1
|
Ntallis C, Tzoupis H, Tselios T, Chasapis CT, Vlamis-Gardikas A. Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands. Antioxidants (Basel) 2023; 13:15. [PMID: 38275635 PMCID: PMC10812433 DOI: 10.3390/antiox13010015] [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: 11/01/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
In silico approaches were employed to examine the characteristics of interactions between human mitochondrial thioredoxin 2 (HsTrx2) and its 38 previously identified mitochondrial protein ligands. All interactions appeared driven mainly by electrostatic forces. The statistically significant residues of HsTrx2 for interactions were characterized as "contact hot spots". Since these were identical/adjacent to putative thermodynamic hot spots, an energy network approach identified their neighbors to highlight possible contact interfaces. Three distinct areas for binding emerged: (i) one around the active site for covalent interactions, (ii) another antipodal to the active site for strong non-covalent interactions, and (iii) a third area involved in both kinds of interactions. The contact interfaces of HsTrx2 were projected as respective interfaces for Escherichia coli Trx1 (EcoTrx1), 2, and HsTrx1. Comparison of the interfaces and contact hot spots of HsTrx2 to the contact residues of EcoTx1 and HsTrx1 from existing crystal complexes with protein ligands supported the hypothesis, except for a part of the cleft/groove adjacent to Trp30 preceding the active site. The outcomes of this study raise the possibility for the rational design of selective inhibitors for the interactions of HsTrx2 with specific protein ligands without affecting the entirety of the functions of the Trx system.
Collapse
Affiliation(s)
- Charalampos Ntallis
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Haralampos Tzoupis
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Theodore Tselios
- Department of Chemistry, University of Patras, 26504 Rion, Greece; (C.N.); (H.T.); (T.T.)
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou 48, 11635 Athens, Greece;
| | | |
Collapse
|
2
|
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
|
3
|
Gao S, Thompson EJ, Barrow SL, Zhang W, Iavarone AT, Klinman JP. Hydrogen-Deuterium Exchange within Adenosine Deaminase, a TIM Barrel Hydrolase, Identifies Networks for Thermal Activation of Catalysis. J Am Chem Soc 2020; 142:19936-19949. [PMID: 33181018 DOI: 10.1021/jacs.0c07866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteins are intrinsically flexible macromolecules that undergo internal motions with time scales spanning femtoseconds to milliseconds. These fluctuations are implicated in the optimization of reaction barriers for enzyme catalyzed reactions. Time, temperature, and mutation dependent hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) has been previously employed to identify spatially resolved, catalysis-linked dynamical regions of enzymes. We now extend this technique to pursue the correlation of protein flexibility and chemical reactivity within the diverse and widespread TIM barrel proteins, targeting murine adenosine deaminase (mADA) that catalyzes the irreversible deamination of adenosine to inosine and ammonia. Following a structure-function analysis of rate and activation energy for a series of mutations at a second sphere phenylalanine positioned in proximity to the bound substrate, the catalytically impaired Phe61Ala with an elevated activation energy (Ea = 7.5 kcal/mol) and the wild type (WT) mADA (Ea = 5.0 kcal/mol) were selected for HDX-MS experiments. The rate constants and activation energies of HDX for peptide segments are quantified and used to assess mutation-dependent changes in local and distal motions. Analyses reveal that approximately 50% of the protein sequence of Phe61Ala displays significant changes in the temperature dependence of HDX behaviors, with the dominant change being an increase in protein flexibility. Utilizing Phe61Ile, which displays the same activation energy for kcat as WT, as a control, we were able to further refine the HDX analysis, highlighting the regions of mADA that are altered in a functionally relevant manner. A map is constructed that illustrates the regions of protein that are proposed to be essential for the thermal optimization of active site configurations that dominate reaction barrier crossings in the native enzyme.
Collapse
Affiliation(s)
| | | | | | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | | | | |
Collapse
|
4
|
Biochemical characterization of 2-phosphinomethylmalate synthase from Streptomyces hygroscopicus: A member of the DRE-TIM metallolyase superfamily. Arch Biochem Biophys 2020; 691:108489. [PMID: 32697946 DOI: 10.1016/j.abb.2020.108489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/23/2022]
Abstract
2-Phosphinomethylmalate synthase (PMMS) from Streptomyces hygroscopicus catalyzes the first step in the biosynthesis of the herbicide bialophos using 3-phosphinopyruvic acid and acetyl coenzyme A as substrates to form 2-phosphinomethylmalic acid and coenzyme A. PMMS belongs to the Claisen condensation-like (CC-like) subgroup of the DRE-TIM metallolyase superfamily, which uses conserved active site architecture to catalyze a functionally-diverse set of reactions. Analysis of a sequence similarity network for the CC-like subgroup identified PMMS and the related R-citrate synthase in an early-diverging cluster suggesting that this group of sequences are more distinct in relation to other Claisen-condensation subgroup members. To better understand the structure/function landscape of the CC-like subgroup PMMS was recombinantly expressed in Escherichia coli, purified, and characterized with respect to its enzymatic properties. Using oxaloacetate as a substrate analog, the recombinantly-produced enzyme exhibited improved Michaelis constants relative to the previously reported natively-produced enzyme. Results from pH rate profiles and kinetic isotope effects were consistent with results from other members of the CC-like subgroup supporting acid-base chemistry and hydrolysis of the direct Claisen-condensation product as the rate-determining step. Results of site-directed mutagenesis experiments indicate that PMMS uses an active-site architecture similar to homocitrate synthase to select for a dicarboxylic acid substrate.
Collapse
|
5
|
Colabroy KL, Horwitz AD, Basciano VR, Fu Y, Travitz KM, Robinson MK, Shimanski BA, Hoffmann TW. A New Way of Belonging: Active-Site Investigation of L-DOPA Dioxygenase, a VOC Family Enzyme from Lincomycin Biosynthesis. Biochemistry 2019; 58:4794-4798. [DOI: 10.1021/acs.biochem.9b00456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Keri L. Colabroy
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Alyssa D. Horwitz
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Victoria R. Basciano
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Yizhi Fu
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Kelly M. Travitz
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Miranda K. Robinson
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Brittany A. Shimanski
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Thomas W. Hoffmann
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| |
Collapse
|
6
|
Wang Y, Shin I, Fu Y, Colabroy KL, Liu A. Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus. Biochemistry 2019; 58:5339-5350. [PMID: 31180203 DOI: 10.1021/acs.biochem.9b00396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extradiol dioxygenases are essential biocatalysts for breaking down catechols. The vicinal oxygen chelate (VOC) superfamily contains a large number of extradiol dioxygenases, most of which are found as part of catabolic pathways degrading a variety of natural and human-made aromatic rings. The l-3,4-dihydroxyphenylalanine (L-DOPA) extradiol dioxygenases compose a multitude of pathways that produce various antibacterial or antitumor natural products. The structural features of these dioxygenases are anticipated to be distinct from those of other VOC extradiol dioxygenases. Herein, we identified a new L-DOPA dioxygenase from the thermophilic bacterium Streptomyces sclerotialus (SsDDO) through a sequence and genome context analysis. The activity of SsDDO was kinetically characterized with L-DOPA using an ultraviolet-visible spectrophotometer and an oxygen electrode. The optimal temperature of the assay was 55 °C, at which the Km and kcat of SsDDO were 110 ± 10 μM and 2.0 ± 0.1 s-1, respectively. We determined the de novo crystal structures of SsDDO in the ligand-free form and as a substrate-bound complex, refined to 1.99 and 2.31 Å resolution, respectively. These structures reveal that SsDDO possesses a form IV arrangement of βαβββ modules, the first characterization of this assembly from among the VOC/type I extradiol dioxygenase protein family. Electron paramagnetic resonance spectra of Fe-NO adducts for the resting and substrate-bound enzyme were obtained. This work contributes to our understanding of a growing class of topologically distinct VOC dioxygenases, and the obtained structural features will improve our understanding of the extradiol cleavage reaction within the VOC superfamily.
Collapse
Affiliation(s)
- Yifan Wang
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Inchul Shin
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Yizhi Fu
- Department of Chemistry , Muhlenberg College , Allentown , Pennsylvania 18104 , United States
| | - Keri L Colabroy
- Department of Chemistry , Muhlenberg College , Allentown , Pennsylvania 18104 , United States
| | - Aimin Liu
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| |
Collapse
|
7
|
Heuberger K, Bailey HJ, Burda P, Chaikuad A, Krysztofinska E, Suormala T, Bürer C, Lutz S, Fowler B, Froese DS, Yue WW, Baumgartner MR. Genetic, structural, and functional analysis of pathogenic variations causing methylmalonyl-CoA epimerase deficiency. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1265-1272. [PMID: 30682498 PMCID: PMC6525113 DOI: 10.1016/j.bbadis.2019.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 11/05/2022]
Abstract
Human methylmalonyl-CoA epimerase (MCEE) catalyzes the interconversion of d-methylmalonyl-CoA and l-methylmalonyl-CoA in propionate catabolism. Autosomal recessive pathogenic variations in MCEE reportedly cause methylmalonic aciduria (MMAuria) in eleven patients. We investigated a cohort of 150 individuals suffering from MMAuria of unknown origin, identifying ten new patients with pathogenic variations in MCEE. Nine patients were homozygous for the known nonsense variation p.Arg47* (c.139C > T), and one for the novel missense variation p.Ile53Arg (c.158T > G). To understand better the molecular basis of MCEE deficiency, we mapped p.Ile53Arg, and two previously described pathogenic variations p.Lys60Gln and p.Arg143Cys, onto our 1.8 Å structure of wild-type (wt) human MCEE. This revealed potential dimeric assembly disruption by p.Ile53Arg, but no clear defects from p.Lys60Gln or p.Arg143Cys. We solved the structure of MCEE-Arg143Cys to 1.9 Å and found significant disruption of two important loop structures, potentially impacting surface features as well as the active-site pocket. Functional analysis of MCEE-Ile53Arg expressed in a bacterial recombinant system as well as patient-derived fibroblasts revealed nearly undetectable soluble protein levels, defective globular protein behavior, and using a newly developed assay, lack of enzymatic activity - consistent with misfolded protein. By contrast, soluble protein levels, unfolding characteristics and activity of MCEE-Lys60Gln were comparable to wt, leaving unclear how this variation may cause disease. MCEE-Arg143Cys was detectable at comparable levels to wt MCEE, but had slightly altered unfolding kinetics and greatly reduced activity. These studies reveal ten new patients with MCEE deficiency and rationalize misfolding and loss of activity as molecular defects in MCEE-type MMAuria. Identification of ten new patients with MCEE-type methylmalonic aciduria. Crystal structures of MCEE wild-type and p.Arg143Cys differ in local conformations. Novel biochemical assay of methylmalonyl-CoA epimerase activity.
Collapse
Affiliation(s)
- Kathrin Heuberger
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Henry J Bailey
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Oxford, OX3 7DQ, UK
| | - Patricie Burda
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Apirat Chaikuad
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Oxford, OX3 7DQ, UK
| | - Ewelina Krysztofinska
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Oxford, OX3 7DQ, UK
| | - Terttu Suormala
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Seraina Lutz
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Brian Fowler
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Oxford, OX3 7DQ, UK.
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland.
| |
Collapse
|
8
|
Miller AF, Park JT, Ferguson KL, Pitsawong W, Bommarius AS. Informing Efforts to Develop Nitroreductase for Amine Production. Molecules 2018; 23:molecules23020211. [PMID: 29364838 PMCID: PMC6017928 DOI: 10.3390/molecules23020211] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/03/2018] [Accepted: 01/12/2018] [Indexed: 12/19/2022] Open
Abstract
Nitroreductases (NRs) hold promise for converting nitroaromatics to aromatic amines. Nitroaromatic reduction rate increases with Hammett substituent constant for NRs from two different subgroups, confirming substrate identity as a key determinant of reactivity. Amine yields were low, but compounds yielding amines tend to have a large π system and electron withdrawing substituents. Therefore, we also assessed the prospects of varying the enzyme. Several different subgroups of NRs include members able to produce aromatic amines. Comparison of four NR subgroups shows that they provide contrasting substrate binding cavities with distinct constraints on substrate position relative to the flavin. The unique architecture of the NR dimer produces an enormous contact area which we propose provides the stabilization needed to offset the costs of insertion of the active sites between the monomers. Thus, we propose that the functional diversity included in the NR superfamily stems from the chemical versatility of the flavin cofactor in conjunction with a structure that permits tremendous active site variability. These complementary properties make NRs exceptionally promising enzymes for development for biocatalysis in prodrug activation and conversion of nitroaromatics to valuable aromatic amines. We provide a framework for identifying NRs and substrates with the greatest potential to advance.
Collapse
Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA.
| | - Jonathan T Park
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
| | - Kyle L Ferguson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
| | - Warintra Pitsawong
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA.
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
| |
Collapse
|
9
|
Baier F, Copp JN, Tokuriki N. Evolution of Enzyme Superfamilies: Comprehensive Exploration of Sequence–Function Relationships. Biochemistry 2016; 55:6375-6388. [DOI: 10.1021/acs.biochem.6b00723] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Baier
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - J. N. Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - N. Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
10
|
Tearing down to build up: Metalloenzymes in the biosynthesis lincomycin, hormaomycin and the pyrrolo [1,4]benzodiazepines. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:724-737. [DOI: 10.1016/j.bbapap.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/24/2016] [Accepted: 03/02/2016] [Indexed: 11/21/2022]
|
11
|
Cupincin: A Unique Protease Purified from Rice (Oryza sativa L.) Bran Is a New Member of the Cupin Superfamily. PLoS One 2016; 11:e0152819. [PMID: 27064905 PMCID: PMC4827828 DOI: 10.1371/journal.pone.0152819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/18/2016] [Indexed: 12/03/2022] Open
Abstract
Cupin superfamily is one of the most diverse super families. This study reports the purification and characterization of a novel cupin domain containing protease from rice bran for the first time. Hypothetical protein OsI_13867 was identified and named as cupincin. Cupincin was purified to 4.4 folds with a recovery of 4.9%. Cupincin had an optimum pH and temperature of pH 4.0 and 60°C respectively. Cupincin was found to be a homotrimer, consisting of three distinct subunits with apparent molecular masses of 33.45 kDa, 22.35 kDa and 16.67 kDa as determined by MALDI-TOF, whereas it eluted as a single unit with an apparent molecular mass of 135.33 ± 3.52 kDa in analytical gel filtration and migrated as a single band in native page, suggesting its homogeneity. Sequence identity of cupincin was deduced by determining the amino-terminal sequence of the polypeptide chains and by and de novo sequencing. For understanding the hydrolysing mechanism of cupincin, its three-dimensional model was developed. Structural analysis indicated that cupincin contains His313, His326 and Glu318 with zinc ion as the putative active site residues, inhibition of enzyme activity by 1,10-phenanthroline and atomic absorption spectroscopy confirmed the presence of zinc ion. The cleavage specificity of cupincin towards oxidized B-chain of insulin was highly specific; cleaving at the Leu15-Tyr16 position, the specificity was also determined using neurotensin as a substrate, where it cleaved only at the Glu1-Tyr2 position. Limited proteolysis of the protease suggests a specific function for cupincin. These results demonstrated cupincin as a completely new protease.
Collapse
|
12
|
Brown SD, Babbitt PC. New insights about enzyme evolution from large scale studies of sequence and structure relationships. J Biol Chem 2014; 289:30221-30228. [PMID: 25210038 PMCID: PMC4215206 DOI: 10.1074/jbc.r114.569350] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes.
Collapse
Affiliation(s)
- Shoshana D Brown
- Departments of Bioengineering and Therapeutic Sciences and University of California, San Francisco, California 94158-2330
| | - Patricia C Babbitt
- Departments of Bioengineering and Therapeutic Sciences and University of California, San Francisco, California 94158-2330; Departments of Pharmaceutical Chemistry, School of Pharmacy, and University of California, San Francisco, California 94158-2330; California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158-2330.
| |
Collapse
|
13
|
Tóth-Petróczy A, Tawfik DS. The robustness and innovability of protein folds. Curr Opin Struct Biol 2014; 26:131-8. [PMID: 25038399 DOI: 10.1016/j.sbi.2014.06.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 11/30/2022]
Abstract
Assignment of protein folds to functions indicates that >60% of folds carry out one or two enzymatic functions, while few folds, for example, the TIM-barrel and Rossmann folds, exhibit hundreds. Are there structural features that make a fold amenable to functional innovation (innovability)? Do these features relate to robustness--the ability to readily accumulate sequence changes? We discuss several hypotheses regarding the relationship between the architecture of a protein and its evolutionary potential. We describe how, in a seemingly paradoxical manner, opposite properties, such as high stability and rigidity versus conformational plasticity and structural order versus disorder, promote robustness and/or innovability. We hypothesize that polarity--differentiation and low connectivity between a protein's scaffold and its active-site--is a key prerequisite for innovability.
Collapse
Affiliation(s)
- Agnes Tóth-Petróczy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
14
|
Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM. The evolution of enzyme function in the isomerases. Curr Opin Struct Biol 2014; 26:121-30. [PMID: 25000289 PMCID: PMC4139412 DOI: 10.1016/j.sbi.2014.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 06/02/2014] [Accepted: 06/10/2014] [Indexed: 01/14/2023]
Abstract
The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an individual EC class, using the isomerases as an exemplar.
Collapse
Affiliation(s)
- Sergio Martinez Cuesta
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Syed Asad Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
| |
Collapse
|
15
|
Mashiyama ST, Malabanan MM, Akiva E, Bhosle R, Branch MC, Hillerich B, Jagessar K, Kim J, Patskovsky Y, Seidel RD, Stead M, Toro R, Vetting MW, Almo SC, Armstrong RN, Babbitt PC. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol 2014; 12:e1001843. [PMID: 24756107 PMCID: PMC3995644 DOI: 10.1371/journal.pbio.1001843] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/14/2014] [Indexed: 12/11/2022] Open
Abstract
Global networks of the cytosolic glutathione S-transferases illuminate sequence-structure-function relationships across more than 13,000 members of this superfamily, including experimental confirmation of enzymatic activity for 82 members and new crystal structures for 27. The cytosolic glutathione transferase (cytGST) superfamily comprises more than 13,000 nonredundant sequences found throughout the biosphere. Their key roles in metabolism and defense against oxidative damage have led to thousands of studies over several decades. Despite this attention, little is known about the physiological reactions they catalyze and most of the substrates used to assay cytGSTs are synthetic compounds. A deeper understanding of relationships across the superfamily could provide new clues about their functions. To establish a foundation for expanded classification of cytGSTs, we generated similarity-based subgroupings for the entire superfamily. Using the resulting sequence similarity networks, we chose targets that broadly covered unknown functions and report here experimental results confirming GST-like activity for 82 of them, along with 37 new 3D structures determined for 27 targets. These new data, along with experimentally known GST reactions and structures reported in the literature, were painted onto the networks to generate a global view of their sequence-structure-function relationships. The results show how proteins of both known and unknown function relate to each other across the entire superfamily and reveal that the great majority of cytGSTs have not been experimentally characterized or annotated by canonical class. A mapping of taxonomic classes across the superfamily indicates that many taxa are represented in each subgroup and highlights challenges for classification of superfamily sequences into functionally relevant classes. Experimental determination of disulfide bond reductase activity in many diverse subgroups illustrate a theme common for many reaction types. Finally, sequence comparison between an enzyme that catalyzes a reductive dechlorination reaction relevant to bioremediation efforts with some of its closest homologs reveals differences among them likely to be associated with evolution of this unusual reaction. Interactive versions of the networks, associated with functional and other types of information, can be downloaded from the Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu). Cytosolic glutathione transferases (cytGSTs) are a large and diverse superfamily of enzymes that have important roles in metabolism and defense against oxidative damage. They have been studied for several decades but because of the synthetic nature of the chemicals used to test these proteins to determine if they have cytGST activity, little is known about the physiological reactions and roles of cytGSTs. In this large, collaborative study, we constructed networks where more than 13,000 cytGST sequences were grouped by sequence similarity and then used these networks to prioritize new targets for experimental characterization in relatively unexplored regions of the superfamily. We report here experimental results confirming GST-like activity for 82 of them, along with 37 new three-dimensional molecular structures determined for 27 targets. These new data, along with experimental data previously reported in the literature, were painted onto the networks to generate a global view of their sequence-structure-function relationships. The results show how proteins of both known and unknown function relate to each other across the entire superfamily and illuminate the complex ways in which their variations in sequence and structure affect our ability to predict unknown functional properties.
Collapse
Affiliation(s)
- Susan T. Mashiyama
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - M. Merced Malabanan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Rahul Bhosle
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Megan C. Branch
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Brandan Hillerich
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Kevin Jagessar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jungwook Kim
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yury Patskovsky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Ronald D. Seidel
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Mark Stead
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Rafael Toro
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Matthew W. Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (SCA); (RNA); (PCB)
| | - Richard N. Armstrong
- Departments of Biochemistry and Chemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail: (SCA); (RNA); (PCB)
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (SCA); (RNA); (PCB)
| |
Collapse
|
16
|
Alderson RG, De Ferrari L, Mavridis L, McDonagh JL, Mitchell JBO, Nath N. Enzyme informatics. Curr Top Med Chem 2014; 12:1911-23. [PMID: 23116471 DOI: 10.2174/156802612804547353] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/12/2012] [Accepted: 09/15/2012] [Indexed: 12/18/2022]
Abstract
Over the last 50 years, sequencing, structural biology and bioinformatics have completely revolutionised biomolecular science, with millions of sequences and tens of thousands of three dimensional structures becoming available. The bioinformatics of enzymes is well served by, mostly free, online databases. BRENDA describes the chemistry, substrate specificity, kinetics, preparation and biological sources of enzymes, while KEGG is valuable for understanding enzymes and metabolic pathways. EzCatDB, SFLD and MACiE are key repositories for data on the chemical mechanisms by which enzymes operate. At the current rate of genome sequencing and manual annotation, human curation will never finish the functional annotation of the ever-expanding list of known enzymes. Hence there is an increasing need for automated annotation, though it is not yet widespread for enzyme data. In contrast, functional ontologies such as the Gene Ontology already profit from automation. Despite our growing understanding of enzyme structure and dynamics, we are only beginning to be able to design novel enzymes. One can now begin to trace the functional evolution of enzymes using phylogenetics. The ability of enzymes to perform secondary functions, albeit relatively inefficiently, gives clues as to how enzyme function evolves. Substrate promiscuity in enzymes is one example of imperfect specificity in protein-ligand interactions. Similarly, most drugs bind to more than one protein target. This may sometimes result in helpful polypharmacology as a drug modulates plural targets, but also often leads to adverse side-effects. Many chemoinformatics approaches can be used to model the interactions between druglike molecules and proteins in silico. We can even use quantum chemical techniques like DFT and QM/MM to compute the structural and energetic course of enzyme catalysed chemical reaction mechanisms, including a full description of bond making and breaking.
Collapse
Affiliation(s)
- Rosanna G Alderson
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, Purdie Building, University of St Andrews, North Haugh, St Andrews, Scotland, UK
| | | | | | | | | | | |
Collapse
|
17
|
Seifried A, Knobloch G, Duraphe PS, Segerer G, Manhard J, Schindelin H, Schultz J, Gohla A. Evolutionary and structural analyses of mammalian haloacid dehalogenase-type phosphatases AUM and chronophin provide insight into the basis of their different substrate specificities. J Biol Chem 2013; 289:3416-31. [PMID: 24338473 DOI: 10.1074/jbc.m113.503359] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian haloacid dehalogenase (HAD)-type phosphatases are an emerging family of phosphatases with important functions in physiology and disease, yet little is known about the basis of their substrate specificity. Here, we characterize a previously unexplored HAD family member (gene annotation, phosphoglycolate phosphatase), which we termed AUM, for aspartate-based, ubiquitous, Mg(2+)-dependent phosphatase. AUM is a tyrosine-specific paralog of the serine/threonine-specific protein and pyridoxal 5'-phosphate-directed HAD phosphatase chronophin. Comparative evolutionary and biochemical analyses reveal that a single, differently conserved residue in the cap domain of either AUM or chronophin is crucial for phosphatase specificity. We have solved the x-ray crystal structure of the AUM cap fused to the catalytic core of chronophin to 2.65 Å resolution and present a detailed view of the catalytic clefts of AUM and chronophin that explains their substrate preferences. Our findings identify a small number of cap domain residues that encode the different substrate specificities of AUM and chronophin.
Collapse
|
18
|
Brain miffed by macrophage migration inhibitory factor. Int J Cell Biol 2012; 2012:139573. [PMID: 22973314 PMCID: PMC3438795 DOI: 10.1155/2012/139573] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 07/06/2012] [Accepted: 07/12/2012] [Indexed: 12/31/2022] Open
Abstract
Macrophage migration inhibitory factor (MIF) is a cytokine which also exhibits enzymatic properties like oxidoreductase and tautomerase. MIF plays a pivotal role in innate and acquired immunity as well as in the neuroendocrine axis. Since it is involved in the pathogenesis of acute and chronic inflammation, neoangiogenesis, and cancer, MIF and its signaling components are considered suitable targets for therapeutic intervention in several fields of medicine. In neurodegenerative and neurooncological diseases, MIF is a highly relevant, but still a hardly investigated mediator. MIF operates via intracellular protein-protein interaction as well as in CD74/CXCR2/CXCR4 receptor-mediated pathways to regulate essential cellular systems such as redox balance, HIF-1, and p53-mediated senescence and apoptosis as well as multiple signaling pathways. Acting as an endogenous glucocorticoid antagonist, MIF thus represents a relevant resistance gene in brain tumor therapies. Alongside this dual action, a functional homolog-annotated D-dopachrome tautomerase/MIF-2 has been uncovered utilizing the same cell surface receptor signaling cascade as MIF. Here we review MIF actions with respect to redox regulation in apoptosis and in tumor growth as well as its extracellular function with a focus on its potential role in brain diseases. We consider the possibility of MIF targeting in neurodegenerative processes and brain tumors by novel MIF-neutralizing approaches.
Collapse
|
19
|
Abstract
Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes.
Collapse
Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
| |
Collapse
|