Acta crystallographica. Section F, Structural biology communications最新文献_第10页

Using structural genomics depositions in undergraduate teaching of protein crystallography: everybody wins 在蛋白质晶体学本科教学中使用结构基因组学沉积：人人皆赢。

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-10-11 DOI: 10.1107/S2053230X2300883X

Jon Agirre

引用次数: 0

Biochemical and X-ray analyses of the players involved in the faRel2/aTfaRel2 toxin–antitoxin operon 参与faRel2/aTfaRel2毒素抗毒素操纵子的参与者的生化和X射线分析。

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-09-20 DOI: 10.1107/S2053230X23007288

Lucia Dominguez-Molina, Ariel Talavera, Albinas Cepauskas, Tatsuaki Kurata, Dannele Echemendia-Blanco, Vasili Hauryliuk, Abel Garcia-Pino

{"title":"Biochemical and X-ray analyses of the players involved in the faRel2/aTfaRel2 toxin–antitoxin operon","authors":"Lucia Dominguez-Molina, Ariel Talavera, Albinas Cepauskas, Tatsuaki Kurata, Dannele Echemendia-Blanco, Vasili Hauryliuk, Abel Garcia-Pino","doi":"10.1107/S2053230X23007288","DOIUrl":"10.1107/S2053230X23007288","url":null,"abstract":"The aTfaRel2/faRel2 operon from Coprobacillus sp. D7 encodes a bicistronic type II toxin–antitoxin (TA) module. The FaRel2 toxin is a toxic small alarmone synthetase (toxSAS) that inhibits translation through the pyrophosphorylation of uncharged tRNAs at the 3′-CCA end. The toxin is neutralized by the antitoxin ATfaRel2 through the formation of an inactive TA complex. Here, the production, biophysical analysis and crystallization of ATfaRel2 and FaRel2 as well as of the ATfaRel2–FaRel2 complex are reported. ATfaRel2 is monomeric in solution. The antitoxin crystallized in space group P21212 with unit-cell parameters a = 53.3, b = 34.2, c = 37.6 Å, and the best crystal diffracted to a resolution of 1.24 Å. Crystals of FaRel2 in complex with APCPP, a nonhydrolysable ATP analogue, belonged to space group P21, with unit-cell parameters a = 31.5, b = 60.6, c = 177.2 Å, β = 90.6°, and diffracted to 2.6 Å resolution. The ATfaRel2–FaRel2Y128F complex forms a heterotetramer in solution composed of two toxins and two antitoxins. This complex crystallized in two space groups: F4132, with unit-cell parameters a = b = c = 227.1 Å, and P212121, with unit-cell parameters a = 51.7, b = 106.2, c = 135.1 Å. The crystals diffracted to 1.98 and 2.1 Å resolution, respectively.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 10","pages":"247-256"},"PeriodicalIF":0.9,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41098188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of a family I inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1 费城嗜肺军团菌一个Ⅰ族无机焦磷酸酶的鉴定1。

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-09-20 DOI: 10.1107/S2053230X23008002

Julia Moorefield, Yagmur Konuk, Jordan O. Norman, Jan Abendroth, Thomas E. Edwards, Donald D. Lorimer, Stephen J. Mayclin, Bart L. Staker, Justin K. Craig, Kayleigh F. Barett, Lynn K. Barrett, Wesley C. Van Voorhis, Peter J. Myler, Krystle J. McLaughlin

{"title":"Characterization of a family I inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1","authors":"Julia Moorefield, Yagmur Konuk, Jordan O. Norman, Jan Abendroth, Thomas E. Edwards, Donald D. Lorimer, Stephen J. Mayclin, Bart L. Staker, Justin K. Craig, Kayleigh F. Barett, Lynn K. Barrett, Wesley C. Van Voorhis, Peter J. Myler, Krystle J. McLaughlin","doi":"10.1107/S2053230X23008002","DOIUrl":"10.1107/S2053230X23008002","url":null,"abstract":"Inorganic pyrophosphate (PPi) is generated as an intermediate or byproduct of many fundamental metabolic pathways, including DNA/RNA synthesis. The intracellular concentration of PPi must be regulated as buildup can inhibit many critical cellular processes. Inorganic pyrophosphatases (PPases) hydrolyze PPi into two orthophosphates (Pi), preventing the toxic accumulation of the PPi byproduct in cells and making Pi available for use in biosynthetic pathways. Here, the crystal structure of a family I inorganic pyrophosphatase from Legionella pneumophila is reported at 2.0 Å resolution. L. pneumophila PPase (LpPPase) adopts a homohexameric assembly and shares the oligonucleotide/oligosaccharide-binding (OB) β-barrel core fold common to many other bacterial family I PPases. LpPPase demonstrated hydrolytic activity against a general substrate, with Mg2+ being the preferred metal cofactor for catalysis. Legionnaires' disease is a severe respiratory infection caused primarily by L. pneumophila, and thus increased characterization of the L. pneumophila proteome is of interest.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 10","pages":"257-266"},"PeriodicalIF":0.9,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23008002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41098189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of the imine reductase from Ajellomyces dermatitidis in three crystal forms. 皮炎胶霉亚胺还原酶的三种晶体结构。

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-09-01 DOI: 10.1107/S2053230X23006672

Mahima Sharma, Anibal Cuetos, Adam Willliams, Daniel González-Martínez, Gideon Grogan

{"title":"Structure of the imine reductase from Ajellomyces dermatitidis in three crystal forms.","authors":"Mahima Sharma, Anibal Cuetos, Adam Willliams, Daniel González-Martínez, Gideon Grogan","doi":"10.1107/S2053230X23006672","DOIUrl":"https://doi.org/10.1107/S2053230X23006672","url":null,"abstract":"The NADPH-dependent imine reductase from Ajellomyces dermatitidis (AdRedAm) catalyzes the reductive amination of certain ketones with amine donors supplied in an equimolar ratio. The structure of AdRedAm has been determined in three forms. The first form, which belongs to space group P3121 and was refined to 2.01 Å resolution, features two molecules (one dimer) in the asymmetric unit in complex with the redox-inactive cofactor NADPH4. The second form, which belongs to space group C21 and was refined to 1.73 Å resolution, has nine molecules (four and a half dimers) in the asymmetric unit, each complexed with NADP+. The third form, which belongs to space group P3121 and was refined to 1.52 Å resolution, has one molecule (one half-dimer) in the asymmetric unit. This structure was again complexed with NADP+ and also with the substrate 2,2-difluoroacetophenone. The different data sets permit the analysis of AdRedAm in different conformational states and also reveal the molecular basis of stereoselectivity in the transformation of fluorinated acetophenone substrates by the enzyme.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 Pt 9","pages":"224-230"},"PeriodicalIF":0.9,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10158600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-resolution crystal structure of the Mu8.1 conotoxin from Conus mucronatus. 松果Mu8.1型松果毒素的高分辨率晶体结构。

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-09-01 DOI: 10.1107/S2053230X23007070

Emilie Müller, Celeste Menuet Hackney, Lars Ellgaard, Jens Preben Morth

{"title":"High-resolution crystal structure of the Mu8.1 conotoxin from Conus mucronatus.","authors":"Emilie Müller, Celeste Menuet Hackney, Lars Ellgaard, Jens Preben Morth","doi":"10.1107/S2053230X23007070","DOIUrl":"https://doi.org/10.1107/S2053230X23007070","url":null,"abstract":"Marine cone snails produce a wealth of peptide toxins (conotoxins) that bind their molecular targets with high selectivity and potency. Therefore, conotoxins constitute valuable biomolecular tools with a variety of biomedical purposes. The Mu8.1 conotoxin from Conus mucronatus is the founding member of the newly identified saposin-like conotoxin class of conotoxins and has been shown to target Cav2.3, a voltage-gated calcium channel. Two crystal structures have recently been determined of Mu8.1 at 2.3 and 2.1 Å resolution. Here, a high-resolution crystal structure of Mu8.1 was determined at 1.67 Å resolution in the high-symmetry space group I4122. The asymmetric unit contained one molecule, with a symmetry-related molecule generating a dimer equivalent to that observed in the two previously determined structures. The high resolution allows a detailed atomic analysis of a water-filled cavity buried at the dimer interface, revealing a tightly coordinated network of waters that shield a lysine residue (Lys55) with a predicted unusually low side-chain pKa value. These findings are discussed in terms of a potential functional role of Lys55 in target interaction.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 Pt 9","pages":"240-246"},"PeriodicalIF":0.9,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10159123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Drastic alterations in the loop structure around colchicine upon complex formation with an engineered lipocalin indicate a conformational selection mechanism 秋水仙碱与工程脂钙蛋白形成复合物后，环结构的剧烈变化表明存在构象选择机制

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-08-16 DOI: 10.1107/S2053230X23006817

Elena Jerschke, Andreas Eichinger, Arne Skerra

{"title":"Drastic alterations in the loop structure around colchicine upon complex formation with an engineered lipocalin indicate a conformational selection mechanism","authors":"Elena Jerschke, Andreas Eichinger, Arne Skerra","doi":"10.1107/S2053230X23006817","DOIUrl":"10.1107/S2053230X23006817","url":null,"abstract":"Using Anticalin technology, a lipocalin protein dubbed Colchicalin, with the ability to bind the toxic plant alkaloid colchicine with picomolar affinity, has previously been engineered, thus offering a potential antidote in vivo and also allowing its sensitive detection in biological samples. To further analyze the mode of ligand recognition, the crystal structure of Colchicalin is now reported in its unliganded form and is compared with the colchicine complex. A superposition of the protein structures revealed major rearrangements in the four structurally variable loops of the engineered lipocalin. Notably, the binding pocket in the unbound protein is largely occupied by the inward-bent loop #3, in particular Ile97, as well as by the phenylalanine side chain at position 71 in loop #2. Upon binding of colchicine, a dramatic shift of loop #3 by up to 11.1 Å occurs, in combination with a side-chain flip of Phe71, thus liberating the necessary space within the ligand pocket. Interestingly, the proline residue at the neighboring position 72, which arose during the combinatorial engineering of Colchicalin, remained in a cis configuration in both structures. These findings provide a striking example of a conformational adaptation mechanism, which is a long-known phenomenon for antibodies in immunochemistry, during the recognition of a small ligand by an engineered lipocalin, thus illustrating the general similarity between the mode of antigen/ligand binding by immunoglobulins and lipocalins.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 9","pages":"231-239"},"PeriodicalIF":0.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23006817","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10521368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal structure of a GCN5-related N-acetyltransferase from Lactobacillus curiae 居里乳杆菌GCN5相关N-乙酰转移酶的晶体结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-08-11 DOI: 10.1107/S2053230X2300571X

Jennifer R. Fleming, Franziskus Hauth, Jörg S. Hartig, Olga Mayans

{"title":"Crystal structure of a GCN5-related N-acetyltransferase from Lactobacillus curiae","authors":"Jennifer R. Fleming, Franziskus Hauth, Jörg S. Hartig, Olga Mayans","doi":"10.1107/S2053230X2300571X","DOIUrl":"10.1107/S2053230X2300571X","url":null,"abstract":"Members of the GCN5-related N-acetyltransferase (GNAT) family are found in all domains of life and are involved in processes ranging from protein synthesis and gene expression to detoxification and virulence. Due to the variety of their macromolecular targets, GNATs are a highly diverse family of proteins. Currently, 3D structures of only a small number of GNAT representatives are available and thus the family remains poorly characterized. Here, the crystal structure of the guanidine riboswitch-associated GNAT from Lactobacillus curiae (LcGNAT) that acetylates canavanine, a structural analogue of arginine with antimetabolite properties, is reported. LcGNAT shares the conserved fold of the members of the GNAT superfamily, but does not contain an N-terminal β0 strand and instead contains a C-terminal β7 strand. Its P-loop, which coordinates the pyrophosphate moiety of the acetyl-coenzyme A cosubstrate, is degenerated. These features are shared with its closest homologues in the polyamine acetyltransferase subclass. Site-directed mutagenesis revealed a central role of the conserved residue Tyr142 in catalysis, as well as the semi-conserved Tyr97 and Glu92, suggesting that despite its individual substrate specificity LcGNAT performs the classical reaction mechanism of this family.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 8","pages":"217-223"},"PeriodicalIF":0.9,"publicationDate":"2023-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X2300571X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10358400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal structure of Prp16 in complex with ADP Prp16与ADP复合物的晶体结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-08-07 DOI: 10.1107/S2053230X23005721

Tim Benedict Garbers, Marieke Enders, Piotr Neumann, Ralf Ficner

引用次数: 0

Structural basis for the development of potential inhibitors targeting FadD23 from Mycobacterium tuberculosis 结核分枝杆菌FadD23潜在抑制剂开发的结构基础

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-07-31 DOI: 10.1107/S2053230X23005836

Mengrong Yan, Mengyuan Ma, Rong Chen, Yangzi Cao, Wei Zhang, Xiang Liu

{"title":"Structural basis for the development of potential inhibitors targeting FadD23 from Mycobacterium tuberculosis","authors":"Mengrong Yan, Mengyuan Ma, Rong Chen, Yangzi Cao, Wei Zhang, Xiang Liu","doi":"10.1107/S2053230X23005836","DOIUrl":"10.1107/S2053230X23005836","url":null,"abstract":"Sulfolipid-1 (SL-1) is a lipid that is abundantly found in the cell wall of Mycobacterium tuberculosis (Mtb). MtbFadD23 is crucial in the SL-1 synthesis pathway. Previously, 5′-O-[N-(11-phenoxyundecanoyl)sulfamoyl]adenosine (PhU-AMS) has been shown to be a general inhibitor of fatty-acid-adenylating enzymes (FadDs) in Mtb. However, the fatty acyl-AMP ligase (FAAL) class of FadDs, which includes MtbFadD23, appears to be functionally nonredundant in the production of multiple fatty acids. In this study, the ability of PhU-AMS to bind to MtbFadD23 was examined under in vitro conditions. The crystal structure of the MtbFadD23–PhU-AMS complex was determined at a resolution of 2.64 Å. Novel features were identified by structural analysis and comparison. Although PhU-AMS could bind to MtbFadD23, it did not inhibit the FAAL adenylation activity of MtbFadD23. However, PhU-AMS improved the main Tm value in a differential scanning fluorimetry assay, and a structural comparison of MtbFadD23–PhU-AMS with FadD32 and PA1221 suggested that PhU-AMS blocks the loading of the acyl chain onto Pks2. This study sheds light on the structure-based design of specific inhibitors of MtbFadD23 and general inhibitors of FAALs.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 8","pages":"208-216"},"PeriodicalIF":0.9,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23005836","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10040082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1 一种缓步动物的超氧化物歧化酶结构:异种野梭菌株YOKOZUNA-1

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-07-05 DOI: 10.1107/S2053230X2300523X

Kee-Shin Sim, Tsuyoshi Inoue

{"title":"Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1","authors":"Kee-Shin Sim, Tsuyoshi Inoue","doi":"10.1107/S2053230X2300523X","DOIUrl":"10.1107/S2053230X2300523X","url":null,"abstract":"Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or β3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 7","pages":"169-179"},"PeriodicalIF":0.9,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X2300523X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9790666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0