1
|
Medvedev KE, Schaeffer RD, Grishin NV. DrugDomain: The evolutionary context of drugs and small molecules bound to domains. Protein Sci 2024; 33:e5116. [PMID: 38979784 PMCID: PMC11231930 DOI: 10.1002/pro.5116] [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: 03/22/2024] [Revised: 06/27/2024] [Accepted: 06/29/2024] [Indexed: 07/10/2024]
Abstract
Interactions between proteins and small organic compounds play a crucial role in regulating protein functions. These interactions can modulate various aspects of protein behavior, including enzymatic activity, signaling cascades, and structural stability. By binding to specific sites on proteins, small organic compounds can induce conformational changes, alter protein-protein interactions, or directly affect catalytic activity. Therefore, many drugs available on the market today are small molecules (72% of all approved drugs in the last 5 years). Proteins are composed of one or more domains: evolutionary units that convey function or fitness either singly or in concert with others. Understanding which domain(s) of the target protein binds to a drug can lead to additional opportunities for discovering novel targets. The evolutionary classification of protein domains (ECOD) classifies domains into an evolutionary hierarchy that focuses on distant homology. Previously, no structure-based protein domain classification existed that included information about both the interaction between small molecules or drugs and the structural domains of a target protein. This data is especially important for multidomain proteins and large complexes. Here, we present the DrugDomain database that reports the interaction between ECOD of human target proteins and DrugBank molecules and drugs. The pilot version of DrugDomain describes the interaction of 5160 DrugBank molecules associated with 2573 human proteins. It describes domains for all experimentally determined structures of these proteins and incorporates AlphaFold models when such structures are unavailable. The DrugDomain database is available online: http://prodata.swmed.edu/DrugDomain/.
Collapse
Affiliation(s)
- Kirill E. Medvedev
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - R. Dustin Schaeffer
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Nick V. Grishin
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| |
Collapse
|
2
|
Baird LM, Berndsen CE, Monroe JD. Malate dehydrogenase in plants: evolution, structure, and a myriad of functions. Essays Biochem 2024:EBC20230089. [PMID: 38868915 DOI: 10.1042/ebc20230089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 06/14/2024]
Abstract
Malate dehydrogenase (MDH) catalyzes the interconversion of oxaloacetate and malate coupled to the oxidation/reduction of coenzymes NAD(P)H/NAD(P)+. While most animals have two isoforms of MDH located in the cytosol and mitochondria, all major groups of land plants have at least six MDHs localized to the cytosol, mitochondria, plastids, and peroxisomes. This family of enzymes participates in important reactions in plant cells including photosynthesis, photorespiration, lipid metabolism, and NH4+ metabolism. MDH also helps to regulate the energy balance in the cell and may help the plant cope with various environmental stresses. Despite their functional diversity, all of the plant MDH enzymes share a similar structural fold and act as dimers. In this review, we will introduce readers to our current understanding of the plant MDHs, including their evolution, structure, and function. The focus will be on the MDH enzymes of the model plant Arabidopsis thaliana.
Collapse
Affiliation(s)
- Lisa M Baird
- Department of Biology, University of San Diego, -5998 Alcalá Park, San Diego, CA 92110, U.S.A
| | - Christopher E Berndsen
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr. MSC 4501, Harrisonburg, VA 22807, U.S.A
| | - Jonathan D Monroe
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr. MSC 4501, Harrisonburg, VA 22807, U.S.A
| |
Collapse
|
3
|
Kita A, Ishida Y, Shimosaka T, Michimori Y, Makarova K, Koonin E, Atomi H, Miki K. Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis. Proteins 2024; 92:768-775. [PMID: 38235908 DOI: 10.1002/prot.26666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/17/2023] [Accepted: 01/01/2024] [Indexed: 01/19/2024]
Abstract
The biosynthesis pathways of coenzyme A (CoA) in most archaea involve several unique enzymes including dephospho-CoA kinase (DPCK) that converts dephospho-CoA to CoA in the final step of CoA biosynthesis in all domains of life. The archaeal DPCK is unrelated to the analogous bacterial and eukaryotic enzymes and shows no significant sequence similarity to any proteins with known structures. Unusually, the archaeal DPCK utilizes GTP as the phosphate donor although the analogous bacterial and eukaryotic enzymes are ATP-dependent kinases. Here, we report the crystal structure of DPCK and its complex with GTP and a magnesium ion from the archaeal hyperthermophile Thermococcus kodakarensis. The crystal structure demonstrates why GTP is the preferred substrate of this kinase. We also report the activity analyses of site-directed mutants of crucial residues determined based on sequence conservation and the crystal structure. From these results, the key residues involved in the reaction of phosphoryl transfer and the possible dephospho-CoA binding site are inferred.
Collapse
Affiliation(s)
- Akiko Kita
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Yuna Ishida
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Takahiro Shimosaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kira Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Eugene Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| |
Collapse
|
4
|
Medvedev KE, Zhang J, Schaeffer RD, Kinch LN, Cong Q, Grishin NV. Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands. Sci Rep 2024; 14:12260. [PMID: 38806511 PMCID: PMC11133325 DOI: 10.1038/s41598-024-60991-x] [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: 02/20/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from 14 characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters or novel potential pathogenicity islands (NPPIs) within the Salmonella genome, suggesting their potential contribution to the bacterium's virulence. One of the NPPIs revealed significant overrepresentation of potentially pathogenic proteins. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied.
Collapse
Affiliation(s)
- Kirill E Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lisa N Kinch
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| |
Collapse
|
5
|
Yang L, Yi L, Gong B, Chen L, Li M, Zhu X, Duan Y, Huang Y. Chalkophomycin Biosynthesis Revealing Unique Enzyme Architecture for a Hybrid Nonribosomal Peptide Synthetase and Polyketide Synthase. Molecules 2024; 29:1982. [PMID: 38731473 PMCID: PMC11085572 DOI: 10.3390/molecules29091982] [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: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N-hydroxylpyrrole, 2H-oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable of coordinating cupric ions draws interest to unprecedented enzymology responsible for chalkophomycin biosynthesis. To elucidate the biosynthetic machinery for chalkophomycin production, the chm biosynthetic gene cluster from S. sp. CB00271 was identified, and its involvement in chalkophomycin biosynthesis was confirmed by gene replacement. The chm cluster was localized to a ~31 kb DNA region, consisting of 19 open reading frames that encode five nonribosomal peptide synthetases (ChmHIJLO), one modular polyketide synthase (ChmP), six tailoring enzymes (ChmFGMNQR), two regulatory proteins (ChmAB), and four resistance proteins (ChmA'CDE). A model for chalkophomycin biosynthesis is proposed based on functional assignments from sequence analysis and structure modelling, and is further supported by analogy to over 100 chm-type gene clusters in public databases. Our studies thus set the stage to fully investigate chalkophomycin biosynthesis and to engineer chalkophomycin analogues through a synthetic biology approach.
Collapse
Affiliation(s)
- Long Yang
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
| | - Liwei Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Department of Pharmacy, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Bang Gong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- College of Pharmacy, Hunan Vocational College of Science and Technology, Changsha 410004, China
| | - Lili Chen
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
| | - Miao Li
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha 410011, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha 410011, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha 410011, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha 410011, China
| | - Yong Huang
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
| |
Collapse
|
6
|
Fontecilla-Camps JC. Reflections on the Origin of Coded Protein Biosynthesis. Biomolecules 2024; 14:518. [PMID: 38785925 PMCID: PMC11117964 DOI: 10.3390/biom14050518] [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: 04/09/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
The principle of continuity posits that some central features of primordial biocatalytic mechanisms should still be present in the genetically dependent pathway of protein synthesis, a crucial step in the emergence of life. Key bimolecular reactions of this process are catalyzed by DNA-dependent RNA polymerases, aminoacyl-tRNA synthetases, and ribosomes. Remarkably, none of these biocatalysts contribute chemically active groups to their respective reactions. Instead, structural and functional studies have demonstrated that nucleotidic α-phosphate and β-d-ribosyl 2' OH and 3' OH groups can help their own catalysis, a process which, consequently, has been called "substrate-assisted". Furthermore, upon binding, the substrates significantly lower the entropy of activation, exclude water from these catalysts' active sites, and are readily positioned for a reaction. This binding mode has been described as an "entropy trap". The combination of this effect with substrate-assisted catalysis results in reactions that are stereochemically and mechanistically simpler than the ones found in most modern enzymes. This observation is consistent with the way in which primordial catalysts could have operated; it may also explain why, thanks to their complementary reactivities, β-d-ribose and phosphate were naturally selected to be the central components of early coding polymers.
Collapse
|
7
|
Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [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: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
Collapse
Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
| |
Collapse
|
8
|
Kisgeropoulos E, Bharadwaj VS, Ledinina A, Lubner CE, Mulder DW, Smolinski SL, Boehm M, Gutekunst K, King PW, Svedruzic D. Structural and biophysical properties of a [4Fe4S] ferredoxin-like protein from Synechocystis sp. PCC 6803 with a unique two domain structure. J Inorg Biochem 2024; 251:112428. [PMID: 38008043 DOI: 10.1016/j.jinorgbio.2023.112428] [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: 09/06/2023] [Revised: 10/23/2023] [Accepted: 11/11/2023] [Indexed: 11/28/2023]
Abstract
Electron carrier proteins (ECPs), binding iron-sulfur clusters, are vital components within the intricate network of metabolic and photosynthetic reactions. They play a crucial role in the distribution of reducing equivalents. In Synechocystis sp. PCC 6803, the ECP network includes at least nine ferredoxins. Previous research, including global expression analyses and protein binding studies, has offered initial insights into the functional roles of individual ferredoxins within this network. This study primarily focuses on Ferredoxin 9 (slr2059). Through sequence analysis and computational modeling, Ferredoxin 9 emerges as a unique ECP with a distinctive two-domain architecture. It consists of a C-terminal iron‑sulfur binding domain and an N-terminal domain with homology to Nil-domain proteins, connected by a structurally rigid 4-amino acid linker. Notably, in contrast to canonical [2Fe2S] ferredoxins exemplified by PetF (ssl0020), which feature highly acidic surfaces facilitating electron transfer with photosystem I reaction centers, models of Ferredoxin 9 reveal a more neutral to basic protein surface. Using a combination of electron paramagnetic resonance spectroscopy and square-wave voltammetry on heterologously produced Ferredoxin 9, this study demonstrates that the protein coordinates 2×[4Fe4S]2+/1+ redox-active and magnetically interacting clusters, with measured redox potentials of -420 ± 9 mV and - 516 ± 10 mV vs SHE. A more in-depth analysis of Fdx9's unique structure and protein sequence suggests that this type of Nil-2[4Fe4S] multi-domain ferredoxin is well conserved in cyanobacteria, bearing structural similarities to proteins involved in homocysteine synthesis in methanogens.
Collapse
Affiliation(s)
- Effie Kisgeropoulos
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Anastasia Ledinina
- Department of Molecular and Structural Biochemistry, North Carolina State University, USA
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Sharon L Smolinski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Marko Boehm
- Department of Biology, Botanical Institute, Christian-Albrechts-University, Kiel, Germany; Department of Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Kirstin Gutekunst
- Department of Biology, Botanical Institute, Christian-Albrechts-University, Kiel, Germany; Department of Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Drazenka Svedruzic
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
| |
Collapse
|
9
|
Schaeffer RD, Zhang J, Medvedev KE, Kinch LN, Cong Q, Grishin NV. ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. PLoS Comput Biol 2024; 20:e1011586. [PMID: 38416793 PMCID: PMC10927120 DOI: 10.1371/journal.pcbi.1011586] [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] [Received: 10/10/2023] [Revised: 03/11/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
Protein structure prediction has now been deployed widely across several different large protein sets. Large-scale domain annotation of these predictions can aid in the development of biological insights. Using our Evolutionary Classification of Protein Domains (ECOD) from experimental structures as a basis for classification, we describe the detection and cataloging of domains from 48 whole proteomes deposited in the AlphaFold Database. On average, we can provide positive classification (either of domains or other identifiable non-domain regions) for 90% of residues in all proteomes. We classified 746,349 domains from 536,808 proteins comprised of over 226,424,000 amino acid residues. We examine the varying populations of homologous groups in both eukaryotes and bacteria. In addition to containing a higher fraction of disordered regions and unassigned domains, eukaryotes show a higher proportion of repeated proteins, both globular and small repeats. We enumerate those highly populated domains that are shared in both eukaryotes and bacteria, such as the Rossmann domains, TIM barrels, and P-loop domains. Additionally, we compare the sampling of homologous groups from this whole proteome set against our stable ECOD reference and discuss groups that have been enriched by structure predictions. Finally, we discuss the implication of these results for protein target selection for future classification strategies for very large protein sets.
Collapse
Affiliation(s)
- R. Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Kirill E. Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Department of Molecular Biology, 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
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| |
Collapse
|
10
|
Gao J, Xu W, Liu T, Sun W, Wang N, Ma J, Ge H. Structural Characterization of an N-Acetyl Sugar Amidotransferase Involved in the Lipopolysaccharide Biosynthesis in Bacteria. Int J Mol Sci 2023; 24:15491. [PMID: 37895170 PMCID: PMC10607449 DOI: 10.3390/ijms242015491] [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: 09/22/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
N-acetyl sugar amidotransferase (NASAT) is involved in the lipopolysaccharide (LPS) biosynthesis pathway that catalyzes the formation of the acetamido moiety (sugar-NC(=NH)CH3) on the O-chain. So far, little is known about its structural and functional properties. Here, we report the crystal structure of an N-acetyl sugar amidotransferase from Legionella pneumophila (LpNASAT) at 2.33 Å resolution. LpNASAT folds into a compact basin-shaped architecture with an unusually wide and open putative substrate-binding pocket and a conserved zinc ion-binding tetracysteine motif. The pocket contains a Rossmann-like fold with a PP-loop, suggesting that the NASAT-catalyzed amidotransfer reaction probably requires the conversion of ATP to AMP and PPi. Our data provide structural insights into the NASAT family of proteins, and allow us to possibly identify its functionally important regions.
Collapse
Affiliation(s)
- Jiajia Gao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; (J.G.); (N.W.)
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Wenwen Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; (J.G.); (N.W.)
| | - Tianqi Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; (J.G.); (N.W.)
| | - Wenjie Sun
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; (J.G.); (N.W.)
| | - Na Wang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; (J.G.); (N.W.)
| | - Jinming Ma
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; (J.G.); (N.W.)
| | - Honghua Ge
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, China; (J.G.); (N.W.)
| |
Collapse
|
11
|
Kojima Y, Mishiro-Sato E, Fujishita T, Satoh K, Kajino-Sakamoto R, Oze I, Nozawa K, Narita Y, Ogata T, Matsuo K, Muro K, Taketo MM, Soga T, Aoki M. Decreased liver B vitamin-related enzymes as a metabolic hallmark of cancer cachexia. Nat Commun 2023; 14:6246. [PMID: 37803016 PMCID: PMC10558488 DOI: 10.1038/s41467-023-41952-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/20/2023] [Indexed: 10/08/2023] Open
Abstract
Cancer cachexia is a complex metabolic disorder accounting for ~20% of cancer-related deaths, yet its metabolic landscape remains unexplored. Here, we report a decrease in B vitamin-related liver enzymes as a hallmark of systemic metabolic changes occurring in cancer cachexia. Metabolomics of multiple mouse models highlights cachexia-associated reductions of niacin, vitamin B6, and a glycine-related subset of one-carbon (C1) metabolites in the liver. Integration of proteomics and metabolomics reveals that liver enzymes related to niacin, vitamin B6, and glycine-related C1 enzymes dependent on B vitamins decrease linearly with their associated metabolites, likely reflecting stoichiometric cofactor-enzyme interactions. The decrease of B vitamin-related enzymes is also found to depend on protein abundance and cofactor subtype. These metabolic/proteomic changes and decreased protein malonylation, another cachexia feature identified by protein post-translational modification analysis, are reflected in blood samples from mouse models and gastric cancer patients with cachexia, underscoring the clinical relevance of our findings.
Collapse
Affiliation(s)
- Yasushi Kojima
- Division of Pathophysiology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan.
| | - Emi Mishiro-Sato
- Division of Pathophysiology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Teruaki Fujishita
- Division of Pathophysiology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Kiyotoshi Satoh
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Rie Kajino-Sakamoto
- Division of Pathophysiology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Kazuki Nozawa
- Department of Clinical Oncology, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Yukiya Narita
- Department of Clinical Oncology, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Takatsugu Ogata
- Department of Clinical Oncology, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Kei Muro
- Department of Clinical Oncology, Aichi Cancer Center Hospital, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan
| | - Makoto Mark Taketo
- Colon Cancer Project, Kyoto University Hospital-iACT, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Masahiro Aoki
- Division of Pathophysiology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, Aichi, 464-8681, Japan.
- Department of Cancer Physiology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan.
| |
Collapse
|
12
|
Medvedev KE, Schaeffer RD, Chen KS, Grishin NV. Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains. Sci Rep 2023; 13:11988. [PMID: 37491511 PMCID: PMC10368619 DOI: 10.1038/s41598-023-39273-5] [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: 04/25/2023] [Accepted: 07/22/2023] [Indexed: 07/27/2023] Open
Abstract
The recent progress in the prediction of protein structures marked a historical milestone. AlphaFold predicted 200 million protein models with an accuracy comparable to experimental methods. Protein structures are widely used to understand evolution and to identify potential drug targets for the treatment of various diseases, including cancer. Thus, these recently predicted structures might convey previously unavailable information about cancer biology. Evolutionary classification of protein domains is challenging and different approaches exist. Recently our team presented a classification of domains from human protein models released by AlphaFold. Here we evaluated the pan-cancer structurome, domains from over and under expressed proteins in 21 cancer types, using the broadest levels of the ECOD classification: the architecture (A-groups) and possible homology (X-groups) levels. Our analysis reveals that AlphaFold has greatly increased the three-dimensional structural landscape for proteins that are differentially expressed in these 21 cancer types. We show that beta sandwich domains are significantly overrepresented and alpha helical domains are significantly underrepresented in the majority of cancer types. Our data suggest that the prevalence of the beta sandwiches is due to the high levels of immunoglobulins and immunoglobulin-like domains that arise during tumor development-related inflammation. On the other hand, proteins with exclusively alpha domains are important elements of homeostasis, apoptosis and transmembrane transport. Therefore cancer cells tend to reduce representation of these proteins to promote successful oncogeneses.
Collapse
Affiliation(s)
- Kirill E Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - R Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kenneth S Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| |
Collapse
|
13
|
Alsohaibani R, Claudel AL, Perchat-Varlet R, Boutserin S, Talfournier F, Boschi-Muller S, Selles B. Rhodanese-Fold Containing Proteins in Humans: Not Just Key Players in Sulfur Trafficking. Antioxidants (Basel) 2023; 12:antiox12040843. [PMID: 37107218 PMCID: PMC10135228 DOI: 10.3390/antiox12040843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The Rhodanese-fold is a ubiquitous structural domain present in various protein subfamilies associated with different physiological functions or pathophysiological conditions in humans. Proteins harboring a Rhodanese domain are diverse in terms of domain architecture, with some representatives exhibiting one or several Rhodanese domains, fused or not to other structural domains. The most famous Rhodanese domains are catalytically active, thanks to an active-site loop containing an essential cysteine residue which allows for catalyzing sulfur transfer reactions involved in sulfur trafficking, hydrogen sulfide metabolism, biosynthesis of molybdenum cofactor, thio-modification of tRNAs or protein urmylation. In addition, they also catalyse phosphatase reactions linked to cell cycle regulation, and recent advances proposed a new role into tRNA hydroxylation, illustrating the catalytic versatility of Rhodanese domain. To date, no exhaustive analysis of Rhodanese containing protein equipment from humans is available. In this review, we focus on structural and biochemical properties of human-active Rhodanese-containing proteins, in order to provide a picture of their established or putative key roles in many essential biological functions.
Collapse
|
14
|
Schaeffer RD, Zhang J, Kinch LN, Pei J, Cong Q, Grishin NV. Classification of domains in predicted structures of the human proteome. Proc Natl Acad Sci U S A 2023; 120:e2214069120. [PMID: 36917664 PMCID: PMC10041065 DOI: 10.1073/pnas.2214069120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/06/2023] [Indexed: 03/16/2023] Open
Abstract
Recent advances in protein structure prediction have generated accurate structures of previously uncharacterized human proteins. Identifying domains in these predicted structures and classifying them into an evolutionary hierarchy can reveal biological insights. Here, we describe the detection and classification of domains from the human proteome. Our classification indicates that only 62% of residues are located in globular domains. We further classify these globular domains and observe that the majority (65%) can be classified among known folds by sequence, with a smaller fraction (33%) requiring structural data to refine the domain boundaries and/or to support their homology. A relatively small number (966 domains) cannot be confidently assigned using our automatic pipelines, thus demanding manual inspection. We classify 47,576 domains, of which only 23% have been included in experimental structures. A portion (6.3%) of these classified globular domains lack sequence-based annotation in InterPro. A quarter (23%) have not been structurally modeled by homology, and they contain 2,540 known disease-causing single amino acid variations whose pathogenesis can now be inferred using AF models. A comparison of classified domains from a series of model organisms revealed expansions of several immune response-related domains in humans and a depletion of olfactory receptors. Finally, we use this classification to expand well-known protein families of biological significance. These classifications are presented on the ECOD website (http://prodata.swmed.edu/ecod/index_human.php).
Collapse
Affiliation(s)
- R. Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Lisa N. Kinch
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX75390
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jimin Pei
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75390
| |
Collapse
|
15
|
Freire MÁ. The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios. Biosystems 2023; 226:104873. [PMID: 36906114 DOI: 10.1016/j.biosystems.2023.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Photosynthesis is the predominant biochemical process of carbon dioxide assimilation in the biosphere. To reduce carbon dioxide into organic compounds, photosynthetic organisms have one or two distinct photochemical reaction centre complexes with which they capture solar energy and generate ATP and reducing power. The core polypeptides of the photosynthetic reaction centres show low homologies but share overlapping structural folds, overall architecture, similar functional properties and highly conserved positions in protein sequences suggesting a common ancestry. However, the other biochemical components of photosynthetic apparatus appear to be a mosaic resulting from different evolutionary trajectories. The current proposal focusses on the nature and biosynthetic pathways of some organic redox cofactors that participate in the photosynthetic systems: quinones, chlorophyll and heme rings and their attached isoprenoid side chains, as well as on the coupled proton motive forces and associated carbon fixation pathways. This perspective highlights clues about the involvement of the phosphorus and sulphur chemistries that would have shaped the different types of photosynthetic systems.
Collapse
Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Exactas, Físicas y Naturales. Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
| |
Collapse
|
16
|
Burroughs A, Aravind L. New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts. NAR Genom Bioinform 2023; 5:lqad029. [PMID: 36968430 PMCID: PMC10034599 DOI: 10.1093/nargab/lqad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The protein-tyrosine/dual-specificity phosphatases and rhodanese domains constitute a sprawling superfamily of Rossmannoid domains that use a conserved active site with a cysteine to catalyze a range of phosphate-transfer, thiotransfer, selenotransfer and redox activities. While these enzymes have been extensively studied in the context of protein/lipid head group dephosphorylation and various thiotransfer reactions, their overall diversity and catalytic potential remain poorly understood. Using comparative genomics and sequence/structure analysis, we comprehensively investigate and develop a natural classification for this superfamily. As a result, we identified several novel clades, both those which retain the catalytic cysteine and those where a distinct active site has emerged in the same location (e.g. diphthine synthase-like methylases and RNA 2' OH ribosyl phosphate transferases). We also present evidence that the superfamily has a wider range of catalytic capabilities than previously known, including a set of parallel activities operating on various sugar/sugar alcohol groups in the context of NAD+-derivatives and RNA termini, and potential phosphate transfer activities involving sugars and nucleotides. We show that such activities are particularly expanded in the RapZ-C-DUF488-DUF4326 clade, defined here for the first time. Some enzymes from this clade are predicted to catalyze novel DNA-end processing activities as part of nucleic-acid-modifying systems that are likely to function in biological conflicts between viruses and their hosts.
Collapse
Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| |
Collapse
|
17
|
van der Weg KJ, Gohlke H. TopEnzyme: a framework and database for structural coverage of the functional enzyme space. Bioinformatics 2023; 39:7072462. [PMID: 36883717 PMCID: PMC10023222 DOI: 10.1093/bioinformatics/btad116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
MOTIVATION TopEnzyme is a database of structural enzyme models created with TopModel and is linked to the SWISS-MODEL repository and AlphaFold Protein Structure Database to provide an overview of structural coverage of the functional enzyme space for over 200 000 enzyme models. It allows the user to quickly obtain representative structural models for 60% of all known enzyme functions. RESULTS We assessed the models with TopScore and contributed 9039 good-quality and 1297 high-quality structures. Furthermore, we compared these models to AlphaFold2 models with TopScore and found that the TopScore differs only by 0.04 on average in favor of AlphaFold2. We tested TopModel and AlphaFold2 for targets not seen in the respective training databases and found that both methods create qualitatively similar structures. When no experimental structures are available, this database will facilitate quick access to structural models across the currently most extensive structural coverage of the functional enzyme space within Swiss-Prot. AVAILABILITY AND IMPLEMENTATION We provide a full web interface to the database at https://cpclab.uni-duesseldorf.de/topenzyme/.
Collapse
Affiliation(s)
- Karel J van der Weg
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Holger Gohlke
- Corresponding author. John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany. E-mail:
| |
Collapse
|
18
|
Schmitz JM, Wolters JF, Murray NH, Guerra RM, Bingman CA, Hittinger CT, Pagliarini DJ. Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae. J Biol Chem 2023; 299:102981. [PMID: 36739946 PMCID: PMC9996372 DOI: 10.1016/j.jbc.2023.102981] [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: 11/15/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Chalcone isomerases (CHIs) have well-established roles in the biosynthesis of plant flavonoid metabolites. Saccharomyces cerevisiae possesses two predicted CHI-like proteins, Aim18p (encoded by YHR198C) and Aim46p (YHR199C), but it lacks other enzymes of the flavonoid pathway, suggesting that Aim18p and Aim46p employ the CHI fold for distinct purposes. Here, we demonstrate using proteinase K protection assays, sodium carbonate extractions, and crystallography that Aim18p and Aim46p reside on the mitochondrial inner membrane and adopt CHI folds, but they lack select active site residues and possess an extra fungal-specific loop. Consistent with these differences, Aim18p and Aim46p lack CHI activity and also the fatty acid-binding capabilities of other CHI-like proteins, but instead bind heme. We further show that diverse fungal homologs also bind heme and that Aim18p and Aim46p possess structural homology to a bacterial hemoprotein. Collectively, our work reveals a distinct function and cellular localization for two CHI-like proteins, introduces a new variation of a hemoprotein fold, and suggests that ancestral CHI-like proteins were hemoproteins.
Collapse
Affiliation(s)
- Jonathan M Schmitz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA
| | - John F Wolters
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan H Murray
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Rachel M Guerra
- Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, USA; Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA.
| |
Collapse
|
19
|
Zhang J, Schaeffer RD, Durham J, Cong Q, Grishin NV. DPAM: A domain parser for AlphaFold models. Protein Sci 2023; 32:e4548. [PMID: 36539305 PMCID: PMC9850437 DOI: 10.1002/pro.4548] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 01/20/2023]
Abstract
The recent breakthroughs in structure prediction, where methods such as AlphaFold demonstrated near-atomic accuracy, herald a paradigm shift in structural biology. The 200 million high-accuracy models released in the AlphaFold Database are expected to guide protein science in the coming decades. Partitioning these AlphaFold models into domains and assigning them to an evolutionary hierarchy provide an efficient way to gain functional insights into proteins. However, classifying such a large number of predicted structures challenges the infrastructure of current structure classifications, including our Evolutionary Classification of protein Domains (ECOD). Better computational tools are urgently needed to parse and classify domains from AlphaFold models automatically. Here we present a Domain Parser for AlphaFold Models (DPAM) that can automatically recognize globular domains from these models based on inter-residue distances in 3D structures, predicted aligned errors, and ECOD domains found by sequence (HHsuite) and structural (Dali) similarity searches. Based on a benchmark of 18,759 AlphaFold models, we demonstrate that DPAM can recognize 98.8% of domains and assign correct boundaries for 87.5%, significantly outperforming structure-based domain parsers and homology-based domain assignment using ECOD domains found by HHsuite or Dali. Application of DPAM to the massive AlphaFold models will enable efficient classification of domains, providing evolutionary contexts and facilitating functional studies.
Collapse
Affiliation(s)
- Jing Zhang
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - R. Dustin Schaeffer
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Jesse Durham
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Nick V. Grishin
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| |
Collapse
|
20
|
Insertions and deletions mediated functional divergence of Rossmann fold enzymes. Proc Natl Acad Sci U S A 2022; 119:e2207965119. [PMID: 36417431 PMCID: PMC9860332 DOI: 10.1073/pnas.2207965119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Nucleobase-containing coenzymes are hypothesized to be relics of an early RNA-based world that preceded the emergence of proteins. Despite the importance of coenzyme-protein synergisms, their emergence and evolution remain understudied. An excellent target to address this issue is the Rossmann fold, the most catalytically diverse and abundant protein architecture in nature. We investigated two main Rossmann lineages: the nicotinamide adenine dinucleotide phosphate (NAD(P)) and the S-adenosyl methionine (SAM)- binding superfamilies. To identify the evolutionary changes that lead to a coenzyme specificity switch on these superfamilies, we performed structural and sequence-based Hidden Markov model analysis to systematically search for key motifs in their coenzyme-binding pockets. Our analyses revealed that through insertions and deletions (InDels) and a residue substitution, the ancient β1-loop-α1 coenzyme-binding structure of NAD(P) could be reshaped into the SAM-binding β1-loop-α1 structure. To experimentally prove this obsevation, we removed three amino acids from the NAD(P)-binding pocket and solved the structure of the resulting mutant, revealing the characteristic loop features of the SAM-binding pocket. To confirm the binding to SAM, we performed isothermal titration calorimetry measurements. Molecular dynamics simulations also corroborated the role of InDels in abolishing NAD binding and acquiring SAM binding. Our results uncovered how nature may have utilized insertions and deletions to optimize the different coenzyme-binding pockets and the distinct functionalities observed for Rossmann superfamilies. This work also proposes a general mechanism by which protein templates could have been recycled through the course of evolution to adopt different coenzymes and confer distinct chemistries.
Collapse
|
21
|
Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022; 31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [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] [Received: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
Abstract
How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.
Collapse
Affiliation(s)
- Vijay Jayaraman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Saacnicteh Toledo‐Patiño
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Lianet Noda‐García
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentHebrew University of JerusalemRehovotIsrael
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| |
Collapse
|
22
|
Yadahalli S, Jayanthi LP, Gosavi S. A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions. Front Mol Biosci 2022; 9:849272. [PMID: 35832734 PMCID: PMC9271847 DOI: 10.3389/fmolb.2022.849272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/27/2022] [Indexed: 12/02/2022] Open
Abstract
Many single-domain proteins are not only stable and water-soluble, but they also populate few to no intermediates during folding. This reduces interactions between partially folded proteins, misfolding, and aggregation, and makes the proteins tractable in biotechnological applications. Natural proteins fold thus, not necessarily only because their structures are well-suited for folding, but because their sequences optimize packing and fit their structures well. In contrast, folding experiments on the de novo designed Top7 suggest that it populates several intermediates. Additionally, in de novo protein design, where sequences are designed for natural and new non-natural structures, tens of sequences still need to be tested before success is achieved. Both these issues may be caused by the specific scaffolds used in design, i.e., some protein scaffolds may be more tolerant to packing perturbations and varied sequences. Here, we report a computational method for assessing the response of protein structures to packing perturbations. We then benchmark this method using designed proteins and find that it can identify scaffolds whose folding gets disrupted upon perturbing packing, leading to the population of intermediates. The method can also isolate regions of both natural and designed scaffolds that are sensitive to such perturbations and identify contacts which when present can rescue folding. Overall, this method can be used to identify protein scaffolds that are more amenable to whole protein design as well as to identify protein regions which are sensitive to perturbations and where further mutations should be avoided during protein engineering.
Collapse
|
23
|
Fontecilla-Camps JC, Volbeda A. Quinolinate Synthase: An Example of the Roles of the Second and Outer Coordination Spheres in Enzyme Catalysis. Chem Rev 2022; 122:12110-12131. [PMID: 35536891 DOI: 10.1021/acs.chemrev.1c00869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The activation energy barrier of biochemical reactions is normally lowered by an enzyme catalyst, which directly helps the weakening of the bond(s) to be broken. In many metalloenzymes, this is a first coordination sphere effect. Besides having a direct catalytic action, enzymes can fix their reactive groups and substrates so that they are optimally positioned and also modify the water activity in the system. They can either activate substrates prior to their reaction or bind preactivated substrates, thereby drastically reducing local entropic effects. The latter type is well represented by some bisubstrate reactions, where they have been defined as "entropic traps". These can be described as "second coordination sphere" processes, but enzymes can also control the reactivity beyond this point through local conformational changes belonging to an "outer coordinate sphere" that can be modulated by substrate binding. We have chosen the [4Fe-4S] cluster-dependent enzyme quinolinate synthase to illustrate each one of these processes. In addition, this very old metalloenzyme shows low in vitro substrate binding specificity, atypical reactivity that produces dead-end products, and a unique modulation of its active site volume.
Collapse
Affiliation(s)
| | - Anne Volbeda
- Université Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| |
Collapse
|
24
|
OUP accepted manuscript. Metallomics 2022; 14:6549566. [DOI: 10.1093/mtomcs/mfac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/02/2022] [Indexed: 11/12/2022]
|
25
|
Gerasimov AS, Rogozhkin SO, Shakhova ES, Chepurnykh TV, Gorokhovatsky AY, Myshkina NM, Balakireva AV, Yampolsky IV. Recombinant Production of Hispidin-3-Hydroxylase: the Key Enzyme in Fungal Luciferin Biosynthesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021040099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
26
|
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: 7] [Impact Index Per Article: 2.3] [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.
Collapse
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
| |
Collapse
|
27
|
Freire MÁ. Short non-coded peptides interacting with cofactors facilitated the integration of early chemical networks. Biosystems 2021; 211:104547. [PMID: 34547425 DOI: 10.1016/j.biosystems.2021.104547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/28/2021] [Accepted: 09/15/2021] [Indexed: 11/02/2022]
Abstract
Independently developed iron-sulphur/thioester- and phosphate-driven chemical reactions would have set up two distinct reaction networks prior to coupling in a proto-metabolic system supporting a minimal organisation closure. Each chemical system assisted initially by simple catalysts and then by more complex cofactors would have provided the precursors of the small metabolites and monomer units along with their respective polymers through dehydrating template-independent assemblies. For example, acylation reactions mediated by activated thioester groups produced peptides, fatty acids and polyhydroxyalkanoates, while phosphorylation reactions by phosphorylating agents allowed the synthesis of polysaccharides, polyribonucleotides and polyphosphates. Here, we address how these independent chemical systems might fit together and shaped a proto-metabolic system, focusing specifically on cofactors as molecular fossils of metabolism. As a result, the proposed overview suggests that non-coded peptides capable of binding a variety of ligands, but in particular with a redox active versatility and/or group transfer potential could have facilitated the chemical connections that led to a minimal closure with a proto-metabolism. Later developments would have made it possible to establish a cellular organisation with more complex and interdependent metabolic pathways.
Collapse
Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC). Facultad de Ciencias Exactas, Físicas y Naturales. Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Schaeffer RD, Kinch LN, Pei J, Medvedev KE, Grishin NV. Completeness and Consistency in Structural Domain Classifications. ACS OMEGA 2021; 6:15698-15707. [PMID: 34179613 PMCID: PMC8223206 DOI: 10.1021/acsomega.1c00950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
Abstract
Domain classifications are a useful resource for computational analysis of the protein structure, but elements of their composition are often opaque to potential users. We perform a comparative analysis of our classification ECOD against the SCOPe, SCOP2, and CATH domain classifications with respect to their constituent domain boundaries and hierarchal organization. The coverage of these domain classifications with respect to ECOD and to the PDB was assessed by structure and by sequence. We also conducted domain pair analysis to determine broad differences in hierarchy between domains shared by ECOD and other classifications. Finally, we present domains from the major facilitator superfamily (MFS) of transporter proteins and provide evidence that supports their split into domains and for multiple conformations within these families. We find that the ECOD and CATH provide the most extensive structural coverage of the PDB. ECOD and SCOPe have the most consistent domain boundary conditions, whereas CATH and SCOP2 both differ significantly.
Collapse
Affiliation(s)
- R. Dustin Schaeffer
- Departments
of Biophysics and Biochemistry, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Lisa N. Kinch
- Howard
Hughes Medical Institute, University of
Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Jimin Pei
- Howard
Hughes Medical Institute, University of
Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Kirill E. Medvedev
- Departments
of Biophysics and Biochemistry, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Nick V. Grishin
- Departments
of Biophysics and Biochemistry, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, University of
Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| |
Collapse
|
30
|
Bujacz A, Rum J, Rutkiewicz M, Pietrzyk-Brzezinska AJ, Bujacz G. Structural Evidence of Active Site Adaptability towards Different Sized Substrates of Aromatic Amino Acid Aminotransferase from Psychrobacter Sp. B6. MATERIALS 2021; 14:ma14123351. [PMID: 34204354 PMCID: PMC8235216 DOI: 10.3390/ma14123351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/27/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023]
Abstract
Aromatic amino acid aminotransferases present a special potential in the production of drugs and synthons, thanks to their ability to accommodate a wider range of substrates in their active site, in contrast to aliphatic amino acid aminotransferases. The mechanism of active site adjustment toward substrates of psychrophilic aromatic amino acid aminotransferase (PsyArAT) from Psychrobacter sp. B6 is discussed based on crystal structures of complexes with four hydroxy-analogs of substrates: phenylalanine, tyrosine, tryptophan and aspartic acid. These competitive inhibitors are bound in the active center of PsyArAT but do not undergo transamination reaction, which makes them an outstanding tool for examination of the enzyme catalytic center. The use of hydroxy-acids enabled insight into substrate binding by native PsyArAT, without mutating the catalytic lysine and modifying cofactor interactions. Thus, the binding mode of substrates and the resulting analysis of the volume of the catalytic site is close to a native condition. Observation of these inhibitors' binding allows for explanation of the enzyme's adaptability to process various sizes of substrates and to gain knowledge about its potential biotechnological application. Depending on the character and size of the used inhibitors, the enzyme crystallized in different space groups and showed conformational changes of the active site upon ligand binding.
Collapse
Affiliation(s)
- Anna Bujacz
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; (J.R.); (A.J.P.-B.); (G.B.)
- Correspondence:
| | - Jedrzej Rum
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; (J.R.); (A.J.P.-B.); (G.B.)
| | - Maria Rutkiewicz
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany;
| | - Agnieszka J. Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; (J.R.); (A.J.P.-B.); (G.B.)
| | - Grzegorz Bujacz
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; (J.R.); (A.J.P.-B.); (G.B.)
| |
Collapse
|
31
|
Terán-Ramírez C, Mares-Alejandre RE, Estrada-González AL, Muñoz-Muñoz PLA, Ramos-Ibarra MA. Structure-Function Relationship Study of a Secretory Amoebic Phosphatase: A Computational-Experimental Approach. Int J Mol Sci 2021; 22:ijms22042164. [PMID: 33671604 PMCID: PMC7926622 DOI: 10.3390/ijms22042164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 11/16/2022] Open
Abstract
Phosphatases are hydrolytic enzymes that cleave the phosphoester bond of numerous substrates containing phosphorylated residues. The typical classification divides them into acid or alkaline depending on the pH at which they have optimal activity. The histidine phosphatase (HP) superfamily is a large group of functionally diverse enzymes characterized by having an active-site His residue that becomes phosphorylated during catalysis. HP enzymes are relevant biomolecules due to their current and potential application in medicine and biotechnology. Entamoeba histolytica, the causative agent of human amoebiasis, contains a gene (EHI_146950) that encodes a putative secretory acid phosphatase (EhHAPp49), exhibiting sequence similarity to histidine acid phosphatase (HAP)/phytase enzymes, i.e., branch-2 of HP superfamily. To assess whether it has the potential as a biocatalyst in removing phosphate groups from natural substrates, we studied the EhHAPp49 structural and functional features using a computational-experimental approach. Although the combined outcome of computational analyses confirmed its structural similarity with HP branch-2 proteins, the experimental results showed that the recombinant enzyme (rEhHAPp49) has negligible HAP/phytase activity. Nonetheless, results from supplementary activity evaluations revealed that rEhHAPp49 exhibits Mg2+-dependent alkaline pyrophosphatase activity. To our knowledge, this study represents the first computational-experimental characterization of EhHAPp49, which offers further insights into the structure-function relationship and the basis for future research.
Collapse
|
32
|
Da Costa M, Gevaert O, Van Overtveldt S, Lange J, Joosten HJ, Desmet T, Beerens K. Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering. Biotechnol Adv 2021; 48:107705. [PMID: 33571638 DOI: 10.1016/j.biotechadv.2021.107705] [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: 07/08/2020] [Revised: 12/18/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
Short-chain Dehydrogenase/Reductase enzymes that are active on nucleotide sugars (abbreviated as NS-SDR) are of paramount importance in the biosynthesis of rare sugars and glycosides. Some family members have already been extensively characterized due to their direct implication in metabolic disorders or in the biosynthesis of virulence factors. In this review, we combine the knowledge gathered from studies that typically focused only on one NS-SDR activity with an in-depth analysis and overview of all of the different NS-SDR families (169,076 enzyme sequences). Through this structure-based multiple sequence alignment of NS-SDRs retrieved from public databases, we could identify clear patterns in conservation and correlation of crucial residues. Supported by this analysis, we suggest updating and extending the UDP-galactose 4-epimerase "hexagonal box model" to an "heptagonal box model" for all NS-SDR enzymes. This specificity model consists of seven conserved regions surrounding the NDP-sugar substrate that serve as fingerprint for each specificity. The specificity fingerprints highlighted in this review will be beneficial for functional annotation of the large group of NS-SDR enzymes and form a guide for future enzyme engineering efforts focused on the biosynthesis of rare and specialty carbohydrates.
Collapse
Affiliation(s)
- Matthieu Da Costa
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Ophelia Gevaert
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Stevie Van Overtveldt
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Joanna Lange
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Henk-Jan Joosten
- Bio-Prodict BV, Nieuwe Marktstraat 54E, 6511, AA, Nijmegen, the Netherlands
| | - Tom Desmet
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| | - Koen Beerens
- Centre for Synthetic Biology - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium.
| |
Collapse
|
33
|
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.
Collapse
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.
| |
Collapse
|
34
|
Su T, Nakamoto R, Chun YY, Chua WZ, Chen JH, Zik JJ, Sham LT. Decoding capsule synthesis in Streptococcus pneumoniae. FEMS Microbiol Rev 2020; 45:6041728. [PMID: 33338218 DOI: 10.1093/femsre/fuaa067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae synthesizes more than one hundred types of capsular polysaccharides (CPS). While the diversity of the enzymes and transporters involved is enormous, it is not limitless. In this review, we summarized the recent progress on elucidating the structure-function relationships of CPS, the mechanisms by which they are synthesized, how their synthesis is regulated, the host immune response against them, and the development of novel pneumococcal vaccines. Based on the genetic and structural information available, we generated provisional models of the CPS repeating units that remain unsolved. In addition, to facilitate cross-species comparisons and assignment of glycosyltransferases, we illustrated the biosynthetic pathways of the known CPS in a standardized format. Studying the intricate steps of pneumococcal CPS assembly promises to provide novel insights for drug and vaccine development as well as improve our understanding of related pathways in other species.
Collapse
Affiliation(s)
- Tong Su
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Rei Nakamoto
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Ye Yu Chun
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Wan Zhen Chua
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Jia Hui Chen
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Justin J Zik
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|