Acta crystallographica. Section F, Structural biology communications最新文献_第9页

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

An unusual disulfide-linked dimerization in the fluorescent protein rsCherryRev1.4 荧光蛋白rsCherryRev1.4中不寻常的二硫化物连接二聚化

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-02-07 DOI: 10.1107/S2053230X23000572

Thi Yen Hang Bui, Peter Dedecker, Luc Van Meervelt

{"title":"An unusual disulfide-linked dimerization in the fluorescent protein rsCherryRev1.4","authors":"Thi Yen Hang Bui, Peter Dedecker, Luc Van Meervelt","doi":"10.1107/S2053230X23000572","DOIUrl":"10.1107/S2053230X23000572","url":null,"abstract":"rsCherryRev1.4 has been reported as one of the reversibly photoswitchable variants of mCherry, and is an improved version with a faster off-switching speed and lower switching fatigue at high light intensities than its precursor rsCherryRev. However, rsCherryRev1.4 still has some limitations such as a tendency to dimerize as well as complex photophysical properties. Here, the crystal structure of rsCherryRev1.4 was determined at a resolution of 2 Å and it was discovered that it forms a dimer that shows disulfide bonding between the protomers. Mutagenesis, gel electrophoresis and size-exclusion chromatography strongly implicate Cys24 in this process. Replacing Cys24 in rsCherryRev1.4 resulted in a much lower tendency towards dimerization, while introducing Cys24 into mCherry correspondingly increased its dimerization. In principle, this finding opens the possibility of developing redox sensors based on controlled dimerization via disulfide cross-linking in fluorescent proteins, even though the actual application of engineering such sensors still requires additional research.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X23000572","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10687866","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 pyridoxal 5′-phosphate-bound d-threonine aldolase from Chlamydomonas reinhardtii 莱茵衣藻吡哆醛5′-磷酸结合d-苏氨酸醛缩酶的结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-02-07 DOI: 10.1107/S2053230X23000304

Yuki Hirato, Masaru Goto, Taichi Mizobuchi, Hisashi Muramatsu, Minoru Tanigawa, Katsushi Nishimura

引用次数: 0

Purification and structure of luminal domain C of human Niemann–Pick C1 protein 人Niemann-Pick C1蛋白管腔结构域C的纯化与结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-02-07 DOI: 10.1107/S2053230X23000705

Laura Odongo, Kaneil K. Zadrozny, William E. Diehl, Jeremy Luban, Judith M. White, Barbie K. Ganser-Pornillos, Lukas K. Tamm, Owen Pornillos

引用次数: 1

Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature. Lentinus similis AA9_A 在室温下的 X 射线/中子联合结构。

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2023-01-01 DOI: 10.1107/S2053230X22011335

Tobias Tandrup, Leila Lo Leggio, Flora Meilleur

引用次数: 1

Crystal structure of the C-terminal domain of the plant-specific microtubule-associated protein Spiral2 植物特异性微管相关蛋白Spiral2 c端结构域的晶体结构

IF 0.9 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-12-20 DOI: 10.1107/S2053230X22011815

Marina Ohno, Yuuki Higuchi, Ikuko Hayashi

{"title":"Crystal structure of the C-terminal domain of the plant-specific microtubule-associated protein Spiral2","authors":"Marina Ohno, Yuuki Higuchi, Ikuko Hayashi","doi":"10.1107/S2053230X22011815","DOIUrl":"10.1107/S2053230X22011815","url":null,"abstract":"Plant cells form microtubule arrays, called `cortical microtubules', beneath the plasma membrane which are critical for cell-wall organization and directional cell growth. Cortical microtubules are nucleated independently of centrosomes. Spiral2 is a land-plant-specific microtubule minus-end-targeting protein that stabilizes the minus ends by inhibiting depolymerization of the filament. Spiral2 possesses an N-terminal microtubule-binding domain and a conserved C-terminal domain whose function is unknown. In this study, the crystal structure of the conserved C-terminal domain of Spiral2 was determined using the single-wavelength anomalous dispersion method. Refinement of the model to a resolution of 2.2 Å revealed a helix–turn–helix fold with seven α-helices. The protein crystallized as a dimer, but SEC-MALS analysis showed the protein to be monomeric. A structural homology search revealed that the protein has similarity to the C-terminal domain of the katanin regulatory subunit p80. The structure presented here suggests that the C-terminal domain of Spiral2 represents a new class of microtubule dynamics modulator across the kingdom.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X22011815","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10559215","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