Acta crystallographica. Section F, Structural biology communications最新文献

Crystal structure of ATP-dependent DNA ligase from Rhizobium phage vB_RleM_P10VF. 根瘤菌噬菌体vB_RleM_P10VF中atp依赖性DNA连接酶的晶体结构

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-06-01 Epub Date: 2025-05-14 DOI: 10.1107/S2053230X2500411X

Ulli Rothweiler, Hanna Kirsti S Leiros, Adele Williamson

{"title":"Crystal structure of ATP-dependent DNA ligase from Rhizobium phage vB_RleM_P10VF.","authors":"Ulli Rothweiler, Hanna Kirsti S Leiros, Adele Williamson","doi":"10.1107/S2053230X2500411X","DOIUrl":"10.1107/S2053230X2500411X","url":null,"abstract":"DNA ligases are foundational molecular-biological tools used for cloning and sequencing workflows, and are essential replicative enzymes for all cellular life forms as well as many viruses and bacteriophage. There is considerable interest in structurally and functionally characterizing novel DNA ligases and profiling their suitability for molecular-biological applications. Here, we report the crystal structure of the ATP-dependent DNA ligase from the Rhizobium phage vB_RleM_P10VF bound to a nicked DNA duplex determined to 2.2 Å resolution. The enzyme crystallized in the DNA-encircling conformation, arrested as a step 2 intermediate in the catalytic cycle with the adenylating cofactor transferred to the 5'-phosphate of the DNA nick. The overall structure of the DNA ligase closely resembles that of the T4 DNA ligase, including an α-helical globular DNA-binding domain. Several secondary-structural elements are abbreviated in the P10VF DNA ligase relative to the T4 DNA ligase enzyme, which may account for its lower specific activity, especially on DNA substrates containing double-stranded breaks.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"249-254"},"PeriodicalIF":1.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958001","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 C1 domain of the surface-layer protein SlpM from Lactobacillus brevis: a module involved in protein self-assembly 短乳杆菌表面层蛋白SlpM C1结构域的晶体结构：参与蛋白质自组装的模块。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-05-19 DOI: 10.1107/S2053230X25004194

Yi Xue, Xue Kang

引用次数: 0

Structural analysis of YcdY, a member of the redox-enzyme maturation protein family 氧化还原酶成熟蛋白家族成员YcdY的结构分析。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-05-19 DOI: 10.1107/S2053230X25003887

Hong Joon Choi, Su-jin Lee, Jee-Hyeon Kim, Young-Bong You, Sung-il Yoon

{"title":"Structural analysis of YcdY, a member of the redox-enzyme maturation protein family","authors":"Hong Joon Choi, Su-jin Lee, Jee-Hyeon Kim, Young-Bong You, Sung-il Yoon","doi":"10.1107/S2053230X25003887","DOIUrl":"10.1107/S2053230X25003887","url":null,"abstract":"Proteins of the NarJ subfamily from facultatively or obligately anaerobic bacteria play key roles as chaperones in folding and cofactor insertion for complex iron–sulfur molybdoenzymes (CISMs), which mediate energy production under anaerobic conditions. YcdY was identified as a NarJ subfamily member but was proposed to increase the catalytic activity of the non-CISM enzyme YcdX phosphatase, presumably by inserting a zinc cofactor into YcdX. To elucidate the structural features of YcdY required for its chaperone function, we determined the crystal structure of Enterobacter cloacae YcdY (enYcdY). enYcdY adopts a single-domain, curved helix-bundle structure decorated with α-helices. enYcdY contains an extensive dent on its concave side. The dent in enYcdY generally forms using hydrophobic or conserved residues. Based on comparative structural and sequence analyses, we propose that enYcdY uses the dent to recognize and fold the client protein. Interestingly, enYcdY did not increase the enzymatic activity of E. cloacae YcdX (enYcdX) in the presence or absence of Zn2+ ions, even for partially denatured enYCdX protein. The same results were obtained for the Escherichia coli counterparts, in contrast to a previous report. These observations suggest that YcdY functions as a chaperone for proteins other than YcdX.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 6","pages":"263-271"},"PeriodicalIF":1.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092573","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: 0

Using resources generated by the Seattle Structural Genomics Center for Infectious Disease (SSGCID) for training early career researchers 利用西雅图传染病结构基因组学中心（SSGCID）产生的资源培训早期职业研究人员

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-05-14 DOI: 10.1107/S2053230X25003930

Julie V. Early, Craig L. Smith, Oluwatoyin A. Asojo, Peter J. Myler

引用次数: 0

Structure of an Fe2+-binding-deficient mimiviral collagen lysyl hydroxylase 缺乏Fe2+结合的mimivirus胶原lysyl羟化酶的结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-05-14 DOI: 10.1107/S2053230X25003735

Tingfei Chen, Christoph Buhlheller, Houfu Guo

{"title":"Structure of an Fe2+-binding-deficient mimiviral collagen lysyl hydroxylase","authors":"Tingfei Chen, Christoph Buhlheller, Houfu Guo","doi":"10.1107/S2053230X25003735","DOIUrl":"10.1107/S2053230X25003735","url":null,"abstract":"Collagen lysyl hydroxylases catalyze the hydroxylation of collagen lysine residues during collagen synthesis in animals and mimiviruses. Lysyl hydroxylation is crucial for collagen fibrogenesis and function. We previously demonstrated that recombinant mimiviral and human collagen lysyl hydroxylases, isolated from bacterial and mammalian cells, have Fe2+ in their active sites, suggesting that lysyl hydroxylases have a high affinity for Fe2+. We found that Fe2+ binding stabilizes lysyl hydroxylase dimers, although the underlying mechanism remains unclear. Crystal structure analysis of mimiviral lysyl hydroxylase revealed that Fe2+ is coordinated by a 2His–1Asp (His825/His877/Asp827) triad, with a nearby highly conserved histidine residue (His869) involved in an alternative 2His–1Asp triad (His869/His877/Asp827). This unique structural architecture suggests that the alternative 2His–1Asp triad may also bind Fe2+. To investigate whether the alternative 2His–1Asp triad binds Fe2+ and how Fe2+ binding regulates lysyl hydroxylase dimerization, we crystallized the mimiviral lysyl hydroxylase mutant His825Ala, which lacks one 2His–1Asp (His825/His877/Asp827) triad but retains the alternative triad (His869/His877/Asp827). Despite providing Fe2+ during crystallization, we found no electron density near the alternative 2His–1Asp triad in the His825Ala mutant, indicating that the alternative 2His–1Asp triad does not bind Fe2+ with high affinity. Although the His825Ala mutant forms a dimer similar to the wild-type enzyme, conformational changes occur in residues near Ala825, including Leu873, which is critical for dimerization. These structural findings provide new insights into the function and regulation of collagen lysyl hydroxylases.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 6","pages":"235-240"},"PeriodicalIF":1.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958263","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: 0

Crystal structure of a recombinant Agaricus bisporus mushroom mannose-binding protein with a longer C-terminal region 具有较长c端区的重组双孢蘑菇甘露糖结合蛋白的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-05-14 DOI: 10.1107/S2053230X25003905

Hiromi Yoshida, Shin-ichi Nakakita, Heni Rachmawati, Raymond R. Tjandrawinata, Wangsa T. Ismaya

{"title":"Crystal structure of a recombinant Agaricus bisporus mushroom mannose-binding protein with a longer C-terminal region","authors":"Hiromi Yoshida, Shin-ichi Nakakita, Heni Rachmawati, Raymond R. Tjandrawinata, Wangsa T. Ismaya","doi":"10.1107/S2053230X25003905","DOIUrl":"10.1107/S2053230X25003905","url":null,"abstract":"A lectin-like protein was discovered in Agaricus bisporus as part of the mushroom tyrosinase complex. The protein has a β-trefoil fold, which is typical of the ricin B-like-type lectin family. The structure of the recombinant protein has been elucidated, and its specific sugar-binding affinity towards mannose and mannitol has also been reported; therefore, the protein was named A. bisporus mannose-binding protein (Abmb). Although the sugar-binding site of Abmb is predicted to be close to the C-terminus, the sugar-binding site has not yet been determined. In this study, a variant of recombinant Abmb with a longer C-terminal region including a 6×His-tag was constructed and its structure was solved at 1.51 and 2.34 Å resolution in an orthorhombic and a monoclinic space group, respectively. The overall structure showed a β-trefoil fold as previously reported; however, several surface loop regions including the C-terminal region showed high flexibility. In addition, a glycan-search assay of this variant showed weak binding affinity towards β-d-galactose but no affinity towards α-d-mannose. The plasticity of the C-terminal tail could be related to the differences in the carbohydrate-binding affinity of Abmb.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 6","pages":"241-248"},"PeriodicalIF":1.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955027","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: 0

Crystal structures of the putative endoribonuclease L-PSP from Entamoeba histolytica 溶组织内阿米巴核糖核酸内切酶L-PSP的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-05-14 DOI: 10.1107/S2053230X25003875

Oladele T. Ojuromi, Abdulazeez O. Giwa, Anna Gardberg, Sandhya Subramanian, Peter J. Myler, Jan Abendroth, Bart Staker, Oluwatoyin A. Asojo

{"title":"Crystal structures of the putative endoribonuclease L-PSP from Entamoeba histolytica","authors":"Oladele T. Ojuromi, Abdulazeez O. Giwa, Anna Gardberg, Sandhya Subramanian, Peter J. Myler, Jan Abendroth, Bart Staker, Oluwatoyin A. Asojo","doi":"10.1107/S2053230X25003875","DOIUrl":"10.1107/S2053230X25003875","url":null,"abstract":"Entamoeba histolytica causes amebiasis, a neglected disease that kills ∼100 000 people globally each year. Due to emerging drug resistance, E. histolytica is one of the target organisms for structure-based drug discovery by the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Purification, crystallization and three structures of the putative drug target endoribonuclease L-PSP from E. histolytica (EhL-PSP) are presented. EhL-PSP has a two-layer α/β-sandwich with structural homology to endoribonuclease L-PSP. All three structures reveal the prototypical YjgF/YER057c/UK114 family trimer topology with accessible allosteric active sites. Citrate molecules from the crystallization solution are bound to the allosteric site in two of the three reported structures. The large allosteric site of EhL-PSP is well conserved with bacterial YjgF/YER057c/UK114 family members and could be targeted for inhibition, drug discovery or repurposing.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 6","pages":"226-234"},"PeriodicalIF":1.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956519","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: 0

Structure of the Saccharolobus solfataricus GINS tetramer. 甘蔗四聚体的结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-05-01 Epub Date: 2025-04-16 DOI: 10.1107/S2053230X25003085

Srihari Shankar, Eric J Enemark

引用次数: 0

Structures of Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in substrate-bound forms. 底物结合形式的结核分枝杆菌异戊二酯二磷酸合酶Rv2173的结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-05-01 Epub Date: 2025-04-01 DOI: 10.1107/S2053230X25002298

James A Titterington, Ngoc Anh Thu Ho, Charles P H Beasley, Francis Mann, Edward N Baker, Timothy M Allison, Jodie M Johnston

{"title":"Structures of Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in substrate-bound forms.","authors":"James A Titterington, Ngoc Anh Thu Ho, Charles P H Beasley, Francis Mann, Edward N Baker, Timothy M Allison, Jodie M Johnston","doi":"10.1107/S2053230X25002298","DOIUrl":"10.1107/S2053230X25002298","url":null,"abstract":"We report structures of the Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in three forms: apo and two substrate-bound forms [isoprenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)]. The protein possesses a canonical all-α-helical trans-isoprenyl diphosphate synthase fold that is dimeric in each form. There are some differences between the structures: the IPP-bound form shows IPP bound in the DMAPP/allylic substrate-binding site with three divalent metal ions bound around the IPP and the complete C-terminus closing around the active site, while the apo and DMAPP-bound forms are more open, with some of the C-terminal region disordered, supporting suggestions that the C-terminus is important in substrate entry/product exit. In the DMAPP form DMAPP occupies the expected allylic substrate site, but only two metal ions are associated with the binding, with the DMAPP diphosphates adopting a slightly different binding pose compared with IPP in the same site, and the third metal-binding site is unoccupied. In no case is the IPP binding site occupied by IPP. There has been some uncertainty regarding product length for Rv2173, with variable lengths being reported. In the structures reported here, the `capping' residue at the bottom of the binding cavity is tryptophan and comparison with other IPP synthases suggests that the structure of Rv2173 is most consistent with a C10-C15 final product size.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"193-200"},"PeriodicalIF":1.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750672","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-throughput protein crystallography to empower natural product-based drug discovery 高通量蛋白质晶体学使基于天然产物的药物发现成为可能

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-17 DOI: 10.1107/S2053230X25001542

Raphael Meneghello, Joane K. Rustiguel, Evandro Ares de Araújo, Rafael de Felício, Arthur Zanetti N. Fernandes, Everton L. F. Ferreira, Juliana R. Gubiani, Agnes A. S. Takeda, Amanda Araujo, Caio C. de Lima Silva, Ariane F. Bertonha, Raquel P. M. Urano, Daniel M. Trindade, Thiago M. Cunha, Alisson C. Cardoso, Roberto G. S. Berlinck, Andrey F. Ziem Nascimento, Daniela B. B. Trivella

{"title":"High-throughput protein crystallography to empower natural product-based drug discovery","authors":"Raphael Meneghello, Joane K. Rustiguel, Evandro Ares de Araújo, Rafael de Felício, Arthur Zanetti N. Fernandes, Everton L. F. Ferreira, Juliana R. Gubiani, Agnes A. S. Takeda, Amanda Araujo, Caio C. de Lima Silva, Ariane F. Bertonha, Raquel P. M. Urano, Daniel M. Trindade, Thiago M. Cunha, Alisson C. Cardoso, Roberto G. S. Berlinck, Andrey F. Ziem Nascimento, Daniela B. B. Trivella","doi":"10.1107/S2053230X25001542","DOIUrl":"https://doi.org/10.1107/S2053230X25001542","url":null,"abstract":"Nature is a rich and largely untapped reservoir of small molecules, the latter historically being the main source of new drugs. Three-dimensional structures of proteins in complex with small-molecule ligands represent key information to progress drug-discovery projects, in particular in the hit-to-lead phase. High-throughput crystallography has been of extensive use in recent years, especially to obtain crystallographic complexes of synthetic ligands and fragments. However, the process of discovering novel bioactive natural products has experienced limitations that have long prevented large drug-discovery programs using this outstanding source of molecules. Recent technologies have contributed to the re-emergence of natural products in modern drug discovery. We present the use of high-throughput protein crystallography to directly capture bioactive natural products from unpurified biota chemical samples using protein crystals. These routines, which are currently in use at the Brazilian Centre for Research in Energy and Materials (CNPEM), are introduced with a description of crystal preparation, automated data collection and processing at the MANACÁ beamline (Sirius, LNLS, CNPEM), along with case examples of bioactive natural product capture using protein crystals. The usefulness of this pipeline, which accelerates the discovery and structural elucidation of both known and previously unknown bioactive natural products, paves the way for the development of innovative therapeutic agents, thus contributing to the new era of natural product-based drug discovery.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 5","pages":"179-192"},"PeriodicalIF":1.1,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143879984","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: 0