1
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Zheng Z, Goncearenco A, Berezovsky IN. Back in time to the Gly-rich prototype of the phosphate binding elementary function. Curr Res Struct Biol 2024; 7:100142. [PMID: 38655428 PMCID: PMC11035071 DOI: 10.1016/j.crstbi.2024.100142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands - phosphate binding. We start from a brief discussion of major participants, conditions, and events in prebiotic evolution that resulted in the Origin of Life. Tracing back to the basic functions, including metal and phosphate binding, and, potentially, formation of primitive protein-protein interactions, we focus here on the phosphate binding. Critically assessing works on the structural, functional, and evolutionary aspects of phosphate binding, we perform a simple computational experiment reconstructing its most ancient and generic sequence prototype. The profiles of the phosphate binding signatures have been derived in form of position-specific scoring matrices (PSSMs), their peculiarities depending on the type of the ligands have been analyzed, and evolutionary connections between them have been delineated. Then, the apparent prototype that gave rise to all relevant phosphate-binding signatures had also been reconstructed. We show that two major signatures of the phosphate binding that discriminate between the binding of dinucleotide- and nucleotide-containing ligands are GxGxxG and GxxGxG, respectively. It appears that the signature archetypal for dinucleotide-containing ligands is more generic, and it can frequently bind phosphate groups in nucleotide-containing ligands as well. The reconstructed prototype's key signature GxGGxG underlies the role of glycine residues in providing flexibility and interactions necessary for binding the phosphate groups. The prototype also contains other ancient amino acids, valine, and alanine, showing versatility towards evolutionary design and functional diversification.
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Affiliation(s)
- Zejun Zheng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | | | - Igor N. Berezovsky
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
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2
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Hudspeth J, Rogge K, Dörner S, Müll M, Hoffmeister D, Rupp B, Werten S. Methyl transfer in psilocybin biosynthesis. Nat Commun 2024; 15:2709. [PMID: 38548735 PMCID: PMC10978996 DOI: 10.1038/s41467-024-46997-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
Psilocybin, the natural hallucinogen produced by Psilocybe ("magic") mushrooms, holds great promise for the treatment of depression and several other mental health conditions. The final step in the psilocybin biosynthetic pathway, dimethylation of the tryptophan-derived intermediate norbaeocystin, is catalysed by PsiM. Here we present atomic resolution (0.9 Å) crystal structures of PsiM trapped at various stages of its reaction cycle, providing detailed insight into the SAM-dependent methylation mechanism. Structural and phylogenetic analyses suggest that PsiM derives from epitranscriptomic N6-methyladenosine writers of the METTL16 family, which is further supported by the observation that bound substrates physicochemically mimic RNA. Inherent limitations of the ancestral monomethyltransferase scaffold hamper the efficiency of psilocybin assembly and leave PsiM incapable of catalysing trimethylation to aeruginascin. The results of our study will support bioengineering efforts aiming to create novel variants of psilocybin with improved therapeutic properties.
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Affiliation(s)
- Jesse Hudspeth
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Chemistry, Colorado School of Mines, Golden, CO, USA
| | - Kai Rogge
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Sebastian Dörner
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Maximilian Müll
- Research Group Biosynthetic Design of Natural Products, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Bernhard Rupp
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- k.-k. Hofkristallamt, San Diego, California, USA
| | - Sebastiaan Werten
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.
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3
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Vasseur CM, Karunasegaram D, Seebeck FP. Structure and Substrate Specificity of S-Methyl Thiourocanate Hydratase. ACS Chem Biol 2024; 19:718-724. [PMID: 38389448 DOI: 10.1021/acschembio.3c00745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a common cofactor in enzyme-catalyzed reactions that involve hydride transfers. In contrast, urocanase and urocanase-like enzymes use NAD+ for covalent electrophilic catalysis. Deciphering avenues by which this unusual catalytic strategy has diversified by evolution may point to approaches for the design of novel enzymes. In this report, we describe the S-methyl thiourocanate hydratase (S-Me-TUC) from Variovorax sp. RA8 as a novel member of this small family of NAD+-dependent hydratases. This enzyme catalyzes the 1,4-addition of water to S-methyl thiourocanate as the second step in the catabolism of S-methyl ergothioneine. The crystal structure of this enzyme in complex with the cofactor and a product analogue identifies critical sequence motifs that explain the narrow and nonoverlapping substrate scopes of S-methyl thiourocanate-, urocanate-, thiourocanate-, and Nτ-methyl urocanate-specific hydratases. The discovery of a S-methyl ergothioneine catabolic pathway also suggests that S-methylation or alkylation may be a significant activity in the biology of ergothioneine.
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Affiliation(s)
- Camille M Vasseur
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, Basel 4002, Switzerland
| | - Dishani Karunasegaram
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, Basel 4002, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, Basel 4002, Switzerland
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4
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Ye W, Krishna Behra PR, Dyrhage K, Seeger C, Joiner JD, Karlsson E, Andersson E, Chi CN, Andersson SGE, Jemth P. Folded Alpha Helical Putative New Proteins from Apilactobacillus kunkeei. J Mol Biol 2024; 436:168490. [PMID: 38355092 DOI: 10.1016/j.jmb.2024.168490] [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: 09/28/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
The emergence of new proteins is a central question in biology. Most tertiary protein folds known to date appear to have an ancient origin, but it is clear from bioinformatic analyses that new proteins continuously emerge in all organismal groups. However, there is a paucity of experimental data on new proteins regarding their structure and biophysical properties. We performed a detailed phylogenetic analysis and identified 48 putative open reading frames in the honeybee-associated bacterium Apilactobacillus kunkeei for which no or few homologs could be identified in closely-related species, suggesting that they could be relatively new on an evolutionary time scale and represent recently evolved proteins. Using circular dichroism-, fluorescence- and nuclear magnetic resonance (NMR) spectroscopy we investigated six of these proteins and show that they are not intrinsically disordered, but populate alpha-helical dominated folded states with relatively low thermodynamic stability (0-3 kcal/mol). The NMR and biophysical data demonstrate that small new proteins readily adopt simple folded conformations suggesting that more complex tertiary structures can be continuously re-invented during evolution by fusion of such simple secondary structure elements. These findings have implications for the general view on protein evolution, where de novo emergence of folded proteins may be a common event.
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Affiliation(s)
- Weihua Ye
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Phani Rama Krishna Behra
- Department of Molecular Evolution, Cell and Molecular Biology, Biomedical Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Karl Dyrhage
- Department of Molecular Evolution, Cell and Molecular Biology, Biomedical Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Christian Seeger
- Department of Molecular Evolution, Cell and Molecular Biology, Biomedical Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden
| | - Joe D Joiner
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden.
| | - Siv G E Andersson
- Department of Molecular Evolution, Cell and Molecular Biology, Biomedical Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden.
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden.
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5
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Sankar S, Preeti P, Ravikumar K, Kumar A, Prasad Y, Pal S, Rao DN, Savithri HS, Chandra N. Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase. Curr Res Struct Biol 2023; 6:100108. [PMID: 38106461 PMCID: PMC10724544 DOI: 10.1016/j.crstbi.2023.100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/05/2023] [Accepted: 10/24/2023] [Indexed: 12/19/2023] Open
Abstract
S-adenosylmethionine (SAM) is a ubiquitous co-factor that serves as a donor for methylation reactions and additionally serves as a donor of other functional groups such as amino and ribosyl moieties in a variety of other biochemical reactions. Such versatility in function is enabled by the ability of SAM to be recognized by a wide variety of protein molecules that vary in their sequences and structural folds. To understand what gives rise to specific SAM binding in diverse proteins, we set out to study if there are any structural patterns at their binding sites. A comprehensive analysis of structures of the binding sites of SAM by all-pair comparison and clustering, indicated the presence of 4 different site-types, only one among them being well studied. For each site-type we decipher the common minimum principle involved in SAM recognition by diverse proteins and derive structural motifs that are characteristic of SAM binding. The presence of the structural motifs with precise three-dimensional arrangement of amino acids in SAM sites that appear to have evolved independently, indicates that these are winning arrangements of residues to bring about SAM recognition. Further, we find high similarity between one of the SAM site types and a well known ATP binding site type. We demonstrate using in vitro experiments that a known SAM binding protein, HpyAII.M1, a type 2 methyltransferase can bind and hydrolyse ATP. We find common structural motifs that explain this, further supported through site-directed mutagenesis. Observation of similar motifs for binding two of the most ubiquitous ligands in multiple protein families with diverse sequences and structural folds presents compelling evidence at the molecular level in favour of convergent evolution.
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Affiliation(s)
- Santhosh Sankar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Preeti Preeti
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Kavya Ravikumar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Amrendra Kumar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Yedu Prasad
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Sukriti Pal
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Desirazu N. Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Handanahal S. Savithri
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
- Department of BioEngineering, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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6
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Gade M, Gardner JM, Jain P, Laurino P. Nucleoside-Driven Specificity of DNA Methyltransferase. Chembiochem 2023; 24:e202300094. [PMID: 37548117 DOI: 10.1002/cbic.202300094] [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: 02/05/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/08/2023]
Abstract
We have studied the adenosine binding specificities of two bacterial DNA methyltransferases, Taq methyltransferase (M.TaqI), and HhaI methyltransferase (M.HhaI). While they have similar cofactor binding pocket interactions, experimental data showed different specificity for novel S-nucleobase-l-methionine cofactors (SNMs; N=guanosyl, cytidyl, uridyl). Protein dynamics corroborate the experimental data on the cofactor specificities. For M.TaqI the specificity for S-adenosyl-l-methionine (SAM) is governed by the tight binding on the nucleoside part of the cofactor, while for M.HhaI the degree of freedom of the nucleoside chain allows the acceptance of other bases. The experimental data prove catalytically productive methylation by the M.HhaI binding pocket for all the SNMs. Our results suggest a new route for successful design of unnatural SNM analogues for methyltransferases as a tool for cofactor engineering.
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Affiliation(s)
- Madhuri Gade
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Jasmine M Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Prashant Jain
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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7
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Loo CE, Hix MA, Wang T, Cisneros GA, Kohli RM. Revealing Drivers for Carboxy- S-adenosyl-l-methionine Use by Neomorphic Variants of a DNA Methyltransferase. ACS Chem Biol 2023; 18:2224-2232. [PMID: 37379458 PMCID: PMC10592258 DOI: 10.1021/acschembio.3c00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Methylation of DNA plays a key role in diverse biological processes spanning from bacteria to mammals. DNA methyltransferases (MTases) typically employ S-adenosyl-l-methionine (SAM) as a critical cosubstrate and the relevant methyl donor for modification of the C5 position of cytosine. Recently, work on the CpG-specific bacterial MTase, M.MpeI, has shown that a single N374K point mutation can confer the enzyme with the neomorphic ability to use the sparse, naturally occurring metabolite carboxy-S-adenosyl-l-methionine (CxSAM) in order to generate the unnatural DNA modification, 5-carboxymethylcytosine (5cxmC). Here, we aimed to investigate the mechanistic basis for this DNA carboxymethyltransferase (CxMTase) activity by employing a combination of computational modeling and in vitro characterization. Modeling of substrate interactions with the enzyme variant allowed us to identify a favorable salt bridge between CxSAM and N374K that helps to rationalize selectivity of the CxMTase. Unexpectedly, we also discovered a potential role for a key active site E45 residue that makes a bidentate interaction with the ribosyl sugar of CxSAM, located on the opposite face of the CxMTase active site. Prompted by these modeling results, we further explored the space-opening E45D mutation and found that the E45D/N374K double mutant in fact inverts selectivity, preferring CxSAM over SAM in biochemical assays. These findings provide new insight into CxMTase active site architecture and may offer broader utility given the numerous opportunities offered by using SAM analogs for selective molecular labeling in concert with nucleic acid or even protein-modifying MTases.
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Affiliation(s)
- Christian E. Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Mark A. Hix
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Tong Wang
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - G. Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75801, United States; Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75801, United States
| | - Rahul M. Kohli
- Department of Medicine and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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8
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Tagami S. Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life. Biophys Physicobiol 2023; 20:e200026. [PMID: 38496239 PMCID: PMC10941967 DOI: 10.2142/biophysico.bppb-v20.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/29/2023] [Indexed: 03/19/2024] Open
Abstract
Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).
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Affiliation(s)
- Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
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9
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Wozniak K, Brzezinski K. Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life. Biomolecules 2023; 13:biom13050782. [PMID: 37238652 DOI: 10.3390/biom13050782] [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: 03/06/2023] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.
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Affiliation(s)
- Katarzyna Wozniak
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
| | - Krzysztof Brzezinski
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
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10
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Shanbhag AP. Stairway to Stereoisomers: Engineering Short- and Medium-Chain Ketoreductases To Produce Chiral Alcohols. Chembiochem 2023; 24:e202200687. [PMID: 36640298 DOI: 10.1002/cbic.202200687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/15/2023]
Abstract
The short- and medium-chain dehydrogenase/reductase superfamilies are responsible for most chiral alcohol production in laboratories and industries. In nature, they participate in diverse roles such as detoxification, housekeeping, secondary metabolite production, and catalysis of several chemicals with commercial and environmental significance. As a result, they are used in industries to create biopolymers, active pharmaceutical intermediates (APIs), and are also used as components of modular enzymes like polyketide synthases for fabricating bioactive molecules. Consequently, random, semi-rational and rational engineering have helped transform these enzymes into product-oriented efficient catalysts. The rise of newer synthetic chemicals and their enantiopure counterparts has proved challenging, and engineering them has been the subject of numerous studies. However, they are frequently limited to the synthesis of a single chiral alcohol. The study attempts to defragment and describe hotspots of engineering short- and medium-chain dehydrogenases/reductases for the production of chiral synthons.
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Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS-TIFR), Bellary Road, Bangalore, 560003, India
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11
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Xie J, Pan G, Li Y, Lai L. How protein topology controls allosteric regulations. J Chem Phys 2023; 158:105102. [PMID: 36922138 DOI: 10.1063/5.0138279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Allostery is an important regulatory mechanism of protein functions. Among allosteric proteins, certain protein structure types are more observed. However, how allosteric regulation depends on protein topology remains elusive. In this study, we extracted protein topology graphs at the fold level and found that known allosteric proteins mainly contain multiple domains or subunits and allosteric sites reside more often between two or more domains of the same fold type. Only a small fraction of fold-fold combinations are observed in allosteric proteins, and homo-fold-fold combinations dominate. These analyses imply that the locations of allosteric sites including cryptic ones depend on protein topology. We further developed TopoAlloSite, a novel method that uses the kernel support vector machine to predict the location of allosteric sites on the overall protein topology based on the subgraph-matching kernel. TopoAlloSite successfully predicted known cryptic allosteric sites in several allosteric proteins like phosphopantothenoylcysteine synthetase, spermidine synthase, and sirtuin 6, demonstrating its power in identifying cryptic allosteric sites without performing long molecular dynamics simulations or large-scale experimental screening. Our study demonstrates that protein topology largely determines how its function can be allosterically regulated, which can be used to find new druggable targets and locate potential binding sites for rational allosteric drug design.
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Affiliation(s)
- Juan Xie
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Gaoxiang Pan
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yibo Li
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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12
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Uegaki T, Takei T, Yamaguchi S, Fujiyama K, Sato Y, Hino T, Nagano S. Anammox Bacterial S-Adenosyl-l-Methionine Dependent Methyltransferase Crystal Structure and Its Interaction with Acyl Carrier Proteins. Int J Mol Sci 2023; 24:ijms24010744. [PMID: 36614187 PMCID: PMC9821293 DOI: 10.3390/ijms24010744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Ladderane lipids (found in the membranes of anaerobic ammonium-oxidizing [anammox] bacteria) have unique ladder-like hydrophobic groups, and their highly strained exotic structure has attracted the attention of scientists. Although enzymes encoded in type II fatty acid biosynthesis (FASII) gene clusters in anammox bacteria, such as S-adenosyl-l-methionine (SAM)-dependent enzymes, have been proposed to construct a ladder-like structure using a substrate connected to acyl carrier protein from anammox bacteria (AmxACP), no experimental evidence to support this hypothesis was reported to date. Here, we report the crystal structure of a SAM-dependent methyltransferase from anammox bacteria (AmxMT1) that has a substrate and active site pocket between a class I SAM methyltransferase-like core domain and an additional α-helix inserted into the core domain. Structural comparisons with homologous SAM-dependent C-methyltransferases in polyketide synthase, AmxACP pull-down assays, AmxACP/AmxMT1 complex structure predictions by AlphaFold, and a substrate docking simulation suggested that a small compound connected to AmxACP could be inserted into the pocket of AmxMT1, and then the enzyme transfers a methyl group from SAM to the substrate to produce branched lipids. Although the enzymes responsible for constructing the ladder-like structure remain unknown, our study, for the first time, supports the hypothesis that biosynthetic intermediates connected to AmxACP are processed by SAM-dependent enzymes, which are not typically involved in the FASII system, to produce the ladder-like structure of ladderane lipids in anammox bacteria.
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Affiliation(s)
- Tesshin Uegaki
- Department of Chemistry, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
| | - Taisei Takei
- Department of Chemistry and Biotechnology, Faculty of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
| | - Shuhei Yamaguchi
- Department of Engineering, Graduate School of Sustainability Science, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
| | - Keisuke Fujiyama
- Department of Chemistry, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
- Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
| | - Tomoya Hino
- Department of Chemistry, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
- Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
| | - Shingo Nagano
- Department of Chemistry, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
- Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan
- Correspondence:
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13
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Noor E, Flamholz AI, Jayaraman V, Ross BL, Cohen Y, Patrick WM, Gruic‐Sovulj I, Tawfik DS. Uniform binding and negative catalysis at the origin of enzymes. Protein Sci 2022; 31:e4381. [PMID: 35900021 PMCID: PMC9281367 DOI: 10.1002/pro.4381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/06/2022] [Accepted: 06/15/2022] [Indexed: 11/06/2022]
Abstract
Enzymes are well known for their catalytic abilities, some even reaching "catalytic perfection" in the sense that the reaction they catalyze has reached the physical bound of the diffusion rate. However, our growing understanding of enzyme superfamilies has revealed that only some share a catalytic chemistry while others share a substrate-handle binding motif, for example, for a particular phosphate group. This suggests that some families emerged through a "substrate-handle-binding-first" mechanism ("binding-first" for brevity) instead of "chemistry-first" and we are, therefore, left to wonder what the role of non-catalytic binders might have been during enzyme evolution. In the last of their eight seminal, back-to-back articles from 1976, John Albery and Jeremy Knowles addressed the question of enzyme evolution by arguing that the simplest mode of enzyme evolution is what they defined as "uniform binding" (parallel stabilization of all enzyme-bound states to the same degree). Indeed, we show that a uniform-binding proto-catalyst can accelerate a reaction, but only when catalysis is already present, that is, when the transition state is already stabilized to some degree. Thus, we sought an alternative explanation for the cases where substrate-handle-binding preceded any involvement of a catalyst. We find that evolutionary starting points that exhibit negative catalysis can redirect the reaction's course to a preferred product without need for rate acceleration or product release; that is, if they do not stabilize, or even destabilize, the transition state corresponding to an undesired product. Such a mechanism might explain the emergence of "binding-first" enzyme families like the aldolase superfamily.
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Affiliation(s)
- Elad Noor
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Avi I. Flamholz
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
- Resnick Sustainability InstituteCalifornia Institute of TechnologyPasadenaCAUSA
| | - Vijay Jayaraman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Brian L. Ross
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Yair Cohen
- Department of Caltech Environmental Science and EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Wayne M. Patrick
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Ita Gruic‐Sovulj
- Department of Chemistry, Faculty of ScienceUniversity of ZagrebZagrebCroatia
| | - Dan S. Tawfik
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
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14
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Essuman K, Milbrandt J, Dangl JL, Nishimura MT. Shared TIR enzymatic functions regulate cell death and immunity across the tree of life. Science 2022; 377:eabo0001. [DOI: 10.1126/science.abo0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the 20th century, researchers studying animal and plant signaling pathways discovered a protein domain shared across diverse innate immune systems: the Toll/Interleukin-1/Resistance-gene (TIR) domain. The TIR domain is found in several protein architectures and was defined as an adaptor mediating protein-protein interactions in animal innate immunity and developmental signaling pathways. However, studies of nerve degeneration in animals, and subsequent breakthroughs in plant, bacterial and archaeal systems, revealed that TIR domains possess enzymatic activities. We provide a synthesis of TIR functions and the role of various related TIR enzymatic products in evolutionarily diverse immune systems. These studies may ultimately guide interventions that would span the tree of life, from treating human neurodegenerative disorders and bacterial infections, to preventing plant diseases.
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Affiliation(s)
- Kow Essuman
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marc T. Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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15
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Nolte TM, Peijnenburg WJGM, Miguel ABR, Zhang YN, Hendriks AJ. Stoichiometric ratios for biotics and xenobiotics capture effective metabolic coupling to re(de)fine biodegradation. WATER RESEARCH 2022; 217:118333. [PMID: 35421691 DOI: 10.1016/j.watres.2022.118333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/07/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Preserving human and environmental health requires anthropogenic pollutants to be biologically degradable. Depending on concentration, both nutrients and pollutants induce and activate metabolic capacity in the endemic bacterial consortium, which in turn aids their degradation. Knowledge on such 'acclimation' is rarely implemented in risk assessment cost-effectively. As a result, an accurate description of the mechanisms and kinetics of biodegradation remains problematic. In this study, we defined a yield 'effectivity', comprising the effectiveness at which a pollutant (substrate) enhances its own degradation by inducing (biomass) cofactors involved therein. Our architecture for calculation represents the interplay between concentration and metabolism via both stoichiometric and thermodynamic concepts. The calculus for yield 'effectivity' is biochemically intuitive, implicitly embeds co-metabolism and distinguishes 'endogenic' from 'exogenic' substances' reflecting various phenomena in biodegradation and bio-transformation studies. We combined data on half-lives of pollutants/nutrients in wastewater and surface water with transition-state rate theory to obtain also experimental values for effective yields. These quantify the state of acclimation: the portion of biodegradation kinetics attributable to (contributed by) 'natural metabolism', in view of similarity to natural substances. Calculated and experimental values showed statistically significant correspondence. Particularly, carbohydrate metabolism and nucleic acid metabolism appeared relevant for acclimation (R2 = 0.11-0.42), affecting rates up to 104.9(±0.7) times: under steady-state acclimation, a compound stoichiometrically identical to carbohydrates or nucleic acids, is 103.2 to 104.9 times faster aerobically degraded than a compound marginally similar. Our new method, simulating (contribution by) the state of acclimation, supplements existing structure-biodegradation and kinetic models for predicting biodegradation in wastewater and surface water. The accuracy of prediction may increase when characterizing nutrients/co-metabolites in terms of, e.g., elemental analysis. We discuss strengths and limitations of our approach by comparison to empirical and mechanism-based methods.
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Affiliation(s)
- Tom M Nolte
- Radboud University Nijmegen, Department of Environmental Science, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands; National Institute of Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, the Netherlands
| | - Ana B Rios- Miguel
- Radboud University Nijmegen, Department of Microbiology, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands
| | - Ya-Nan Zhang
- School of Environment, Northeast Normal University, NO. 2555 Jingyue Street, Changchun, Jilin 130117, China
| | - A Jan Hendriks
- Radboud University Nijmegen, Department of Environmental Science, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands
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16
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Merski M, Macedo-Ribeiro S, Wieczorek RM, Górna MW. The Repeating, Modular Architecture of the HtrA Proteases. Biomolecules 2022; 12:biom12060793. [PMID: 35740918 PMCID: PMC9221053 DOI: 10.3390/biom12060793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
A conserved, 26-residue sequence [AA(X2)[A/G][G/L](X2)GDV[I/L](X2)[V/L]NGE(X1)V(X6)] and corresponding structure repeating module were identified within the HtrA protease family using a non-redundant set (N = 20) of publicly available structures. While the repeats themselves were far from sequence perfect, they had notable conservation to a statistically significant level. Three or more repetitions were identified within each protein despite being statistically expected to randomly occur only once per 1031 residues. This sequence repeat was associated with a six stranded antiparallel β-barrel module, two of which are present in the core of the structures of the PA clan of serine proteases, while a modified version of this module could be identified in the PDZ-like domains. Automated structural alignment methods had difficulties in superimposing these β-barrels, but the use of a target human HtrA2 structure showed that these modules had an average RMSD across the set of structures of less than 2 Å (mean and median). Our findings support Dayhoff’s hypothesis that complex proteins arose through duplication of simpler peptide motifs and domains.
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Affiliation(s)
- Matthew Merski
- Structural Biology Group, Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Correspondence: (M.M.); (M.W.G.); Tel.: +48-225-526-642 (M.M.)
| | - Sandra Macedo-Ribeiro
- Instituto de Investigação e Inovação em Saúde and Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal;
| | - Rafal M. Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Correspondence: (M.M.); (M.W.G.); Tel.: +48-225-526-642 (M.M.)
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17
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Jackson C, Toth-Petroczy A, Kolodny R, Hollfelder F, Fuxreiter M, Caroline Lynn Kamerlin S, Tokuriki N. Adventures on the routes of protein evolution — in memoriam Dan Salah Tawfik (1955 - 2021). J Mol Biol 2022; 434:167462. [DOI: 10.1016/j.jmb.2022.167462] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 12/21/2022]
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18
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Kamiński K, Ludwiczak J, Jasiński M, Bukala A, Madaj R, Szczepaniak K, Dunin-Horkawicz S. Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. Brief Bioinform 2021; 23:6375059. [PMID: 34571541 PMCID: PMC8769691 DOI: 10.1093/bib/bbab371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/04/2021] [Accepted: 08/22/2021] [Indexed: 11/15/2022] Open
Abstract
The Rossmann fold enzymes are involved in essential biochemical pathways such as nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors, small nucleoside-based compounds specifically recognized by a conserved βαβ motif shared by all Rossmann fold proteins. While Rossmann methyltransferases recognize only a single cofactor type, the S-adenosylmethionine, the oxidoreductases, depending on the family, bind nicotinamide (nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate) or flavin-based (flavin adenine dinucleotide) cofactors. In this study, we showed that despite its short length, the βαβ motif unambiguously defines the specificity towards the cofactor. Following this observation, we trained two complementary deep learning models for the prediction of the cofactor specificity based on the sequence and structural features of the βαβ motif. A benchmark on two independent test sets, one containing βαβ motifs bearing no resemblance to those of the training set, and the other comprising 38 experimentally confirmed cases of rational design of the cofactor specificity, revealed the nearly perfect performance of the two methods. The Rossmann-toolbox protocols can be accessed via the webserver at https://lbs.cent.uw.edu.pl/rossmann-toolbox and are available as a Python package at https://github.com/labstructbioinf/rossmann-toolbox.
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Affiliation(s)
- Kamil Kamiński
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.,Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Pasteura 3, 02-093 Warsaw, Poland
| | - Maciej Jasiński
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Adriana Bukala
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Rafal Madaj
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Krzysztof Szczepaniak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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19
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Pinto GP, Corbella M, Demkiv AO, Kamerlin SCL. Exploiting enzyme evolution for computational protein design. Trends Biochem Sci 2021; 47:375-389. [PMID: 34544655 DOI: 10.1016/j.tibs.2021.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 11/15/2022]
Abstract
Recent years have seen an explosion of interest in understanding the physicochemical parameters that shape enzyme evolution, as well as substantial advances in computational enzyme design. This review discusses three areas where evolutionary information can be used as part of the design process: (i) using ancestral sequence reconstruction (ASR) to generate new starting points for enzyme design efforts; (ii) learning from how nature uses conformational dynamics in enzyme evolution to mimic this process in silico; and (iii) modular design of enzymes from smaller fragments, again mimicking the process by which nature appears to create new protein folds. Using showcase examples, we highlight the importance of incorporating evolutionary information to continue to push forward the boundaries of enzyme design studies.
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Affiliation(s)
- Gaspar P Pinto
- Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Marina Corbella
- Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Andrey O Demkiv
- Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
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20
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Ferruz N, Michel F, Lobos F, Schmidt S, Höcker B. Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks. Front Mol Biosci 2021; 8:715972. [PMID: 34485385 PMCID: PMC8416435 DOI: 10.3389/fmolb.2021.715972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Modern proteins have been shown to share evolutionary relationships via subdomain-sized fragments. The assembly of such fragments through duplication and recombination events led to the complex structures and functions we observe today. We previously implemented a pipeline that identified more than 1,000 of these fragments that are shared by different protein folds and developed a web interface to analyze and search for them. This resource named Fuzzle helps structural and evolutionary biologists to identify and analyze conserved parts of a protein but it also provides protein engineers with building blocks for example to design proteins by fragment combination. Here, we describe a new version of this web resource that was extended to include ligand information. This addition is a significant asset to the database since now protein fragments that bind specific ligands can be identified and analyzed. Often the mode of ligand binding is conserved in proteins thereby supporting a common evolutionary origin. The same can now be explored for subdomain-sized fragments within this database. This ligand binding information can also be used in protein engineering to graft binding pockets into other protein scaffolds or to transfer functional sites via recombination of a specific fragment. Fuzzle 2.0 is freely available at https://fuzzle.uni-bayreuth.de/2.0.
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Affiliation(s)
- Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Florian Michel
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Francisco Lobos
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Steffen Schmidt
- Computational Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
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21
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Stodola TJ, Chi YI, De Assuncao TM, Leverence EN, Tripathi S, Dsouza NR, Mathison AJ, Volkman BF, Smith BC, Lomberk G, Zimmermann MT, Urrutia R. Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1-like (DOT1L) and partnering complexes involved in leukemogenesis. Proteins 2021; 90:282-298. [PMID: 34414607 PMCID: PMC8671179 DOI: 10.1002/prot.26219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022]
Abstract
Disruptor of telomeric silencing 1‐like (DOT1L) is the only non‐SET domain histone lysine methyltransferase (KMT) and writer of H3K79 methylation on nucleosomes marked by H2B ubiquitination. DOT1L has elicited significant attention because of its interaction or fusion with members of the AF protein family in blood cell biology and leukemogenic transformation. Here, our goal was to extend previous structural information by performing a robust molecular dynamic study of DOT1L and its leukemogenic partners combined with mutational analysis. We show that statically and dynamically, D161, G163, E186, and F223 make frequent time‐dependent interactions with SAM, while additional residues T139, K187, and N241 interact with SAM only under dynamics. Dynamics models reveal DOT1L, SAM, and H4 moving as one and show that more than twice the number of DOT1L residues interacts with these partners, relative to the static structure. Mutational analyses indicate that six of these residues are intolerant to substitution. We describe the dynamic behavior of DOT1L interacting with AF10 and AF9. Studies on the dynamics of a heterotrimeric complex of DOT1L1‐AF10 illuminated describe coordinated motions that impact the relative position of the DOT1L HMT domain to the nucleosome. The molecular motions of the DOT1L–AF9 complex are less extensive and highly dynamic, resembling a swivel‐like mechanics. Through molecular dynamics and mutational analysis, we extend the knowledge previous provided by static measurements. These results are important to consider when describing the biochemical properties of DOT1L, under normal and in disease conditions, as well as for the development of novel therapeutic agents.
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Affiliation(s)
- Timothy J Stodola
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Young-In Chi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Thiago M De Assuncao
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Elise N Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Swarnendu Tripathi
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nikita R Dsouza
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gwen Lomberk
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael T Zimmermann
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, GSPMC, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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22
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Gruic-Sovulj I, Longo LM, Jabłońska J, Tawfik DS. The evolutionary history of the HUP domain. Crit Rev Biochem Mol Biol 2021; 57:1-15. [PMID: 34384295 DOI: 10.1080/10409238.2021.1957764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Among the enzyme lineages that undoubtedly emerged prior to the last universal common ancestor is the so-called HUP, which includes Class I aminoacyl tRNA synthetases (AARSs) as well as enzymes mediating NAD, FAD, and CoA biosynthesis. Here, we provide a detailed analysis of HUP evolution, from emergence to structural and functional diversification. The HUP is a nucleotide binding domain that uniquely catalyzes adenylation via the release of pyrophosphate. In contrast to other ancient nucleotide binding domains with the αβα sandwich architecture, such as P-loop NTPases, the HUP's most conserved feature is not phosphate binding, but rather ribose binding by backbone interactions to the tips of β1 and/or β4. Indeed, the HUP exhibits unusual evolutionary plasticity and, while ribose binding is conserved, the location and mode of binding to the base and phosphate moieties of the nucleotide, and to the substrate(s) reacting with it, have diverged with time, foremost along the emergence of the AARSs. The HUP also beautifully demonstrates how a well-packed scaffold combined with evolvable surface elements promotes evolutionary innovation. Finally, we offer a scenario for the emergence of the HUP from a seed βαβ fragment, and suggest that despite an identical architecture, the HUP and the Rossmann represent independent emergences.
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Affiliation(s)
- Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Liam M Longo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Jagoda Jabłońska
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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23
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Álvarez-Lugo A, Becerra A. The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach. Front Genet 2021; 12:641817. [PMID: 34335678 PMCID: PMC8318041 DOI: 10.3389/fgene.2021.641817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Gene duplication is a crucial process involved in the appearance of new genes and functions. It is thought to have played a major role in the growth of enzyme families and the expansion of metabolism at the biosphere's dawn and in recent times. Here, we analyzed paralogous enzyme content within each of the seven enzymatic classes for a representative sample of prokaryotes by a comparative approach. We found a high ratio of paralogs for three enzymatic classes: oxidoreductases, isomerases, and translocases, and within each of them, most of the paralogs belong to only a few subclasses. Our results suggest an intricate scenario for the evolution of prokaryotic enzymes, involving different fates for duplicated enzymes fixed in the genome, where around 20-40% of prokaryotic enzymes have paralogs. Intracellular organisms have a lesser ratio of duplicated enzymes, whereas free-living enzymes show the highest ratios. We also found that phylogenetically close phyla and some unrelated but with the same lifestyle share similar genomic and biochemical traits, which ultimately support the idea that gene duplication is associated with environmental adaptation.
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Affiliation(s)
- Alejandro Álvarez-Lugo
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
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24
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Kolodny R, Nepomnyachiy S, Tawfik DS, Ben-Tal N. Bridging Themes: Short Protein Segments Found in Different Architectures. Mol Biol Evol 2021; 38:2191-2208. [PMID: 33502503 PMCID: PMC8136508 DOI: 10.1093/molbev/msab017] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages over ab initio emergence from random sequences. In support of this view, sequence similarities between different proteins is generally indicative of common ancestry, and we collectively refer to such homologous sequences as "themes." At the domain level, sequence homology is routinely detected. However, short themes which are segments, or fragments of intact domains, are particularly interesting because they may provide hints about the emergence of domains, as opposed to divergence of preexisting domains, or their mixing-and-matching to form multi-domain proteins. Here we identified 525 representative short themes, comprising 20-80 residues that are unexpectedly shared between domains considered to have emerged independently. Among these "bridging themes" are ones shared between the most ancient domains, for example, Rossmann, P-loop NTPase, TIM-barrel, flavodoxin, and ferredoxin-like. We elaborate on several particularly interesting cases, where the bridging themes mediate ligand binding. Ligand binding may have contributed to the stability and the plasticity of these building blocks, and to their ability to invade preexisting domains or serve as starting points for completely new domains.
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Affiliation(s)
- Rachel Kolodny
- Department of Computer Science, University of Haifa, Haifa, Israel
| | | | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Ben-Tal
- George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel
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25
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Ferruz N, Noske J, Höcker B. Protlego: A Python package for the analysis and design of chimeric proteins. Bioinformatics 2021; 37:3182-3189. [PMID: 33901273 PMCID: PMC8504633 DOI: 10.1093/bioinformatics/btab253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/05/2021] [Accepted: 04/19/2021] [Indexed: 01/03/2023] Open
Abstract
Motivation Duplication and recombination of protein fragments have led to the highly diverse protein space that we observe today. By mimicking this natural process, the design of protein chimeras via fragment recombination has proven experimentally successful and has opened a new era for the design of customizable proteins. The in silico building of structural models for these chimeric proteins, however, remains a manual task that requires a considerable degree of expertise and is not amenable for high-throughput studies. Energetic and structural analysis of the designed proteins often require the use of several tools, each with their unique technical difficulties and available in different programming languages or web servers. Results We implemented a Python package that enables automated, high-throughput design of chimeras and their structural analysis. First, it fetches evolutionarily conserved fragments from a built-in database (also available at fuzzle.uni-bayreuth.de). These relationships can then be represented via networks or further selected for chimera construction via recombination. Designed chimeras or natural proteins are then scored and minimized with the Charmm and Amber forcefields and their diverse structural features can be analyzed at ease. Here, we showcase Protlego’s pipeline by exploring the relationships between the P-loop and Rossmann superfolds, building and characterizing their offspring chimeras. We believe that Protlego provides a powerful new tool for the protein design community. Availability and implementation Protlego runs on the Linux platform and is freely available at (https://hoecker-lab.github.io/protlego/) with tutorials and documentation. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Jakob Noske
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
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Helicase-like functions in phosphate loop containing beta-alpha polypeptides. Proc Natl Acad Sci U S A 2021; 118:2016131118. [PMID: 33846247 DOI: 10.1073/pnas.2016131118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases, and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple βα repeat proteins bind NTPs but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one β-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes compose a plausible description of the sequence, structure, and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.
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Müller M, Calvert M, Hottmann I, Kluj RM, Teufel T, Balbuchta K, Engelbrecht A, Selim KA, Xu Q, Borisova M, Titz A, Mayer C. The exo-β-N-acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases. J Biol Chem 2021; 296:100519. [PMID: 33684445 PMCID: PMC8054146 DOI: 10.1016/j.jbc.2021.100519] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/27/2021] [Accepted: 03/04/2021] [Indexed: 11/11/2022] Open
Abstract
Endo-β-N-acetylmuramidases, commonly known as lysozymes, are well-characterized antimicrobial enzymes that catalyze an endo-lytic cleavage of peptidoglycan; i.e., they hydrolyze the β-1,4-glycosidic bonds connecting N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc). In contrast, little is known about exo-β-N-acetylmuramidases, which catalyze an exo-lytic cleavage of β-1,4-MurNAc entities from the non-reducing ends of peptidoglycan chains. Such an enzyme was identified earlier in the bacterium Bacillus subtilis, but the corresponding gene has remained unknown so far. We now report that ybbC of B. subtilis, renamed namZ, encodes the reported exo-β-N-acetylmuramidase. A ΔnamZ mutant accumulated specific cell wall fragments and showed growth defects under starvation conditions, indicating a role of NamZ in cell wall turnover and recycling. Recombinant NamZ protein specifically hydrolyzed the artificial substrate para-nitrophenyl β-MurNAc and the peptidoglycan-derived disaccharide MurNAc-β-1,4-GlcNAc. Together with the exo-β-N-acetylglucosaminidase NagZ and the exo-muramoyl-l-alanine amidase AmiE, NamZ degraded intact peptidoglycan by sequential hydrolysis from the non-reducing ends. A structure model of NamZ, built on the basis of two crystal structures of putative orthologs from Bacteroides fragilis, revealed a two-domain structure including a Rossmann-fold-like domain that constitutes a unique glycosidase fold. Thus, NamZ, a member of the DUF1343 protein family of unknown function, is now classified as the founding member of a new family of glycosidases (CAZy GH171; www.cazy.org/GH171.html). NamZ-like peptidoglycan hexosaminidases are mainly present in the phylum Bacteroidetes and less frequently found in individual genomes within Firmicutes (Bacilli, Clostridia), Actinobacteria, and γ-proteobacteria.
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Affiliation(s)
- Maraike Müller
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Matthew Calvert
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany; Department of Chemistry, Saarland University, Saarbrücken, Germany
| | - Isabel Hottmann
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Robert Maria Kluj
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Tim Teufel
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Katja Balbuchta
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Alicia Engelbrecht
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Khaled A Selim
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany; Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Center, Giza, Egypt
| | - Qingping Xu
- GM/CA @ APS, Argonne National Laboratory, Lemont, Illinois, USA
| | - Marina Borisova
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany; Department of Chemistry, Saarland University, Saarbrücken, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
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28
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Medvedev KE, Kinch LN, Dustin Schaeffer R, Pei J, Grishin NV. A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit. J Mol Biol 2020; 433:166788. [PMID: 33387532 DOI: 10.1016/j.jmb.2020.166788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/26/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The Rossmann-like fold is the most prevalent and diversified doubly-wound superfold of ancient evolutionary origin. Rossmann-like domains are present in a variety of metabolic enzymes and are capable of binding diverse ligands. Discerning evolutionary relationships among these domains is challenging because of their diverse functions and ancient origin. We defined a minimal Rossmann-like structural motif (RLM), identified RLM-containing domains among known 3D structures (20%) and classified them according to their homologous relationships. New classifications were incorporated into our Evolutionary Classification of protein Domains (ECOD) database. We defined 156 homology groups (H-groups), which were further clustered into 123 possible homology groups (X-groups). Our analysis revealed that RLM-containing proteins constitute approximately 15% of the human proteome. We found that disease-causing mutations are more frequent within RLM domains than within non-RLM domains of these proteins, highlighting the importance of RLM-containing proteins for human health.
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Affiliation(s)
- Kirill E Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States.
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, United States; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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29
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Brzezinski K. S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains. Biomolecules 2020; 10:biom10121682. [PMID: 33339190 PMCID: PMC7765604 DOI: 10.3390/biom10121682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/27/2022] Open
Abstract
S-adenosyl-l-homocysteine hydrolase (SAHase) is a major regulator of cellular methylation reactions that occur in eukaryotic and prokaryotic organisms. SAHase activity is also a significant source of l-homocysteine and adenosine, two compounds involved in numerous vital, as well as pathological processes. Therefore, apart from cellular methylation, the enzyme may also influence other processes important for the physiology of particular organisms. Herein, presented is the structural characterization and comparison of SAHases of eukaryotic and prokaryotic origin, with an emphasis on the two principal domains of SAHase subunit based on the Rossmann motif. The first domain is involved in the binding of a substrate, e.g., S-adenosyl-l-homocysteine or adenosine and the second domain binds the NAD+ cofactor. Despite their structural similarity, the molecular interactions between an adenosine-based ligand molecule and macromolecular environment are different in each domain. As a consequence, significant differences in the conformation of d-ribofuranose rings of nucleoside and nucleotide ligands, especially those attached to adenosine moiety, are observed. On the other hand, the chemical nature of adenine ring recognition, as well as an orientation of the adenine ring around the N-glycosidic bond are of high similarity for the ligands bound in the substrate- and cofactor-binding domains.
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Affiliation(s)
- Krzysztof Brzezinski
- Laboratory of Structural Microbiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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30
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Longo LM, Jabłońska J, Vyas P, Kanade M, Kolodny R, Ben-Tal N, Tawfik DS. On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment. eLife 2020; 9:e64415. [PMID: 33295875 PMCID: PMC7758060 DOI: 10.7554/elife.64415] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
This article is dedicated to the memory of Michael G. Rossmann. Dating back to the last universal common ancestor, P-loop NTPases and Rossmanns comprise the most ubiquitous and diverse enzyme lineages. Despite similarities in their overall architecture and phosphate binding motif, a lack of sequence identity and some fundamental structural differences currently designates them as independent emergences. We systematically searched for structure and sequence elements shared by both lineages. We detected homologous segments that span the first βαβ motif of both lineages, including the phosphate binding loop and a conserved aspartate at the tip of β2. The latter ligates the catalytic metal in P-loop NTPases, while in Rossmanns it binds the nucleotide's ribose moiety. Tubulin, a Rossmann GTPase, demonstrates the potential of the β2-Asp to take either one of these two roles. While convergence cannot be completely ruled out, we show that both lineages likely emerged from a common βαβ segment that comprises the core of these enzyme families to this very day.
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Affiliation(s)
- Liam M Longo
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
| | - Jagoda Jabłońska
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
| | - Pratik Vyas
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
| | - Manil Kanade
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
| | - Rachel Kolodny
- University of Haifa, Department of Computer ScienceHaifaIsrael
| | - Nir Ben-Tal
- Tel Aviv University, George S. Wise Faculty of Life Sciences, Department of Biochemistry and Molecular BiologyTel AvivIsrael
| | - Dan S Tawfik
- Weizmann Institute of Science, Department of Biomolecular SciencesRehovotIsrael
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31
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Sridhar S, Schmitz W, Hiltunen JK, Venkatesan R, Bergmann U, Kiema TR, Wierenga RK. Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1256-1269. [DOI: 10.1107/s2059798320013819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/15/2020] [Indexed: 11/11/2022]
Abstract
The peroxisomal multifunctional enzyme type 1 (MFE1) catalyzes two successive reactions in the β-oxidation cycle: the 2E-enoyl-CoA hydratase (ECH) and NAD+-dependent 3S-hydroxyacyl-CoA dehydrogenase (HAD) reactions. MFE1 is a monomeric enzyme that has five domains. The N-terminal part (domains A and B) adopts the crotonase fold and the C-terminal part (domains C, D and E) adopts the HAD fold. A new crystal form of MFE1 has captured a conformation in which both active sites are noncompetent. This structure, at 1.7 Å resolution, shows the importance of the interactions between Phe272 in domain B (the linker helix; helix H10 of the crotonase fold) and the beginning of loop 2 (of the crotonase fold) in stabilizing the competent ECH active-site geometry. In addition, protein crystallographic binding studies using optimized crystal-treatment protocols have captured a structure with both the 3-ketodecanoyl-CoA product and NAD+bound in the HAD active site, showing the interactions between 3-ketodecanoyl-CoA and residues of the C, D and E domains. Structural comparisons show the importance of domain movements, in particular of the C domain with respect to the D/E domains and of the A domain with respect to the HAD part. These comparisons suggest that the N-terminal part of the linker helix, which interacts tightly with domains A and E, functions as a hinge region for movement of the A domain with respect to the HAD part.
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32
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Steinbeck J, Fuchs P, Negroni YL, Elsässer M, Lichtenauer S, Stockdreher Y, Feitosa-Araujo E, Kroll JB, Niemeier JO, Humberg C, Smith EN, Mai M, Nunes-Nesi A, Meyer AJ, Zottini M, Morgan B, Wagner S, Schwarzländer M. In Vivo NADH/NAD + Biosensing Reveals the Dynamics of Cytosolic Redox Metabolism in Plants. THE PLANT CELL 2020; 32:3324-3345. [PMID: 32796121 PMCID: PMC7534465 DOI: 10.1105/tpc.20.00241] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/13/2020] [Accepted: 08/12/2020] [Indexed: 05/04/2023]
Abstract
NADH and NAD+ are a ubiquitous cellular redox couple. Although the central role of NAD in plant metabolism and its regulatory role have been investigated extensively at the biochemical level, analyzing the subcellular redox dynamics of NAD in living plant tissues has been challenging. Here, we established live monitoring of NADH/NAD+ in plants using the genetically encoded fluorescent biosensor Peredox-mCherry. We established Peredox-mCherry lines of Arabidopsis (Arabidopsis thaliana) and validated the biophysical and biochemical properties of the sensor that are critical for in planta measurements, including specificity, pH stability, and reversibility. We generated an NAD redox atlas of the cytosol of living Arabidopsis seedlings that revealed pronounced differences in NAD redox status between different organs and tissues. Manipulating the metabolic status through dark-to-light transitions, respiratory inhibition, sugar supplementation, and elicitor exposure revealed a remarkable degree of plasticity of the cytosolic NAD redox status and demonstrated metabolic redox coupling between cell compartments in leaves. Finally, we used protein engineering to generate a sensor variant that expands the resolvable NAD redox range. In summary, we established a technique for in planta NAD redox monitoring to deliver important insight into the in vivo dynamics of plant cytosolic redox metabolism.
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Affiliation(s)
- Janina Steinbeck
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
| | - Philippe Fuchs
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Yuri L Negroni
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Marlene Elsässer
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
- Institute for Cellular and Molecular Botany (IZMB), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany
| | - Sophie Lichtenauer
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
| | - Yvonne Stockdreher
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Elias Feitosa-Araujo
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Johanna B Kroll
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
| | - Jan-Ole Niemeier
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
| | - Christoph Humberg
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
| | - Edward N Smith
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, United Kingdom
| | - Marie Mai
- Institute of Biochemistry, Zentrum für Human- und Molekularbiologie (ZHMB), Saarland University, D-66123 Saarbrücken, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Michela Zottini
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Bruce Morgan
- Institute of Biochemistry, Zentrum für Human- und Molekularbiologie (ZHMB), Saarland University, D-66123 Saarbrücken, Germany
| | - Stephan Wagner
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
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Schall P, Marutschke L, Grimm B. The Flavoproteome of the Model Plant Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21155371. [PMID: 32731628 PMCID: PMC7432721 DOI: 10.3390/ijms21155371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022] Open
Abstract
Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are essential cofactors for enzymes, which catalyze a broad spectrum of vital reactions. This paper intends to compile all potential FAD/FMN-binding proteins encoded by the genome of Arabidopsis thaliana. Several computational approaches were applied to group the entire flavoproteome according to (i) different catalytic reactions in enzyme classes, (ii) the localization in subcellular compartments, (iii) different protein families and subclasses, and (iv) their classification to structural properties. Subsequently, the physiological significance of several of the larger flavoprotein families was highlighted. It is conclusive that plants, such as Arabidopsis thaliana, use many flavoenzymes for plant-specific and pivotal metabolic activities during development and for signal transduction pathways in response to biotic and abiotic stress. Thereby, often two up to several homologous genes are found encoding proteins with high protein similarity. It is proposed that these gene families for flavoproteins reflect presumably their need for differential transcriptional control or the expression of similar proteins with modified flavin-binding properties or catalytic activities.
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Crean RM, Gardner JM, Kamerlin SCL. Harnessing Conformational Plasticity to Generate Designer Enzymes. J Am Chem Soc 2020; 142:11324-11342. [PMID: 32496764 PMCID: PMC7467679 DOI: 10.1021/jacs.0c04924] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Indexed: 02/08/2023]
Abstract
Recent years have witnessed an explosion of interest in understanding the role of conformational dynamics both in the evolution of new enzymatic activities from existing enzymes and in facilitating the emergence of enzymatic activity de novo on scaffolds that were previously non-catalytic. There are also an increasing number of examples in the literature of targeted engineering of conformational dynamics being successfully used to alter enzyme selectivity and activity. Despite the obvious importance of conformational dynamics to both enzyme function and evolvability, many (although not all) computational design approaches still focus either on pure sequence-based approaches or on using structures with limited flexibility to guide the design. However, there exist a wide variety of computational approaches that can be (re)purposed to introduce conformational dynamics as a key consideration in the design process. Coupled with laboratory evolution and more conventional existing sequence- and structure-based approaches, these techniques provide powerful tools for greatly expanding the protein engineering toolkit. This Perspective provides an overview of evolutionary studies that have dissected the role of conformational dynamics in facilitating the emergence of novel enzymes, as well as advances in computational approaches that allow one to target conformational dynamics as part of enzyme design. Harnessing conformational dynamics in engineering studies is a powerful paradigm with which to engineer the next generation of designer biocatalysts.
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Affiliation(s)
- Rory M. Crean
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Jasmine M. Gardner
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites. PLoS Comput Biol 2020; 16:e1007904. [PMID: 32453784 PMCID: PMC7319350 DOI: 10.1371/journal.pcbi.1007904] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 06/26/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023] Open
Abstract
S-adenosylmethionine (SAM) is one of the most important enzyme substrates. It is vital for the function of various proteins, including large group of methyltransferases (MTs). Intriguingly, some bacterial and eukaryotic MTs, while catalysing the same reaction, possess significantly different topologies, with the former being a knotted one. Here, we conducted a comprehensive analysis of SAM conformational space and factors that affect its vastness. We investigated SAM in two forms: free in water (via NMR studies and explicit solvent simulations) and bound to proteins (based on all data available in the PDB and on all-atom molecular dynamics simulations in water). We identified structural descriptors—angles which show the major differences in SAM conformation between unknotted and knotted methyltransferases. Moreover, we report that this is caused mainly by a characteristic for knotted MTs compact binding site formed by the knot and the presence of adenine-binding loop. Additionally, we elucidate conformational restrictions imposed on SAM molecules by other protein groups in comparison to conformational space in water. The topology of a folded polypeptide chain has great impact on the resulting protein function and its interaction with ligands. Interestingly, topological constraints appear to affect binding of one of the most ubiquitous substrates in the cell, S-adenosylmethionine (SAM), to its target proteins. Here, we demonstrate how binding sites of specific proteins restrict SAM conformational freedom in comparison to its unbound state, with a special interest in proteins with non-trivial topology, including an exciting group of knotted methyltransferases. Using a vast array of computational methods combined with NMR experiments, we identify key structural features of knotted methyltransferases that impose unorthodox SAM conformations. We compare them with the characteristics of standard, unknotted SAM binding proteins. These results are significant for understanding differences between analogous, yet topologically different enzymes, as well as for future rational drug design.
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36
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Takénaka A, Moras D. Correlation between equi-partition of aminoacyl-tRNA synthetases and amino-acid biosynthesis pathways. Nucleic Acids Res 2020; 48:3277-3285. [PMID: 31965182 PMCID: PMC7102985 DOI: 10.1093/nar/gkaa013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
The partition of aminoacyl-tRNA synthetases (aaRSs) into two classes of equal size and the correlated amino acid distribution is a puzzling still unexplained observation. We propose that the time scale of the amino-acid synthesis, assumed to be proportional to the number of reaction steps (NE) involved in the biosynthesis pathway, is one of the parameters that controlled the timescale of aaRSs appearance. Because all pathways are branched at fructose-6-phosphate on the metabolic pathway, this product is defined as the common origin for the NE comparison. For each amino-acid, the NE value, counted from the origin to the final product, provides a timescale for the pathways to be established. An archeological approach based on NE reveals that aaRSs of the two classes are generated in pair along this timescale. The results support the coevolution theory for the origin of the genetic code with an earlier appearance of class II aaRSs.
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Affiliation(s)
- Akio Takénaka
- Research Institute, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan.,Faculty of Pharmacy, Shenyang Pharmaceutical University, Benxi, Liaoning 117004, China
| | - Dino Moras
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) 1 rue Laurent Fries, Illkirch 67404, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, France.,Université de Strasbourg, Illkirch, France
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37
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Ferruz N, Lobos F, Lemm D, Toledo-Patino S, Farías-Rico JA, Schmidt S, Höcker B. Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design. J Mol Biol 2020; 432:3898-3914. [PMID: 32330481 PMCID: PMC7322520 DOI: 10.1016/j.jmb.2020.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
Natural evolution has generated an impressively diverse protein universe via duplication and recombination from a set of protein fragments that served as building blocks. The application of these concepts to the design of new proteins using subdomain-sized fragments from different folds has proven to be experimentally successful. To better understand how evolution has shaped our protein universe, we performed an all-against-all comparison of protein domains representing all naturally existing folds and identified conserved homologous protein fragments. Overall, we found more than 1000 protein fragments of various lengths among different folds through similarity network analysis. These fragments are present in very different protein environments and represent versatile building blocks for protein design. These data are available in our web server called F(old P)uzzle (fuzzle.uni-bayreuth.de), which allows to individually filter the dataset and create customized networks for folds of interest. We believe that our results serve as an invaluable resource for structural and evolutionary biologists and as raw material for the design of custom-made proteins.
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Affiliation(s)
- Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Francisco Lobos
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dominik Lemm
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Saacnicteh Toledo-Patino
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Steffen Schmidt
- Max Planck Institute for Developmental Biology, Tübingen, Germany; Computational Biochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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38
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Abstract
Life on Earth is driven by electron transfer reactions catalyzed by a suite of enzymes that comprise the superfamily of oxidoreductases (Enzyme Classification EC1). Most modern oxidoreductases are complex in their structure and chemistry and must have evolved from a small set of ancient folds. Ancient oxidoreductases from the Archean Eon between ca. 3.5 and 2.5 billion years ago have been long extinct, making it challenging to retrace evolution by sequence-based phylogeny or ancestral sequence reconstruction. However, three-dimensional topologies of proteins change more slowly than sequences. Using comparative structure and sequence profile-profile alignments, we quantify the similarity between proximal cofactor-binding folds and show that they are derived from a common ancestor. We discovered that two recurring folds were central to the origin of metabolism: ferredoxin and Rossmann-like folds. In turn, these two folds likely shared a common ancestor that, through duplication, recruitment, and diversification, evolved to facilitate electron transfer and catalysis at a very early stage in the origin of metabolism.
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39
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Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes. Proc Natl Acad Sci U S A 2020; 117:5310-5318. [PMID: 32079722 DOI: 10.1073/pnas.1911742117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ubiquity of phospho-ligands suggests that phosphate binding emerged at the earliest stage of protein evolution. To evaluate this hypothesis and unravel its details, we identified all phosphate-binding protein lineages in the Evolutionary Classification of Protein Domains database. We found at least 250 independent evolutionary lineages that bind small molecule cofactors and metabolites with phosphate moieties. For many lineages, phosphate binding emerged later as a niche functionality, but for the oldest protein lineages, phosphate binding was the founding function. Across some 4 billion y of protein evolution, side-chain binding, in which the phosphate moiety does not interact with the backbone at all, emerged most frequently. However, in the oldest lineages, and most characteristically in αβα sandwich enzyme domains, N-helix binding sites dominate, where the phosphate moiety sits atop the N terminus of an α-helix. This discrepancy is explained by the observation that N-helix binding is uniquely realized by short, contiguous sequences with reduced amino acid diversity, foremost Gly, Ser, and Thr. The latter two amino acids preferentially interact with both the backbone amide and the side-chain hydroxyl (bidentate interaction) to promote binding by short sequences. We conclude that the first αβα sandwich domains emerged from shorter and simpler polypeptides that bound phospho-ligands via N-helix sites.
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40
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Northover DE, Shank SD, Liberles DA. Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates. BMC Evol Biol 2020; 20:24. [PMID: 32046633 PMCID: PMC7011509 DOI: 10.1186/s12862-020-1585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 01/16/2020] [Indexed: 11/21/2022] Open
Abstract
Background Understanding the origins of genome content has long been a goal of molecular evolution and comparative genomics. By examining genome evolution through the guise of lineage-specific evolution, it is possible to make inferences about the evolutionary events that have given rise to species-specific diversification. Here we characterize the evolutionary trends found in chordate species using The Adaptive Evolution Database (TAED). TAED is a database of phylogenetically indexed gene families designed to detect episodes of directional or diversifying selection across chordates. Gene families within the database have been assessed for lineage-specific estimates of dN/dS and have been reconciled to the chordate species to identify retained duplicates. Gene families have also been mapped to the functional pathways and amino acid changes which occurred on high dN/dS lineages have been mapped to protein structures. Results An analysis of this exhaustive database has enabled a characterization of the processes of lineage-specific diversification in chordates. A pathway level enrichment analysis of TAED determined that pathways most commonly found to have elevated rates of evolution included those involved in metabolism, immunity, and cell signaling. An analysis of protein fold presence on proteins, after normalizing for frequency in the database, found common folds such as Rossmann folds, Jelly Roll folds, and TIM barrels were overrepresented on proteins most likely to undergo directional selection. A set of gene families which experience increased numbers of duplications within short evolutionary times are associated with pathways involved in metabolism, olfactory reception, and signaling. An analysis of protein secondary structure indicated more relaxed constraint in β-sheets and stronger constraint on alpha Helices, amidst a general preference for substitutions at exposed sites. Lastly a detailed analysis of the ornithine decarboxylase gene family, a key enzyme in the pathway for polyamine synthesis, revealed lineage-specific evolution along the lineage leading to Cetacea through rapid sequence evolution in a duplicate gene with amino acid substitutions causing active site rearrangement. Conclusion Episodes of lineage-specific evolution are frequent throughout chordate species. Both duplication and directional selection have played large roles in the evolution of the phylum. TAED is a powerful tool for facilitating this understanding of lineage-specific evolution.
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Affiliation(s)
- David E Northover
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Stephen D Shank
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA. .,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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41
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Medvedev KE, Kinch LN, Schaeffer RD, Grishin NV. Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. PLoS Comput Biol 2019; 15:e1007569. [PMID: 31869345 PMCID: PMC6957218 DOI: 10.1371/journal.pcbi.1007569] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 01/13/2020] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
Rossmann folds are ancient, frequently diverged domains found in many biological reaction pathways where they have adapted for different functions. Consequently, discernment and classification of their homologous relations and function can be complicated. We define a minimal Rossmann-like structure motif (RLM) that corresponds for the common core of known Rossmann domains and use this motif to identify all RLM domains in the Protein Data Bank (PDB), thus finding they constitute about 20% of all known 3D structures. The Evolutionary Classification of protein structure Domains (ECOD) classifies RLM domains in a number of groups that lack evidence for homology (X-groups), which suggests that they could have evolved independently multiple times. Closely related, homologous RLM enzyme families can diverge to bind different ligands using similar binding sites and to catalyze different reactions. Conversely, non-homologous RLM domains can converge to catalyze the same reactions or to bind the same ligand with alternate binding modes. We discuss a special case of such convergent evolution that is relevant to the polypharmacology paradigm, wherein the same drug (methotrexate) binds to multiple non-homologous RLM drug targets with different topologies. Finally, assigning proteins with RLM domain to the Enzyme Commission classification suggest that RLM enzymes function mainly in metabolism (and comprise 38% of reference metabolic pathways) and are overrepresented in extant pathways that represent ancient biosynthetic routes such as nucleotide metabolism, energy metabolism, and metabolism of amino acids. In fact, RLM enzymes take part in five out of eight enzymatic reactions of the Wood-Ljungdahl metabolic pathway thought to be used by the last universal common ancestor (LUCA). The prevalence of RLM domains in this ancient metabolism might explain their wide distribution among enzymes.
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Affiliation(s)
- Kirill E. Medvedev
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - R. Dustin Schaeffer
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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42
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Afanasieva E, Chaudhuri I, Martin J, Hertle E, Ursinus A, Alva V, Hartmann MD, Lupas AN. Structural diversity of oligomeric β-propellers with different numbers of identical blades. eLife 2019; 8:49853. [PMID: 31613220 PMCID: PMC6805158 DOI: 10.7554/elife.49853] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/25/2019] [Indexed: 12/29/2022] Open
Abstract
β-Propellers arise through the amplification of a supersecondary structure element called a blade. This process produces toroids of between four and twelve repeats, which are almost always arranged sequentially in a single polypeptide chain. We found that new propellers evolve continuously by amplification from single blades. We therefore investigated whether such nascent propellers can fold as homo-oligomers before they have been fully amplified within a single chain. One- to six-bladed building blocks derived from two seven-bladed WD40 propellers yielded stable homo-oligomers with six to nine blades, depending on the size of the building block. High-resolution structures for tetramers of two blades, trimers of three blades, and dimers of four and five blades, respectively, show structurally diverse propellers and include a novel fold, highlighting the inherent flexibility of the WD40 blade. Our data support the hypothesis that subdomain-sized fragments can provide structural versatility in the evolution of new proteins.
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Affiliation(s)
- Evgenia Afanasieva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Indronil Chaudhuri
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eva Hertle
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Astrid Ursinus
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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43
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Berezovsky IN. Towards descriptor of elementary functions for protein design. Curr Opin Struct Biol 2019; 58:159-165. [PMID: 31352188 DOI: 10.1016/j.sbi.2019.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/18/2019] [Indexed: 11/18/2022]
Abstract
We review studies of the protein evolution that help to formulate rules for protein design. Acknowledging the fundamental importance of Dayhoff's provision on the emergence of functional proteins from short peptides, we discuss multiple evidences of the omnipresent partitioning of protein globules into structural/functional units, using which greatly facilitates the engineering and design efforts. Closed loops and elementary functional loops, which are descendants of ancient ring-like peptides that formed fist protein domains in agreement with Dayhoff's hypothesis, can be considered as basic units of protein structure and function. We argue that future developments in protein design approaches should consider descriptors of the elementary functions, which will help to complement designed scaffolds with functional signatures and flexibility necessary for their functions.
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Affiliation(s)
- Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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44
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Bower EKM, Cooper LP, Roberts GA, White JH, Luyten Y, Morgan RD, Dryden DTF. A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes. Nucleic Acids Res 2019; 46:9067-9080. [PMID: 30165537 PMCID: PMC6158711 DOI: 10.1093/nar/gky760] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 08/21/2018] [Indexed: 12/28/2022] Open
Abstract
Restriction Modification (RM) systems prevent the invasion of foreign genetic material into bacterial cells by restriction and protect the host's genetic material by methylation. They are therefore important in maintaining the integrity of the host genome. RM systems are currently classified into four types (I to IV) on the basis of differences in composition, target recognition, cofactors and the manner in which they cleave DNA. Comparing the structures of the different types, similarities can be observed suggesting an evolutionary link between these different types. This work describes the ‘deconstruction’ of a large Type I RM enzyme into forms structurally similar to smaller Type II RM enzymes in an effort to elucidate the pathway taken by Nature to form these different RM enzymes. Based upon the ability to engineer new enzymes from the Type I ‘scaffold’, an evolutionary pathway and the evolutionary pressures required to move along the pathway from Type I RM systems to Type II RM systems are proposed. Experiments to test the evolutionary model are discussed.
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Affiliation(s)
- Edward K M Bower
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Laurie P Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Gareth A Roberts
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - John H White
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FJ, UK
| | - Yvette Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | - Richard D Morgan
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | - David T F Dryden
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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45
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Identification of functional signatures in the metabolism of the three cellular domains of life. PLoS One 2019; 14:e0217083. [PMID: 31136618 PMCID: PMC6538242 DOI: 10.1371/journal.pone.0217083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/04/2019] [Indexed: 11/19/2022] Open
Abstract
In order to identify common and specific enzymatic activities associated with the metabolism of the three cellular domains of life, the conservation and variations between the enzyme contents of Bacteria, Archaea, and Eukarya organisms were evaluated. To this end, the content of enzymes belonging to a particular pathway and their abundance and distribution in 1507 organisms that have been annotated and deposited in the KEGG database were assessed. In addition, we evaluated the consecutive enzymatic reaction pairs obtained from metabolic pathway reactions and transformed into sequences of enzymatic reactions, with catalytic activities encoded in the Enzyme Commission numbers, which are linked by a substrate. Both analyses are complementary: the first considers individual reactions associated with each organism and metabolic map, and the second evaluates the functional associations between pairs of consecutive reactions. From these comparisons, we found a set of five enzymatic reactions that were widely distributed in all the organisms and considered here as universal to Bacteria, Archaea, and Eukarya; whereas 132 pairs out of 3151 reactions were identified as significant, only 5 of them were found to be widely distributed in all the taxonomic divisions. However, these universal reactions are not widely distributed along the metabolic maps, suggesting their dispensability to all metabolic processes. Finally, we found that universal reactions are also associated with ancestral domains, such as those related to phosphorus-containing groups with a phosphate group as acceptor or those related to the ribulose-phosphate binding barrel, triosephosphate isomerase, and D-ribose-5-phosphate isomerase (RpiA) lid domain, among others. Therefore, we consider that this analysis provides clues about the functional constraints associated with the repertoire of enzymatic functions per organism.
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46
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Nguyen TD, Choi GE, Gu DH, Seo PW, Kim JW, Park JB, Kim JS. Structural basis for the selective addition of an oxygen atom to cyclic ketones by Baeyer-Villiger monooxygenase from Parvibaculum lavamentivorans. Biochem Biophys Res Commun 2019; 512:564-570. [PMID: 30914200 DOI: 10.1016/j.bbrc.2019.03.114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 03/18/2019] [Indexed: 11/17/2022]
Abstract
Baeyer-Villiger monooxygenase (BVMO) catalyzes insertion of an oxygen atom into aliphatic or cyclic ketones with high regioselectivity. The BVMOs from Parvibaculum lavamentivorans (BVMOParvi) and Oceanicola batsensis (BVMOOcean) are interesting because of their homologies, with >40% sequence identity, and reaction with the same cyclic ketones with a methyl moiety to give different products. The revealed BVMOParvi structure shows that BVMOParvi forms a two-domain structure like other BVMOs. It has two inserted residues, compared with BVMOOcean, that form a bulge near the bound flavin adenine dinucleotide in the active site. Furthermore, this bulge is linked to a nearby α-helix via a disulfide bond, probably restricting access of the bulky methyl group of the substrate to this bulge. Another sequence motif at the entrance of the active site (Ala-Ser in BVMOParvi and Ser-Thr in BVMOOcean) allows a large volume in BVMOParvi. These minute differences may discriminate a substrate orientation in both BVMOs from the initial substrate binding pocket to the final oxygenation site, resulting in the inserted oxygen atom being in different positions of the same substrate.
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Affiliation(s)
- Tien Duc Nguyen
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Go-Eun Choi
- Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Do-Heon Gu
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jin-Byung Park
- Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.
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47
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Lenz M, Fademrecht S, Sharma M, Pleiss J, Grogan G, Nestl BM. New imine-reducing enzymes from β-hydroxyacid dehydrogenases by single amino acid substitutions. Protein Eng Des Sel 2018; 31:109-120. [PMID: 29733377 DOI: 10.1093/protein/gzy006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 04/10/2018] [Indexed: 11/14/2022] Open
Abstract
We report the exploration of the evolutionary relationship between imine reductases (IREDs) and other dehydrogenases. This approach is informed by the sequence similarity between these enzyme families and the recently described promiscuous activity of IREDs for the highly reactive carbonyl compound 2,2,2-trifluoroacetophenone. Using the structure of the R-selective IRED from Streptosporangium roseum (R-IRED-Sr) as a model, β-hydroxyacid dehydrogenases (βHADs) were identified as the dehydrogenases most similar to IREDs. To understand how active site differences in IREDs and βHADs enable the reduction of predominantly C = N or C = O bonds respectively, we substituted amino acid residues in βHADs with the corresponding residues from the R-IRED-Sr and were able to increase the promiscuous activity of βHADs for C = N functions by a single amino acid substitution. Variants βHADAt_K170D and βHADAt_K170F lost mainly their keto acid reduction activity and gained the ability to catalyze the reduction of imines. Moreover, the product enantiomeric purity for a bulky imine substrate could be increased from 23% ee (R-IRED-Sr) to 97% ee (βHADAt_K170D/F_F231A) outcompeting already described IRED selectivity.
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Affiliation(s)
- Maike Lenz
- Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - Bettina M Nestl
- Institute of Biochemistry and Technical Biochemistry, Department of Chemistry, Universitaet Stuttgart, Allmandring 31, Stuttgart, Germany
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48
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Abstract
Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein's scaffold. Can motifs such as P-loops confer function in a simpler context? We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop's key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif.
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49
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Chouhan BPS, Maimaiti S, Gade M, Laurino P. Rossmann-Fold Methyltransferases: Taking a "β-Turn" around Their Cofactor, S-Adenosylmethionine. Biochemistry 2018; 58:166-170. [PMID: 30406995 DOI: 10.1021/acs.biochem.8b00994] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methyltransferases (MTases) are superfamilies of enzymes that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM), a nucleoside-based cofactor, to a wide variety of substrates such as DNA, RNA, proteins, small molecules, and lipids. Depending upon their structural features, the MTases can be further classified into different classes; we consider exclusively the largest class of MTases, the Rossmann-fold MTases. It has been shown that the nucleoside cofactor-binding Rossmann enzymes, particularly the nicotinamide adenine dinucleotide (NAD)-, flavin adenine dinucleotide (FAD)-, and SAM-binding MTases enzymes, share common binding motifs that include a Gly-rich loop region that interacts with the cofactor and a highly conserved acidic residue (Asp/Glu) that interacts with the ribose moiety of the cofactor. Here, we observe that the Gly-rich loop region of the Rossmann MTases adapts a specific type II' β-turn in the proximity of the cofactor (<4 Å), and it appears to be a key feature of these superfamilies. Additionally, we demonstrate that the conservation of this β-turn could play a critical role in the enzyme-cofactor interaction, thereby shedding new light on the structural conformation of the Gly-rich loop region from Rossmann MTases.
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Affiliation(s)
- Bhanu Pratap Singh Chouhan
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Shayida Maimaiti
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Madhuri Gade
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Paola Laurino
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
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Davidi D, Longo LM, Jabłońska J, Milo R, Tawfik DS. A Bird’s-Eye View of Enzyme Evolution: Chemical, Physicochemical, and Physiological Considerations. Chem Rev 2018; 118:8786-8797. [DOI: 10.1021/acs.chemrev.8b00039] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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