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

Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2 甲基黄曲霉SB2株NADPH依赖性黄素单加氧酶MbnF的晶体结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-05-05 DOI: 10.1107/S2053230X23003035

Andrew Stewart, Philip Dershwitz, Charles Stewart Jr, Michael R. Sawaya, Todd O. Yeates, Jeremy D. Semrau, Hans Zischka, Alan A. DiSpirito, Thomas A. Bobik

{"title":"Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2","authors":"Andrew Stewart, Philip Dershwitz, Charles Stewart Jr, Michael R. Sawaya, Todd O. Yeates, Jeremy D. Semrau, Hans Zischka, Alan A. DiSpirito, Thomas A. Bobik","doi":"10.1107/S2053230X23003035","DOIUrl":"10.1107/S2053230X23003035","url":null,"abstract":"Methanobactins (MBs) are ribosomally produced and post-translationally modified peptides (RiPPs) that are used by methanotrophs for copper acquisition. The signature post-translational modification of MBs is the formation of two heterocyclic groups, either an oxazolone, pyrazinedione or imidazolone group, with an associated thioamide from an X-Cys dipeptide. The precursor peptide (MbnA) for MB formation is found in a gene cluster of MB-associated genes. The exact biosynthetic pathway of MB formation is not yet fully understood, and there are still uncharacterized proteins in some MB gene clusters, particularly those that produce pyrazinedione or imidazolone rings. One such protein is MbnF, which is proposed to be a flavin monooxygenase (FMO) based on homology. To help to elucidate its possible function, MbnF from Methylocystis sp. strain SB2 was recombinantly produced in Escherichia coli and its X-ray crystal structure was resolved to 2.6 Å resolution. Based on its structural features, MbnF appears to be a type A FMO, most of which catalyze hydroxylation reactions. Preliminary functional characterization shows that MbnF preferentially oxidizes NADPH over NADH, supporting NAD(P)H-mediated flavin reduction, which is the initial step in the reaction cycle of several type A FMO enzymes. It is also shown that MbnF binds the precursor peptide for MB, with subsequent loss of the leader peptide sequence as well as the last three C-terminal amino acids, suggesting that MbnF might be needed for this process to occur. Finally, molecular-dynamics simulations revealed a channel in MbnF that is capable of accommodating the core MbnA fragment minus the three C-terminal amino acids.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23003035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9442518","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 the engineered endolysin mtEC340M 工程内溶素mtEC340M的晶体结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-05-03 DOI: 10.1107/S2053230X23002583

Jee-Min Wang, Seung-Hyeon Seok, Won-Su Yoon, Ji-Hun Kim, Min-Duk Seo

引用次数: 0

Crystal structure of MAB_4123, a putative flavin-dependent monooxygenase from Mycobacterium abscessus 推测来自脓肿分枝杆菌黄素依赖性单加氧酶MAB_4123的晶体结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-05-03 DOI: 10.1107/S2053230X2300345X

Kien Lam Ung, Chloé Poussineau, Julie Couston, Husam M. A. B. Alsarraf, Mickaël Blaise

{"title":"Crystal structure of MAB_4123, a putative flavin-dependent monooxygenase from Mycobacterium abscessus","authors":"Kien Lam Ung, Chloé Poussineau, Julie Couston, Husam M. A. B. Alsarraf, Mickaël Blaise","doi":"10.1107/S2053230X2300345X","DOIUrl":"10.1107/S2053230X2300345X","url":null,"abstract":"Numerous bacteria from different phylae can perform desulfurization reactions of organosulfur compounds. In these degradation or detoxification pathways, two-component flavin-dependent monooxygenases that use flavins (FMN or FAD) as a cofactor play important roles as they catalyse the first steps of these metabolic routes. The TdsC or DszC and MsuC proteins belong to this class of enzymes as they process dibenzothiophene (DBT) and methanesulfinate. Elucidation of their X-ray structures in apo, ligand-bound and cofactor-bound forms has provided important molecular insights into their catalytic reaction. Mycobacterial species have also been shown to possess a DBT degradation pathway, but no structural information is available on these two-component flavin-dependent monooxygenases. In this study, the crystal structure of the uncharacterized MAB_4123 protein from the human pathogen Mycobacterium abscessus is presented. The structure solved at high resolution displays high similarity to homologs from Rhodococcus, Paenibacillus and Pseudomonas species. In silico docking approaches suggest that MAB_4123 binds FMN and may use it as a cofactor. Structural analysis strongly suggests that MAB_4123 is a two-component flavin-dependent monooxygenase that could act as a detoxifying enzyme of organosulfur compounds in mycobacteria.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X2300345X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9812714","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

Introduction to the virtual thematic issue on room-temperature biological crystallography 介绍室温生物晶体学虚拟专题问题

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-04-04 DOI: 10.1107/S2053230X23002935

Roberto A. Steiner

引用次数: 0

Monomeric crystal structure of the vaccine carrier protein CRM197 and implications for vaccine development 疫苗载体蛋白CRM197的单体晶体结构及其对疫苗开发的意义

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-03-30 DOI: 10.1107/S2053230X23002364

D. Travis Gallagher, Natalia Oganesyan, Andrew Lees

{"title":"Monomeric crystal structure of the vaccine carrier protein CRM197 and implications for vaccine development","authors":"D. Travis Gallagher, Natalia Oganesyan, Andrew Lees","doi":"10.1107/S2053230X23002364","DOIUrl":"https://doi.org/10.1107/S2053230X23002364","url":null,"abstract":"CRM197 is a genetically detoxified mutant of diphtheria toxin (DT) that is widely used as a carrier protein in conjugate vaccines. Protective immune responses to several bacterial diseases are obtained by coupling CRM197 to glycans from these pathogens. Wild-type DT has been described in two oligomeric forms: a monomer and a domain-swapped dimer. Their proportions depend on the chemical conditions and especially the pH, with a large kinetic barrier to interconversion. A similar situation occurs in CRM197, where the monomer is preferred for vaccine synthesis. Despite 30 years of research and the increasing application of CRM197 in conjugate vaccines, until now all of its available crystal structures have been dimeric. Here, CRM197 was expressed as a soluble, intracellular protein in an Escherichia coli strain engineered to have an oxidative cytoplasm. The purified product, called EcoCRM, remained monomeric throughout crystallization. The structure of monomeric EcoCRM is reported at 2.0 Å resolution with the domain-swapping hinge loop (residues 379–387) in an extended, exposed conformation, similar to monomeric wild-type DT. The structure enables comparisons across expression systems and across oligomeric states, with implications for monomer–dimer interconversion and for the optimization of conjugation.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50155868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Structural and enzymatic characterization of the sialidase SiaPG from Porphyromonas gingivalis 牙龈卟啉单胞菌唾液酸酶SiaPG的结构和酶学表征

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-03-30 DOI: 10.1107/S2053230X23001735

Wen-Bo Dong, Yong-Liang Jiang, Zhong-Liang Zhu, Jie Zhu, Yang Li, Rong Xia, Kang Zhou

{"title":"Structural and enzymatic characterization of the sialidase SiaPG from Porphyromonas gingivalis","authors":"Wen-Bo Dong, Yong-Liang Jiang, Zhong-Liang Zhu, Jie Zhu, Yang Li, Rong Xia, Kang Zhou","doi":"10.1107/S2053230X23001735","DOIUrl":"10.1107/S2053230X23001735","url":null,"abstract":"The sialidases, which catalyze the hydrolysis of sialic acid from extracellular glycoconjugates, are a group of major virulence factors in various pathogenic bacteria. In Porphyromonas gingivalis, which causes human periodontal disease, sialidase contributes to bacterial pathogenesis via promoting the formation of biofilms and capsules, reducing the ability for macrophage clearance, and providing nutrients for bacterial colonization. Here, the crystal structure of the P. gingivalis sialidase SiaPG is reported at 2.1 Å resolution, revealing an N-terminal carbohydrate-binding domain followed by a canonical C-terminal catalytic domain. Simulation of the product sialic acid in the active-site pocket together with functional analysis enables clear identification of the key residues that are required for substrate binding and catalysis. Moreover, structural comparison with other sialidases reveals distinct features of the active-site pocket which might confer substrate specificity. These findings provide the structural basis for the further design and optimization of effective inhibitors to target SiaPG to fight against P. gingivalis-derived oral diseases.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23001735","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9323544","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: 1

A partially open conformation of an androgen receptor ligand-binding domain with drug-resistance mutations 具有耐药性突变的雄激素受体配体结合域的部分开放构象

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-03-30 DOI: 10.1107/S2053230X23002224

Selom K. Doamekpor, Panfeng Peng, Ruo Xu, Liandong Ma, Youzhi Tong, Liang Tong

{"title":"A partially open conformation of an androgen receptor ligand-binding domain with drug-resistance mutations","authors":"Selom K. Doamekpor, Panfeng Peng, Ruo Xu, Liandong Ma, Youzhi Tong, Liang Tong","doi":"10.1107/S2053230X23002224","DOIUrl":"10.1107/S2053230X23002224","url":null,"abstract":"Mutations in the androgen receptor (AR) ligand-binding domain (LBD) can cause resistance to drugs used to treat prostate cancer. Commonly found mutations include L702H, W742C, H875Y, F877L and T878A, while the F877L mutation can convert second-generation antagonists such as enzalutamide and apalutamide into agonists. However, pruxelutamide, another second-generation AR antagonist, has no agonist activity with the F877L and F877L/T878A mutants and instead maintains its inhibitory activity against them. Here, it is shown that the quadruple mutation L702H/H875Y/F877L/T878A increases the soluble expression of AR LBD in complex with pruxelutamide in Escherichia coli. The crystal structure of the quadruple mutant in complex with the agonist dihydrotestosterone (DHT) reveals a partially open conformation of the AR LBD due to conformational changes in the loop connecting helices H11 and H12 (the H11–H12 loop) and Leu881. This partially open conformation creates a larger ligand-binding site for AR. Additional structural studies suggest that both the L702H and F877L mutations are important for conformational changes. This structural variability in the AR LBD could affect ligand binding as well as the resistance to antagonists.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23002224","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9323545","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

Structural and biophysical characterization of the Borna disease virus 1 phosphoprotein 博尔纳病病毒1型磷蛋白的结构和生物物理特性

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-02-23 DOI: 10.1107/S2053230X23000717

Jack D. Whitehead, Jonathan M. Grimes, Jeremy R. Keown

{"title":"Structural and biophysical characterization of the Borna disease virus 1 phosphoprotein","authors":"Jack D. Whitehead, Jonathan M. Grimes, Jeremy R. Keown","doi":"10.1107/S2053230X23000717","DOIUrl":"10.1107/S2053230X23000717","url":null,"abstract":"Bornaviruses are RNA viruses with a mammalian, reptilian, and avian host range. The viruses infect neuronal cells and in rare cases cause a lethal encephalitis. The family Bornaviridae are part of the Mononegavirales order of viruses, which contain a nonsegmented viral genome. Mononegavirales encode a viral phosphoprotein (P) that binds both the viral polymerase (L) and the viral nucleoprotein (N). The P protein acts as a molecular chaperone and is required for the formation of a functional replication/transcription complex. In this study, the structure of the oligomerization domain of the phosphoprotein determined by X-ray crystallography is reported. The structural results are complemented with biophysical characterization using circular dichroism, differential scanning calorimetry and small-angle X-ray scattering. The data reveal the phosphoprotein to assemble into a stable tetramer, with the regions outside the oligomerization domain remaining highly flexible. A helix-breaking motif is observed between the α-helices at the midpoint of the oligomerization domain that appears to be conserved across the Bornaviridae. These data provide information on an important component of the bornavirus replication complex.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23000717","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9083525","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

Expression, purification and crystallization of N-acetyl-(R)-β-phenylalanine acylases derived from Burkholderia sp. AJ110349 and Variovorax sp. AJ110348 and structure determination of the Burkholderia enzyme Burkholderia sp. AJ110349和Variovorax sp. AJ110348 n -乙酰基-(R)-β-苯丙氨酸酰化酶的表达、纯化、结晶及结构测定

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-02-23 DOI: 10.1107/S2053230X23000730

Yuki Kato, Hisashi Kawasaki, Tsuyoshi Nakamatsu, Namio Matsuda, Ryo Natsume

{"title":"Expression, purification and crystallization of N-acetyl-(R)-β-phenylalanine acylases derived from Burkholderia sp. AJ110349 and Variovorax sp. AJ110348 and structure determination of the Burkholderia enzyme","authors":"Yuki Kato, Hisashi Kawasaki, Tsuyoshi Nakamatsu, Namio Matsuda, Ryo Natsume","doi":"10.1107/S2053230X23000730","DOIUrl":"10.1107/S2053230X23000730","url":null,"abstract":"N-Acetyl-(R)-β-phenylalanine acylase is an enzyme that hydrolyzes the amide bond of N-acetyl-(R)-β-phenylalanine to produce enantiopure (R)-β-phenylalanine. In previous studies, Burkholderia sp. AJ110349 and Variovorax sp. AJ110348 were isolated as (R)-enantiomer-specific N-acetyl-(R)-β-phenylalanine acylase-producing organisms and the properties of the native enzyme from Burkholderia sp. AJ110349 were characterized. In this study, structural analyses were carried out in order to investigate the structure–function relationships of the enzymes derived from both organisms. The recombinant N-acetyl-(R)-β-phenylalanine acylases were crystallized by the hanging-drop vapor-diffusion method under multiple crystallization solution conditions. The crystals of the Burkholderia enzyme belonged to space group P41212, with unit-cell parameters a = b = 112.70–112.97, c = 341.50–343.32 Å, and were likely to contain two subunits in the asymmetric unit. The crystal structure was solved by the Se-SAD method, suggesting that two subunits in the asymmetric unit form a dimer. Each subunit was composed of three domains, and they showed structural similarity to the corresponding domains of the large subunit of N,N-dimethylformamidase from Paracoccus sp. strain DMF. The crystals of the Variovorax enzyme grew as twinned crystals and were not suitable for structure determination. Using size-exclusion chromatography with online static light-scattering analysis, the N-acetyl-(R)-β-phenylalanine acylases were clarified to be dimeric in solution.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23000730","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10837329","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

Structures of chloramphenicol acetyltransferase III and Escherichia coli β-ketoacylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(dethia)CoA 氯霉素乙酰转移酶III和大肠杆菌β-酮酰合酶III与部分水解的乙酰氧(dethia)辅酶a共结晶的结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-02-23 DOI: 10.1107/S2053230X23001206

Aaron B. Benjamin, Lee M. Stunkard, Jianheng Ling, Jaelen N. Nice, Jeremy R. Lohman

{"title":"Structures of chloramphenicol acetyltransferase III and Escherichia coli β-ketoacylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(dethia)CoA","authors":"Aaron B. Benjamin, Lee M. Stunkard, Jianheng Ling, Jaelen N. Nice, Jeremy R. Lohman","doi":"10.1107/S2053230X23001206","DOIUrl":"10.1107/S2053230X23001206","url":null,"abstract":"Acetyl coenzyme A (acetyl-CoA) is a reactive metabolite that nonproductively hydrolyzes in a number of enzyme active sites in the crystallization time frame. In order to elucidate the enzyme–acetyl-CoA interactions leading to catalysis, acetyl-CoA substrate analogs are needed. One possible analog for use in structural studies is acetyl-oxa(dethia)CoA (AcOCoA), in which the thioester S atom of CoA is replaced by an O atom. Here, structures of chloramphenicol acetyltransferase III (CATIII) and Escherichia coli ketoacylsynthase III (FabH) from crystals grown in the presence of partially hydrolyzed AcOCoA and the respective nucleophile are presented. Based on the structures, the behavior of AcOCoA differs between the enzymes, with FabH reacting with AcOCoA and CATIII being unreactive. The structure of CATIII reveals insight into the catalytic mechanism, with one active site of the trimer having relatively clear electron density for AcOCoA and chloramphenicol and the other active sites having weaker density for AcOCoA. One FabH structure contains a hydrolyzed AcOCoA product oxa(dethia)CoA (OCoA), while the other FabH structure contains an acyl-enzyme intermediate with OCoA. Together, these structures provide preliminary insight into the use of AcOCoA for enzyme structure–function studies with different nucleophiles.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9979976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9588835","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