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Takahashi D, Fujiwara I, Sasajima Y, Narita A, Imada K, Miyata M. ATP-dependent polymerization dynamics of bacterial actin proteins involved in Spiroplasma swimming. Open Biol 2022; 12:220083. [PMID: 36285441 PMCID: PMC9597168 DOI: 10.1098/rsob.220083] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MreB is a bacterial protein belonging to the actin superfamily. This protein polymerizes into an antiparallel double-stranded filament that determines cell shape by maintaining cell wall synthesis. Spiroplasma eriocheiris, a helical wall-less bacterium, has five MreB homologous (SpeMreB1-5) that probably contribute to swimming motility. Here, we investigated the structure, ATPase activity and polymerization dynamics of SpeMreB3 and SpeMreB5. SpeMreB3 polymerized into a double-stranded filament with possible antiparallel polarity, while SpeMreB5 formed sheets which contained the antiparallel filament, upon nucleotide binding. SpeMreB3 showed slow Pi release owing to the lack of an amino acid motif conserved in the catalytic centre of MreB family proteins. Our SpeMreB3 crystal structures and analyses of SpeMreB3 and SpeMreB5 variants showed that the amino acid motif probably plays a role in eliminating a nucleophilic water proton during ATP hydrolysis. Sedimentation assays suggest that SpeMreB3 has a lower polymerization activity than SpeMreB5, though their polymerization dynamics are qualitatively similar to those of other actin superfamily proteins, in which pre-ATP hydrolysis and post-Pi release states are unfavourable for them to remain as filaments.
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Affiliation(s)
- Daichi Takahashi
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan
| | - Ikuko Fujiwara
- Graduate School of Science, Osaka City University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan,Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yuya Sasajima
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan
| | - Akihiro Narita
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Katsumi Imada
- Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,The OMU Advanced Research Center for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan,Graduate School of Science, Osaka City University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
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2
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Michalska K, Chang C, Maltseva NI, Jedrzejczak R, Robertson GT, Gusovsky F, McCarren P, Schreiber SL, Nag PP, Joachimiak A. Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase. Protein Sci 2020; 29:779-788. [PMID: 31930594 PMCID: PMC7020977 DOI: 10.1002/pro.3825] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Global dispersion of multidrug resistant bacteria is very common and evolution of antibiotic-resistance is occurring at an alarming rate, presenting a formidable challenge for humanity. The development of new therapeuthics with novel molecular targets is urgently needed. Current drugs primarily affect protein, nucleic acid, and cell wall synthesis. Metabolic pathways, including those involved in amino acid biosynthesis, have recently sparked interest in the drug discovery community as potential reservoirs of such novel targets. Tryptophan biosynthesis, utilized by bacteria but absent in humans, represents one of the currently studied processes with a therapeutic focus. It has been shown that tryptophan synthase (TrpAB) is required for survival of Mycobacterium tuberculosis in macrophages and for evading host defense, and therefore is a promising drug target. Here we present crystal structures of TrpAB with two allosteric inhibitors of M. tuberculosis tryptophan synthase that belong to sulfolane and indole-5-sulfonamide chemical scaffolds. We compare our results with previously reported structural and biochemical studies of another, azetidine-containing M. tuberculosis tryptophan synthase inhibitor. This work shows how structurally distinct ligands can occupy the same allosteric site and make specific interactions. It also highlights the potential benefit of targeting more variable allosteric sites of important metabolic enzymes.
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Affiliation(s)
- Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Changsoo Chang
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Natalia I. Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Gregory T. Robertson
- Colorado State UniversityMycobacteria Research Laboratories, Department of Microbiology, Immunology and PathologyFort CollinsColorado
| | | | | | | | - Partha P. Nag
- Broad Institute of MIT and HarvardCambridgeMassachusetts
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
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3
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4
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Giegé R. What macromolecular crystallogenesis tells us - what is needed in the future. IUCRJ 2017; 4:340-349. [PMID: 28875021 PMCID: PMC5571797 DOI: 10.1107/s2052252517006595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 05/05/2023]
Abstract
Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallo-graphers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105 X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing either in vitro or in vivo or participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, under in vivo conditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization under in vivo conditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg and CNRS, F-67084 Strasbourg, France
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5
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Looking Inside the Intramolecular C-H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine. Molecules 2017; 22:molecules22030361. [PMID: 28264508 PMCID: PMC6155423 DOI: 10.3390/molecules22030361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 11/25/2022] Open
Abstract
Recently, strong evidence that supports the presence of an intramolecular C−H···O hydrogen bond in amides derived from the chiral auxiliary α-methylbenzylamine was disclosed. Due to the high importance of this chiral auxiliary in asymmetric synthesis, the inadvertent presence of this C−H···O interaction may lead to new interpretations upon stereochemical models in which this chiral auxiliary is present. Therefore, a series of lactams containing the chiral auxiliary α-methylbenzylamine (from three to eight-membered ring) were theoretically studied at the MP2/cc-pVDZ level of theory with the purpose of studying the origin and nature of the C−Hα···O interaction. NBO analysis revealed that rehybridization at C atom of the C−Hα bond (s-character at C is ~23%) and the subsequent bond polarization are the dominant effect over the orbital interaction energy n(O)→σ*C−Hα (E(2) < 2 kcal/mol), causing an important shortening of the C−Hα bond distance and an increment in the positive charge in the Hα atom.
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6
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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7
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Shang G, Feng D, Lu F, Zhang H, Cang H, Gao W, Bi R. Purification, crystallization and preliminary crystallographic analysis of a ribosome-recycling factor from Thermoanaerobacter tengcongensis (TteRRF). ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:588-91. [PMID: 24817715 DOI: 10.1107/s2053230x1400507x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 03/05/2014] [Indexed: 11/10/2022]
Abstract
Ribosome-recycling factor (RRF) plays an essential role in the fourth step of protein synthesis in prokaryotes. RRF combined with elongation factor G (EF-G) disassembles the post-termination ribosome complex and recycles the protein synthesis machine for the next round of translation. A reductive-methylation-modified RRF from Thermoanaerobacter tengcongensis (TteRRF) has been crystallized using the vapour-diffusion method. The crystal grew in a condition consisting of 0.1 M citric acid pH 3.5, 3.0 M NaCl and 50 mg ml(-1) methylated protein solution at 289 K. A complete data set was collected from a crystal to 2.80 Å resolution using synchrotron radiation at 100 K. The crystal belonged to space group P6122/P6522 with unit-cell parameters a = b = 103.26, c = 89.17 Å. The asymmetric unit was estimated to contain one molecule of TteRRF.
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Affiliation(s)
- Guijun Shang
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Duo Feng
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Fang Lu
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Hongjie Zhang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China
| | - Huaixing Cang
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Wei Gao
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Ruchang Bi
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China
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8
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Tan K, Kim Y, Hatzos-Skintges C, Chang C, Cuff M, Chhor G, Osipiuk J, Michalska K, Nocek B, An H, Babnigg G, Bigelow L, Joachimiak G, Li H, Mack J, Makowska-Grzyska M, Maltseva N, Mulligan R, Tesar C, Zhou M, Joachimiak A. Salvage of failed protein targets by reductive alkylation. Methods Mol Biol 2014; 1140:189-200. [PMID: 24590719 PMCID: PMC4078742 DOI: 10.1007/978-1-4939-0354-2_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.
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Affiliation(s)
- Kemin Tan
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL, 60439, USA
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9
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Sledz P, Zheng H, Murzyn K, Chruszcz M, Zimmerman MD, Chordia MD, Joachimiak A, Minor W. New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization. Protein Sci 2010; 19:1395-404. [PMID: 20506323 DOI: 10.1002/pro.420] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Surface lysine methylation (SLM) is a technique for improving the rate of success of protein crystallization by chemically methylating lysine residues. The exact mechanism by which SLM enhances crystallization is still not clear. To study these mechanisms, and to analyze the conditions where SLM will provide the optimal benefits for rescuing failed crystallization experiments, we compared 40 protein structures containing N,N-dimethyl-lysine (dmLys) to a nonredundant set of 18,972 nonmethylated structures from the PDB. By measuring the relative frequency of intermolecular contacts (where contacts are defined as interactions between the residues in proximity with a distance of 3.5 A or less) of basic residues in the methylated versus nonmethylated sets, dmLys-Glu contacts are seen more frequently than Lys-Glu contacts. Based on observation of the 10 proteins with both native and methylated structures, we propose that the increased rate of contact for dmLys-Glu is due to both a slight increase in the number of amine-carboxyl H-bonds and to the formation of methyl C--H...O interactions. By comparing the relative contact frequencies of dmLys with other residues, the mechanism by which methylation of lysines improves the formation of crystal contacts appears to be similar to that of Lys to Arg mutation. Moreover, analysis of methylated structures with the surface entropy reduction (SER) prediction server suggests that in many cases SLM of predicted SER sites may contribute to improved crystallization. Thus, tools that analyze protein sequences and mark residues for SER mutation may identify proteins with good candidate sites for SLM.
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Affiliation(s)
- Pawel Sledz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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10
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Crystal structure of a novel non-Pfam protein PF2046 solved using low resolution B-factor sharpening and multi-crystal averaging methods. Protein Cell 2010; 1:453-8. [PMID: 21203960 DOI: 10.1007/s13238-010-0045-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022] Open
Abstract
Sometimes crystals cannot diffract X-rays beyond 3.0 Å resolution due to the intrinsic flexibility associated with the protein. Low resolution diffraction data not only pose a challenge to structure determination, but also hamper interpretation of mechanistic details. Crystals of a 25.6 kDa non-Pfam, hypothetical protein, PF2046, diffracted X-rays to 3.38 Å resolution. A combination of Se-Met derived heavy atom positions with multiple cycles of B-factor sharpening, multi-crystal averaging, restrained refinement followed by manual inspection of electron density and model building resulted in a final model with a R value of 23.5 (R(free)= 24.7). The asymmetric unit was large and consisted of six molecules arranged as a homodimer of trimers. Analysis of the structure revealed the presence of a RNA binding domain suggesting a role for PF2046 in the processing of nucleic acids.
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11
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Fan Y, Joachimiak A. Enhanced crystal packing due to solvent reorganization through reductive methylation of lysine residues in oxidoreductase from Streptococcus pneumoniae. ACTA ACUST UNITED AC 2010; 11:101-11. [PMID: 20127187 DOI: 10.1007/s10969-010-9079-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 01/12/2010] [Indexed: 10/19/2022]
Abstract
Protein crystallization is in part driven by the changes in the entropy of the system, but opinions differ as to whether the solute (protein) or solvent (water) molecules make more of a contribution to the overall entropic change. Methylation of lysine residues in proteins has been used to enhance protein crystallization. We investigated using molecular dynamics simulations with explicit solvent molecules, the behavior of several native proteins and their methylated counterparts chosen from an earlier large-scale study. Methylated lysines are capable of making a variety of interactions including H-bonds with protein residues and solvent. We demonstrate that methylation on the lysine slightly increases its side chain conformational entropy by about 3.5 J mol(-1) K(-1). Analysis of the radial and spatial distributions of the water molecules around the methylated lysine surface in oxidoreductase from Streptococcus pneumoniae revealed a larger sphere of water molecules with low entropy, as compared with solvent associated with unmethylated lysine. If methylated lysine were to make interactions at the protein-protein interface, the low-entropy water molecules associated with methylated lysines would be released, resulting in a gain of entropy. We show that this gain more than compensates for the loss of protein entropy. Therefore, we propose that lysine methylation favors the formation of crystals through solvent entropic gain.
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Affiliation(s)
- Yao Fan
- Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL 60439, USA
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12
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Vetting MW, Hegde SS, Blanchard JS. Crystallization of a pentapeptide-repeat protein by reductive cyclic pentylation of free amines with glutaraldehyde. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:462-9. [PMID: 19390151 DOI: 10.1107/s0907444909008324] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/06/2009] [Indexed: 11/10/2022]
Abstract
The pentapeptide-repeat protein EfsQnr from Enterococcus faecalis protects DNA gyrase from inhibition by fluoroquinolones. EfsQnr was cloned and purified to homogeneity, but failed to produce diffraction-quality crystals in initial crystallization screens. Treatment of EfsQnr with glutaraldehyde and the strong reducing agent borane-dimethylamine resulted in a derivatized protein which produced crystals that diffracted to 1.6 A resolution; their structure was subsequently determined by single-wavelength anomalous dispersion. Analysis of the derivatized protein using Fourier transform ion cyclotron resonance mass spectrometry indicated a mass increase of 68 Da per free amino group. Electron-density maps about a limited number of structurally ordered lysines indicated that the modification was a cyclic pentylation of free amines, producing piperidine groups.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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13
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Yin J, Li L, Shaw N, Li Y, Song JK, Zhang W, Xia C, Zhang R, Joachimiak A, Zhang HC, Wang LX, Liu ZJ, Wang P. Structural basis and catalytic mechanism for the dual functional endo-beta-N-acetylglucosaminidase A. PLoS One 2009; 4:e4658. [PMID: 19252736 PMCID: PMC2646837 DOI: 10.1371/journal.pone.0004658] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 01/07/2009] [Indexed: 11/18/2022] Open
Abstract
Endo-β-N-acetylglucosaminidases (ENGases) are dual specificity enzymes with an ability to catalyze hydrolysis and transglycosylation reactions. Recently, these enzymes have become the focus of intense research because of their potential for synthesis of glycopeptides. We have determined the 3D structures of an ENGase from Arthrobacter protophormiae (Endo-A) in 3 forms, one in native form, one in complex with Man3GlcNAc-thiazoline and another in complex with GlcNAc-Asn. The carbohydrate moiety sits above the TIM-barrel in a cleft region surrounded by aromatic residues. The conserved essential catalytic residues – E173, N171 and Y205 are within hydrogen bonding distance of the substrate. W216 and W244 regulate access to the active site during transglycosylation by serving as “gate-keepers”. Interestingly, Y299F mutation resulted in a 3 fold increase in the transglycosylation activity. The structure provides insights into the catalytic mechanism of GH85 family of glycoside hydrolases at molecular level and could assist rational engineering of ENGases.
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Affiliation(s)
- Jie Yin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Lei Li
- National Glycoengineering Research Center and The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Shandong, China
- Departments of Biochemistry and Chemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Neil Shaw
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yang Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Jing Katherine Song
- Departments of Biochemistry and Chemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Wenpeng Zhang
- Departments of Biochemistry and Chemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Chengfeng Xia
- Departments of Biochemistry and Chemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Rongguang Zhang
- Structural Biology Center, Advanced Photon Source, Argonne National Laboratory, Illinois, United States of America
| | - Andrzej Joachimiak
- Structural Biology Center, Advanced Photon Source, Argonne National Laboratory, Illinois, United States of America
| | - Hou-Cheng Zhang
- National Glycoengineering Research Center and The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Shandong, China
| | - Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (Z-JL); (PW)
| | - Peng Wang
- National Glycoengineering Research Center and The State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Shandong, China
- Departments of Biochemistry and Chemistry, The Ohio State University, Columbus, Ohio, United States of America
- College of Pharmacy and The State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
- * E-mail: (Z-JL); (PW)
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14
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Kim Y, Quartey P, Li H, Volkart L, Hatzos C, Chang C, Nocek B, Cuff M, Osipiuk J, Tan K, Fan Y, Bigelow L, Maltseva N, Wu R, Borovilos M, Duggan E, Zhou M, Binkowski TA, Zhang RG, Joachimiak A. Large-scale evaluation of protein reductive methylation for improving protein crystallization. Nat Methods 2008; 5:853-4. [PMID: 18825126 DOI: 10.1038/nmeth1008-853] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Li Y, Bahti P, Shaw N, Song G, Chen S, Zhang X, Zhang M, Cheng C, Yin J, Zhu JY, Zhang H, Che D, Xu H, Abbas A, Wang BC, Liu ZJ. Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source. Proteins 2008; 71:2109-13. [PMID: 18361456 DOI: 10.1002/prot.22025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yang Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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16
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Bahti P, Chen S, Li Y, Shaw N, Zhang X, Zhang M, Cheng C, Song G, Yin J, Zhang H, Che D, Abbas A, Xu H, Wang BC, Liu ZJ. Purification, crystallization and preliminary crystallographic analysis of the non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:91-3. [PMID: 18259057 PMCID: PMC2374175 DOI: 10.1107/s1744309107068649] [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: 10/12/2007] [Accepted: 12/28/2007] [Indexed: 11/11/2022]
Abstract
A 10.5 kDa non-Pfam hypothetical protein, AF1514, from the hyperthermophilic archaeon Archeoglobus fulgidus has been overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted X-rays to 2.09 A resolution and a data set was collected at 100 K using Cu K alpha radiation from a rotating-anode X-ray source. The crystals belong to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 49.27, c = 106.61 A. The calculated Matthews coefficient was 3.16 A(3) Da(-1), suggesting the presence of one molecule in the asymmetric unit.
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Affiliation(s)
- Pazilat Bahti
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, People’s Republic of China
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Shunmei Chen
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yang Li
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Neil Shaw
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xuejun Zhang
- Department of Immunology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| | - Min Zhang
- Life Sciences College, Anhui University, Hefei 230039, People’s Republic of China
| | - Chongyun Cheng
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Gaojie Song
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Jie Yin
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hua Zhang
- SECSG, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30605, USA
| | - Dongsheng Che
- SECSG, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30605, USA
| | - Abdulla Abbas
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, People’s Republic of China
| | - Hao Xu
- SECSG, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30605, USA
| | - Bi-Cheng Wang
- SECSG, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30605, USA
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institution of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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