland, Cortland, New York 13045, United States
| | - Andrew T Torelli
- Department of Chemistry, Ithaca College, Ithaca, New York 14850, United States
| | - Jarrod B French
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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2
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Aleshin VA, Bunik VI. Protein-Protein Interfaces as Druggable Targets: A Common Motif of the Pyridoxal-5'-Phosphate-Dependent Enzymes to Receive the Coenzyme from Its Producers. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1022-1033. [PMID: 37751871 DOI: 10.1134/s0006297923070131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 09/28/2023]
Abstract
Pyridoxal-5'-phosphate (PLP), a phosphorylated form of vitamin B6, acts as a coenzyme for numerous reactions, including those changed in cancer and/or associated with the disease prognosis. Since highly reactive PLP can modify cellular proteins, it is hypothesized to be directly transferred from its donors to acceptors. Our goal is to validate the hypothesis by finding common motif(s) in the multitude of PLP-dependent enzymes for binding the limited number of PLP donors, namely pyridoxal kinase (PdxK), pyridox(am)in-5'-phosphate oxidase (PNPO), and PLP-binding protein (PLPBP). Experimentally confirmed interactions between the PLP donors and acceptors reveal that PdxK and PNPO interact with the most abundant PLP acceptors belonging to structural folds I and II, while PLPBP - with those belonging to folds III and V. Aligning sequences and 3D structures of the identified interactors of PdxK and PNPO, we have identified a common motif in the PLP-dependent enzymes of folds I and II. The motif extends from the enzyme surface to the neighborhood of the PLP binding site, represented by an exposed alfa-helix, a partially buried beta-strand, and residual loops. Pathogenicity of mutations in the human PLP-dependent enzymes within or in the vicinity of the motif, but outside of the active sites, supports functional significance of the motif that may provide an interface for the direct transfer of PLP from the sites of its synthesis to those of coenzyme binding. The enzyme-specific amino acid residues of the common motif may be useful to develop selective inhibitors blocking PLP delivery to the PLP-dependent enzymes critical for proliferation of malignant cells.
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Affiliation(s)
- Vasily A Aleshin
- Department of Biokinetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Biochemistry, Sechenov University, Moscow, 119048, Russia
| | - Victoria I Bunik
- Department of Biokinetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Department of Biochemistry, Sechenov University, Moscow, 119048, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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3
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Qureshi IA, Saini M, Are S. Pyridoxal Kinase of Disease-causing Human Parasites: Structural and
Functional Insights to Understand its Role in Drug Discovery. Curr Protein Pept Sci 2022; 23:271-289. [DOI: 10.2174/1389203723666220519155025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Human parasites cause several diseased conditions with high morbidity and mortality in a
large section of the population residing in various geographical areas. Nearly three billion people suffer
from either one or many parasitic infections globally, with almost one million deaths annually. In spite
of extensive research and advancement in the medical field, no effective vaccine is available against
prominent human parasitic diseases that necessitate identification of novel targets for designing specific
inhibitors. Vitamin B6 is an important ubiquitous co-enzyme that participates in several biological processes
and plays an important role in scavenging ROS (reactive oxygen species) along with providing
resistance to oxidative stress. Moreover, the absence of the de novo vitamin B6 biosynthetic pathway in
human parasites makes this pathway indispensable for the survival of these pathogens. Pyridoxal kinase
(PdxK) is a crucial enzyme for vitamin B6 salvage pathway and participates in the process of vitamers
B6 phosphorylation. Since the parasites are dependent on pyridoxal kinase for their survival and infectivity
to the respective hosts, it is considered a promising candidate for drug discovery. The detailed
structural analysis of PdxK from disease-causing parasites has provided insights into the catalytic
mechanism of this enzyme as well as significant differences from their human counterpart. Simultaneously,
structure-based studies have identified small lead molecules that can be exploited for drug discovery
against protozoan parasites. The present review provides structural and functional highlights of
pyridoxal kinase for its implication in developing novel and potent therapeutics to combat fatal parasitic
diseases.
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Affiliation(s)
- Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao
Road, Hyderabad 500046, India
| | - Mayank Saini
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao
Road, Hyderabad 500046, India
| | - Sayanna Are
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao
Road, Hyderabad 500046, India
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4
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Cloning and Characterization of Pyridoxal Kinase from Geobacillus sp. H6a. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyridoxal kinase encoded by pdxK gene, is the important key enzyme in the salvage pathway of vitamin B6 biosynthesis. The enzyme catalyzes the phosphorylation of the 5′ alcohol groups of free form vitamin B6 into their 5′-phosphate forms that requires metal ion and ATP. Pyridoxal kinase have been reported in many organisms except in the thermophilic bacterium. Therefore, this study aimed to clone, express and characterize pyridoxal kinase of Geobacillus sp. H6a isolated from the hot spring in the North of Thailand. The GhpdxK gene (810 base pairs) was inserted into pET28a(+) plasmids at restriction site of NdeI and BamHI and transformed into E.coli BL21(DE3). The expressed pyridoxal kinase of this bacterium exhibits a homodimer, in which each subunit had a molecular mass of about 32 kDa when examined by SDS-PAGE and gel filtration. The enzyme showed maximal activity at 70°C and at pH 8.0. The expressed enzyme obtained in this study was found to be more active (>50%) in the broad pH range (6.0 – 9.0) than those previously reported. This enzyme prefers Mg2+ and also accepts other cations to the less extent. Under optimal conditions, the expressed enzyme has higher affinity toward PN (20 ± 1.35 µM), while it showed the same affinity to pyridoxal (100 ± 0.76 µM) and pyridoxamine (100 ± 1.21 µM). The Km value for ATP and 4-amino-5-hydroxymethyl-2-methylpyridine were 8.99 ± 1.76 µM and 19 ± 0.85 µM, respectively. With high activity at high temperature and active in the broad pH range, it could be considered as a potential candidate for future application particularly bioconversion of vitamin B6.
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5
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Bunik V, Aleshin V, Nogues I, Kähne T, Parroni A, Contestabile R, Salvo ML, Graf A, Tramonti A. Thiamine‐dependent regulation of mammalian brain pyridoxal kinase
in vitro
and
in vivo. J Neurochem 2022; 161:20-39. [DOI: 10.1111/jnc.15576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Victoria Bunik
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University 19991 Moscow Russia
- Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow 119991 Russia
- Sechenov University 119048 Moscow Russia
| | - Vasily Aleshin
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University 19991 Moscow Russia
- Sechenov University 119048 Moscow Russia
| | - Isabel Nogues
- Research Institute of Terrestrial Ecosystems Italian National Research Council Via Salaria Km. 29 300–00015 Monterotondo Scalo
| | - Thilo Kähne
- Institute of Exptl. Internal Medicine Otto‐von‐Guericke‐Universität Magdeburg 39120 Magdeburg Germany
| | - Alessia Parroni
- Istituto Pasteur Italia‐ Fondazione Cenci Bolognetti Department of Biochemical Sciences “A. Rossi Fanelli” Sapienza University of Rome P.le A. Moro 5 ‐ 00185 Rome Italy
| | - Roberto Contestabile
- Istituto Pasteur Italia‐ Fondazione Cenci Bolognetti Department of Biochemical Sciences “A. Rossi Fanelli” Sapienza University of Rome P.le A. Moro 5 ‐ 00185 Rome Italy
| | - Martino Luigi Salvo
- Istituto Pasteur Italia‐ Fondazione Cenci Bolognetti Department of Biochemical Sciences “A. Rossi Fanelli” Sapienza University of Rome P.le A. Moro 5 ‐ 00185 Rome Italy
| | - Anastasia Graf
- Moscow Institute of Physics and Technology 123098 Moscow Russia
- Faculty of Biology Lomonosov Moscow State University 19991 Moscow Russia
| | - Angela Tramonti
- Istituto Pasteur Italia‐ Fondazione Cenci Bolognetti Department of Biochemical Sciences “A. Rossi Fanelli” Sapienza University of Rome P.le A. Moro 5 ‐ 00185 Rome Italy
- Istitute of Molecular Biology and Pathology Italian National Research Council P.le A. Moro 5 ‐ 00185 Rome Italy
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Are S, Gatreddi S, Jakkula P, Qureshi IA. Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani. Int J Biol Macromol 2020; 152:812-827. [PMID: 32105687 DOI: 10.1016/j.ijbiomac.2020.02.257] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/22/2020] [Accepted: 02/23/2020] [Indexed: 11/26/2022]
Abstract
The enzyme pyridoxal kinase (PdxK) catalyzes the conversion of pyridoxal to pyridoxal-5'-phosphate (PLP) using ATP as the co-factor. The product pyridoxal-5'-phosphate plays a key role in several biological processes such as transamination, decarboxylation and deamination. In the present study, full-length ORF of PdxK from Leishmania donovani (LdPdxK) was cloned and then purified using affinity chromatography. LdPdxK exists as a homo-dimer in solution and shows more activity at near to physiological pH. Biochemical analysis of LdPdxK with pyridoxal, pyridoxamine, pyridoxine and ginkgotoxin revealed its affinity preference towards different substrates. The secondary structure analysis using circular dichroism spectroscopy showed LdPdxK to be predominantly α-helical in organization which tends to decline at lower and higher pH. Simultaneously, LdPdxK was crystallized and its three-dimensional structure in complex with ADP and different substrates were determined. Crystal structure of LdPdxK delineated that it has a central core of β-sheets surrounded by α-helices with a conserved GTGD ribokinase motif. The structures of LdPdxK disclosed no major structural changes between ADP and ADP- substrate bound structures. In addition, comparative structural analysis highlighted the key differences between the active site pockets of leishmanial and human PdxK, rendering LdPdxK an attractive candidate for the designing of novel and specific inhibitors.
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Affiliation(s)
- Sayanna Are
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Santhosh Gatreddi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Pranay Jakkula
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India.
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