1
|
Andress Huacachino A, Joo J, Narayanan N, Tehim A, Himes BE, Penning TM. Aldo-keto reductase (AKR) superfamily website and database: An update. Chem Biol Interact 2024; 398:111111. [PMID: 38878851 DOI: 10.1016/j.cbi.2024.111111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/09/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
The aldo-keto reductase (AKR) superfamily is a large family of proteins found across the kingdoms of life. Shared features of the family include 1) structural similarities such as an (α/β)8-barrel structure, disordered loop structure, cofactor binding site, and a catalytic tetrad, and 2) the ability to catalyze the nicotinamide adenine dinucleotide (phosphate) reduced (NAD(P)H)-dependent reduction of a carbonyl group. A criteria of family membership is that the protein must have a measured function, and thus, genomic sequences suggesting the transcription of potential AKR proteins are considered pseudo-members until evidence of a functionally expressed protein is available. Currently, over 200 confirmed AKR superfamily members are reported to exist. A systematic nomenclature for the AKR superfamily exists to facilitate family and subfamily designations of the member to be communicated easily. Specifically, protein names include the root "AKR", followed by the family represented by an Arabic number, the subfamily-if one exists-represented by a letter, and finally, the individual member represented by an Arabic number. The AKR superfamily database has been dedicated to tracking and reporting the current knowledge of the AKRs since 1997, and the website was last updated in 2003. Here, we present an updated version of the website and database that were released in 2023. The database contains genetic, functional, and structural data drawn from various sources, while the website provides alignment information and family tree structure derived from bioinformatics analyses.
Collapse
Affiliation(s)
- Andrea Andress Huacachino
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA; Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA
| | - Jaehyun Joo
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA
| | - Nisha Narayanan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA
| | - Anisha Tehim
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA; Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA
| | - Trevor M Penning
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104-6061, USA.
| |
Collapse
|
2
|
Tramonti A, Donkor AK, Parroni A, Musayev FN, Barile A, Ghatge MS, Graziani C, Alkhairi M, AlAwadh M, di Salvo ML, Safo MK, Contestabile R. Functional and structural properties of pyridoxal reductase (PdxI) from Escherichia coli: a pivotal enzyme in the vitamin B6 salvage pathway. FEBS J 2023; 290:5628-5651. [PMID: 37734924 PMCID: PMC10872706 DOI: 10.1111/febs.16962] [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: 07/19/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/23/2023]
Abstract
Pyridoxine 4-dehydrogenase (PdxI), a NADPH-dependent pyridoxal reductase, is one of the key players in the Escherichia coli pyridoxal 5'-phosphate (PLP) salvage pathway. This enzyme, which catalyses the reduction of pyridoxal into pyridoxine, causes pyridoxal to be converted into PLP via the formation of pyridoxine and pyridoxine phosphate. The structural and functional properties of PdxI were hitherto unknown, preventing a rational explanation of how and why this longer, detoured pathway occurs, given that, in E. coli, two pyridoxal kinases (PdxK and PdxY) exist that could convert pyridoxal directly into PLP. Here, we report a detailed characterisation of E. coli PdxI that explains this behaviour. The enzyme efficiently catalyses the reversible transformation of pyridoxal into pyridoxine, although the reduction direction is thermodynamically strongly favoured, following a compulsory-order ternary-complex mechanism. In vitro, the enzyme is also able to catalyse PLP reduction and use NADH as an electron donor, although with lower efficiency. As with all members of the aldo-keto reductase (AKR) superfamily, the enzyme has a TIM barrel fold; however, it shows some specific features, the most important of which is the presence of an Arg residue that replaces the catalytic tetrad His residue that is present in all AKRs and appears to be involved in substrate specificity. The above results, in conjunction with kinetic and static measurements of vitamins B6 in cell extracts of E. coli wild-type and knockout strains, shed light on the role of PdxI and both kinases in determining the pathway followed by pyridoxal in its conversion to PLP, which has a precise regulatory function.
Collapse
Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Akua K. Donkor
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Alessia Parroni
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Faik N. Musayev
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Anna Barile
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Mohini. S. Ghatge
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Claudio Graziani
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
| | - Mona Alkhairi
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammed AlAwadh
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Martino Luigi di Salvo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
| | - Martin K. Safo
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Roberto Contestabile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
| |
Collapse
|
3
|
Akbary Z, Yu H, Lorenzo I, Paez K, Lee ND, DeBeVoise K, Moses J, Sanders N, Connors N, Cassano A. Electron withdrawing group-dependent substrate inhibition of an α-ketoamide reductase from Saccharomyces cerevisiae. Biochem Biophys Res Commun 2023; 676:97-102. [PMID: 37499370 DOI: 10.1016/j.bbrc.2023.07.030] [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: 06/29/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Aldo-keto reductases remain enzymes of interest in biocatalysis due to their ability to reduce carbonyls to alcohols stereospecifically. Based on genomic sequence, we identified aldo-keto reductases of a S. cerevisiae strain extracted from an ancient amber sample. One of the putative enzymes, AKR 163, displays 99% identity with α-amide ketoreductases from the S288C and YJM248 S. cerevisiae strains, which have been investigated for biocatalytic applications. To further investigate AKR 163, we successfully cloned, expressed in E.coli as a glutathione-S-transferase fusion protein, and affinity purified AKR 163. Kinetic studies revealed that AKR 163 experiences strong substrate inhibition by substrates containing halogen atoms or other electron withdrawing groups adjacent to the reactive carbonyl, with Ki values ranging from 0.29 to 0.6 mM and KM values ranging from 0.38 to 0.9 mM at pH 8.0. Substrates without electron withdrawing groups do not display substrate inhibition kinetics and possess much larger KM values between 83 and 260 mM under the same conditions. The kcat values ranged from 0.5 to 2.5s-1 for substrates exhibiting substrate inhibition and 0.22 to 0.52s-1 for substrates that do not engage in substrate inhibition. Overall, the results are consistent with rate-limiting dissociation of the NADP+ cofactor after hydride transfer when electron withdrawing groups are present and activating the reduction step. This process leads to a buildup of enzyme-NADP+ complex that is susceptible to binding and inhibition by a second substrate molecule.
Collapse
Affiliation(s)
- Zarina Akbary
- Program in Biochemistry and Molecular Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Honglin Yu
- Program in Biochemistry and Molecular Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Ivelisse Lorenzo
- Department of Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Karyme Paez
- Program in Biochemistry and Molecular Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Narisa Diana Lee
- Program in Biochemistry and Molecular Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Kayla DeBeVoise
- Department of Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Joel Moses
- Program in Biochemistry and Molecular Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Nathaniel Sanders
- Program in Biochemistry and Molecular Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Neal Connors
- Research Institute for Scientists Emeriti, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States
| | - Adam Cassano
- Program in Biochemistry and Molecular Biology, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States; Department of Chemistry, Drew University, 36 Madison Ave, Madison, NJ, 07940, United States.
| |
Collapse
|
4
|
Liang JJ, Rasmusson AM. Overview of the Molecular Steps in Steroidogenesis of the GABAergic Neurosteroids Allopregnanolone and Pregnanolone. CHRONIC STRESS (THOUSAND OAKS, CALIF.) 2018; 2:2470547018818555. [PMID: 32440589 PMCID: PMC7219929 DOI: 10.1177/2470547018818555] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/19/2018] [Indexed: 12/23/2022]
Abstract
Allopregnanolone and pregnanolone-neurosteroids synthesized from progesterone in the brain, adrenal gland, ovary and testis-have been implicated in a range of neuropsychiatric conditions including seizure disorders, post-traumatic stress disorder, major depression, post-partum depression, pre-menstrual dysphoric disorder, chronic pain, Parkinson's disease, Alzheimer's disease, neurotrauma, and stroke. Allopregnanolone and pregnanolone equipotently facilitate the effects of gamma-amino-butyric acid (GABA) at GABAA receptors, and when sulfated, antagonize N-methyl-D-aspartate receptors. They play myriad roles in neurophysiological homeostasis and adaptation to stress while exerting anxiolytic, antidepressant, anti-nociceptive, anticonvulsant, anti-inflammatory, sleep promoting, memory stabilizing, neuroprotective, pro-myelinating, and neurogenic effects. Given that these neurosteroids are synthesized de novo on demand, this review details the molecular steps involved in the biochemical conversion of cholesterol to allopregnanolone and pregnanolone within steroidogenic cells. Although much is known about the early steps in neurosteroidogenesis, less is known about transcriptional, translational, and post-translational processes in allopregnanolone- and pregnanolone-specific synthesis. Further research to elucidate these mechanisms as well as to optimize the timing and dose of interventions aimed at altering the synthesis or levels of these neurosteroids is much needed. This should include the development of novel therapeutics for the many neuropsychiatric conditions to which dysregulation of these neurosteroids contributes.
Collapse
Affiliation(s)
| | - Ann M. Rasmusson
- Boston
University School of Medicine, Boston, MA,
USA
- National Center for PTSD, Women’s Health
Science Division, Department of Veterans Affairs, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA,
USA
| |
Collapse
|
5
|
Kapedanovska Nestorovska A, Naumovska Z, Jakovski K, Sterjev Z, Matevska Geskovska N, Dimovski A, Suturkova L. Allele frequency and genotype distribution of aldo keto reductase 1D1 (AKR1D1) rs1872930 genetic variant in a Macedonian population. MAKEDONSKO FARMACEVTSKI BILTEN 2018. [DOI: 10.33320/maced.pharm.bull.2018.64.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AKR1D1 has been recently recognized as novel candidate gene regulating CYP450 coexpression. The AKR1D1 3’-UTR SNP (rs1872930) functional genetic variation was considered as important source of phenotypic variation in the activity of CYP450. The minor allele frequency of rs1872930 varies among populations suggesting population specific pharmacogenetic implications. The aim of the present study was to determine the AKR1D1 (rs1872930) minor allele frequencies and genotypes distribution in a population from Republic of Macedonia. Four hundred and fifty unrelated Macedonian subjects were studied. AKR1D1 variant allele was detected by real time polymerase chain reaction. The distribution of AKR1D1*1/*1, *1/*36 and *36/*36 genotypes was 0.569, 0.360 and 0.071, respectively. The overall frequency of AKR1D1*36 variant allele was 0.251. Our study is the first to assess the frequency distribution of the AKR1D1*36 (rs1872930) genetic variant in population from Republic of Macedonia and the findings are in accordance with the frequency reported for the Caucasian population.
Keywords: AKR1D1, rs1872930, CYP450, variability, gene expression, enzyme activity
Collapse
Affiliation(s)
- Aleksandra Kapedanovska Nestorovska
- Center for Biomolecular and Pharmaceutical Analysis, Faculty of Pharmacy, Ss. Cyril and Methodius University, Mother Theresa St. 47, Skopje 1000, Republic of Macedonia
| | - Zorica Naumovska
- Center for Biomolecular and Pharmaceutical Analysis, Faculty of Pharmacy, Ss. Cyril and Methodius University, Mother Theresa St. 47, Skopje 1000, Republic of Macedonia
| | - Krume Jakovski
- Department of Preclinical and Clinical Pharmacology and Toxicology, Faculty of Medicine, Ss. Cyril and Methodius University, St.50 Division-6 Skopje 1000, Republic of Macedonia
| | - Zoran Sterjev
- Center for Biomolecular and Pharmaceutical Analysis, Faculty of Pharmacy, Ss. Cyril and Methodius University, Mother Theresa St. 47, Skopje 1000, Republic of Macedonia
| | - Nadica Matevska Geskovska
- Center for Biomolecular and Pharmaceutical Analysis, Faculty of Pharmacy, Ss. Cyril and Methodius University, Mother Theresa St. 47, Skopje 1000, Republic of Macedonia
| | - Aleksandar Dimovski
- Center for Biomolecular and Pharmaceutical Analysis, Faculty of Pharmacy, Ss. Cyril and Methodius University, Mother Theresa St. 47, Skopje 1000, Republic of Macedonia
| | - Ljubica Suturkova
- Center for Biomolecular and Pharmaceutical Analysis, Faculty of Pharmacy, Ss. Cyril and Methodius University, Mother Theresa St. 47, Skopje 1000, Republic of Macedonia
| |
Collapse
|