Acta Crystallographica. Section D, Structural Biology最新文献

Structural basis for the allosteric pathway of 4-amino-4-deoxychorismate synthase. 4-氨基-4-脱氧氯合酶变构途径的结构基础。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-10-01 Epub Date: 2023-09-15 DOI: 10.1107/S2059798323006320

Yusuke Nakamichi, Jyumpei Kobayashi, Koichi Toyoda, Masako Suda, Kazumi Hiraga, Masayuki Inui, Masahiro Watanabe

{"title":"Structural basis for the allosteric pathway of 4-amino-4-deoxychorismate synthase.","authors":"Yusuke Nakamichi, Jyumpei Kobayashi, Koichi Toyoda, Masako Suda, Kazumi Hiraga, Masayuki Inui, Masahiro Watanabe","doi":"10.1107/S2059798323006320","DOIUrl":"10.1107/S2059798323006320","url":null,"abstract":"4-Amino-4-deoxychorismate synthase (ADCS), a chorismate-utilizing enzyme, is composed of two subunits: PabA and PabB. PabA is a glutamine amidotransferase that hydrolyzes glutamine into glutamate and ammonia. PabB is an aminodeoxychorismate synthase that converts chorismate to 4-amino-4-deoxychorismate (ADC) using the ammonia produced by PabA. ADCS functions under allosteric regulation between PabA and PabB. However, the allosteric mechanism remains unresolved because the structure of the PabA-PabB complex has not been determined. Here, the crystal structure and characterization of PapA from Streptomyces venezuelae (SvPapA), a bifunctional enzyme comprising the PabA and PabB domains, is reported. SvPapA forms a unique dimer in which PabA and PabB domains from different monomers complement each other and form an active structure. The chorismate-bound structure revealed that recognition of the C1 carboxyl group by Thr501 and Gly502 of the 498-PIKTG-502 motif in the PabB domain is essential for the catalytic Lys500 to reach the C2 atom, a reaction-initiation site. SvPapA demonstrated ADCS activity in the presence of Mg2+ when glutamate or NH+4 was used as the amino donor. The crystal structure indicated that the Mg2+-binding position changed depending on the binding of chorismate. In addition, significant structural changes were observed in the PabA domain depending on the presence or absence of chorismate. This study provides insights into the structural factors that are involved in the allosteric regulation of ADCS.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"895-908"},"PeriodicalIF":2.2,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10247141","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

Increasing the bulk of the 1TEL-target linker and retaining the 10×His tag in a 1TEL-CMG2-vWa construct improves crystal order and diffraction limits. 增加1TEL靶连接体的体积并在1TEL-CMG2-vWa结构中保留10×His标签提高了晶体的有序性和衍射极限。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-10-01 Epub Date: 2023-09-25 DOI: 10.1107/S2059798323007246

Parag L Gajjar, Maria J Pedroza Romo, Celeste M Litchfield, Miles Callahan, Nathan Redd, Supeshala Nawarathnage, Sara Soleimani, Jacob Averett, Elijah Wilson, Andrew Lewis, Cameron Stewart, Yi Jie Tseng, Tzanko Doukov, Andrey Lebedev, James D Moody

{"title":"Increasing the bulk of the 1TEL-target linker and retaining the 10×His tag in a 1TEL-CMG2-vWa construct improves crystal order and diffraction limits.","authors":"Parag L Gajjar, Maria J Pedroza Romo, Celeste M Litchfield, Miles Callahan, Nathan Redd, Supeshala Nawarathnage, Sara Soleimani, Jacob Averett, Elijah Wilson, Andrew Lewis, Cameron Stewart, Yi Jie Tseng, Tzanko Doukov, Andrey Lebedev, James D Moody","doi":"10.1107/S2059798323007246","DOIUrl":"10.1107/S2059798323007246","url":null,"abstract":"TELSAM-fusion crystallization has the potential to become a revolutionary tool for the facile crystallization of proteins. TELSAM fusion can increase the crystallization rate and enable crystallization at low protein concentrations, in some cases with minimal crystal contacts [Nawarathnage et al. (2022), Open Biol. 12, 210271]. Here, requirements for the linker composition between 1TEL and a fused CMG2 vWa domain were investigated. Ala-Ala, Ala-Val, Thr-Val and Thr-Thr linkers were evaluated, comparing metrics for crystallization propensity and crystal order. The effect on crystallization of removing or retaining the purification tag was then tested. It was discovered that increasing the linker bulk and retaining the 10×His purification tag improved the diffraction resolution, likely by decreasing the number of possible vWa-domain orientations in the crystal. Additionally, it was discovered that some vWa-domain binding modes are correlated with scrambling of the 1TEL polymer orientation in crystals and an effective mitigation strategy for this pathology is presented.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"925-943"},"PeriodicalIF":2.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41111269","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

Elucidating polymorphs of crystal structures by intensity-based hierarchical clustering analysis of multiple diffraction data sets. 通过多个衍射数据集的基于强度的层次聚类分析来阐明晶体结构的多晶型。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-10-01 Epub Date: 2023-10-25 DOI: 10.1107/S2059798323007039

Hiroaki Matsuura, Naoki Sakai, Sachiko Toma-Fukai, Norifumi Muraki, Koki Hayama, Hironari Kamikubo, Shigetoshi Aono, Yoshiaki Kawano, Masaki Yamamoto, Kunio Hirata

{"title":"Elucidating polymorphs of crystal structures by intensity-based hierarchical clustering analysis of multiple diffraction data sets.","authors":"Hiroaki Matsuura, Naoki Sakai, Sachiko Toma-Fukai, Norifumi Muraki, Koki Hayama, Hironari Kamikubo, Shigetoshi Aono, Yoshiaki Kawano, Masaki Yamamoto, Kunio Hirata","doi":"10.1107/S2059798323007039","DOIUrl":"10.1107/S2059798323007039","url":null,"abstract":"In macromolecular structure determination using X-ray diffraction from multiple crystals, the presence of different structures (structural polymorphs) necessitates the classification of the diffraction data for appropriate structural analysis. Hierarchical clustering analysis (HCA) is a promising technique that has so far been used to extract isomorphous data, mainly for single-structure determination. Although in principle the use of HCA can be extended to detect polymorphs, the absence of a reference to define the threshold used to group the isomorphous data sets (the `isomorphic threshold') poses a challenge. Here, unit-cell-based and intensity-based HCAs have been applied to data sets for apo trypsin and inhibitor-bound trypsin that were mixed post data acquisition to investigate the efficacy of HCA in classifying polymorphous data sets. Single-step intensity-based HCA successfully classified polymorphs with a certain `isomorphic threshold'. In data sets for several samples containing an unknown degree of structural heterogeneity, polymorphs could be identified by intensity-based HCA using the suggested `isomorphic threshold'. Polymorphs were also detected in single crystals using data collected using the continuous helical scheme. These findings are expected to facilitate the determination of multiple structural snapshots by exploiting automated data collection and analysis.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 10","pages":"909-924"},"PeriodicalIF":2.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41187822","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

A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography. 一种用户友好的即插即用的基于环烯烃共聚物的微流控芯片，用于室温、固定靶序列晶体学。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-10-01 Epub Date: 2023-09-25 DOI: 10.1107/S2059798323007027

Zhongrui Liu, Kevin K Gu, Megan L Shelby, Deepshika Gilbile, Artem Y Lyubimov, Silvia Russi, Aina E Cohen, Sankar Raju Narayanasamy, Sabine Botha, Christopher Kupitz, Raymond G Sierra, Fredric Poitevin, Antonio Gilardi, Stella Lisova, Matthew A Coleman, Matthias Frank, Tonya L Kuhl

{"title":"A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography.","authors":"Zhongrui Liu, Kevin K Gu, Megan L Shelby, Deepshika Gilbile, Artem Y Lyubimov, Silvia Russi, Aina E Cohen, Sankar Raju Narayanasamy, Sabine Botha, Christopher Kupitz, Raymond G Sierra, Fredric Poitevin, Antonio Gilardi, Stella Lisova, Matthew A Coleman, Matthias Frank, Tonya L Kuhl","doi":"10.1107/S2059798323007027","DOIUrl":"10.1107/S2059798323007027","url":null,"abstract":"Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip, 21, 4831-4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"944-952"},"PeriodicalIF":2.2,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41096155","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 structures of human and mouse ketohexokinase provide a structural basis for species- and isoform-selective inhibitor design. 人和小鼠酮己糖激酶的晶体结构为物种和异构体选择性抑制剂的设计提供了结构基础。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-10-01 Epub Date: 2023-09-15 DOI: 10.1107/S2059798323006137

Rebecca Ebenhoch, Margit Bauer, Helmut Romig, Dirk Gottschling, Jörg Thomas Kley, Niklas Heine, Alexander Weber, Ingo Uphues, Herbert Nar, Alexander Pautsch

引用次数: 0

Michael James (1940-2023). 迈克尔·詹姆斯（1940-2023）。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-10-01 Epub Date: 2023-09-15 DOI: 10.1107/S2059798323006976

J N Mark Glover, Cyril M Kay, Joanne Lemieux, Randy J Read

引用次数: 0

X-ray structure of the metastable SEPT14-SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization. 亚稳SEPT14-SEPT7线圈的X射线结构揭示了一个对异二聚至关重要的hendeca区域。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-10-01 Epub Date: 2023-09-15 DOI: 10.1107/S2059798323006514

Italo A Cavini, Ashley J Winter, Humberto D'Muniz Pereira, Derek N Woolfson, Matthew P Crump, Richard C Garratt

{"title":"X-ray structure of the metastable SEPT14-SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization.","authors":"Italo A Cavini, Ashley J Winter, Humberto D'Muniz Pereira, Derek N Woolfson, Matthew P Crump, Richard C Garratt","doi":"10.1107/S2059798323006514","DOIUrl":"10.1107/S2059798323006514","url":null,"abstract":"Septins are membrane-associated, GTP-binding proteins that are present in most eukaryotes. They polymerize to play important roles as scaffolds and/or diffusion barriers as part of the cytoskeleton. α-Helical coiled-coil domains are believed to contribute to septin assembly, and those observed in both human SEPT6 and SEPT8 form antiparallel homodimers. These are not compatible with their parallel heterodimeric organization expected from the current model for protofilament assembly, but they could explain the interfilament cross-bridges observed by microscopy. Here, the first structure of a heterodimeric septin coiled coil is presented, that between SEPT14 and SEPT7; the former is a SEPT6/SEPT8 homolog. This new structure is parallel, with two long helices that are axially shifted by a full helical turn with reference to their sequence alignment. The structure also has unusual knobs-into-holes packing of side chains. Both standard seven-residue (heptad) and the less common 11-residue (hendecad) repeats are present, creating two distinct regions with opposite supercoiling, which gives rise to an overall straight coiled coil. Part of the hendecad region is required for heterodimerization and therefore may be crucial for selective septin recognition. These unconventional sequences and structural features produce a metastable heterocomplex that nonetheless has enough specificity to promote correct protofilament assembly. For instance, the lack of supercoiling may facilitate unzipping and transitioning to the antiparallel homodimeric state.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"881-894"},"PeriodicalIF":2.6,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10247137","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

Raimond B. G. Ravelli (25 March 1968-30 June 2023). raymond B. G. Ravelli(1968年3月25日- 2023年6月30日)。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-09-01 DOI: 10.1107/S2059798323006897

Elspeth F Garman

引用次数: 0

A Python package based on robust statistical analysis for serial crystallography data processing. 基于稳健统计分析的 Python 软件包，用于序列晶体学数据处理。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-09-01 Epub Date: 2023-08-16 DOI: 10.1107/S2059798323005855

Marjan Hadian-Jazi, Alireza Sadri

{"title":"A Python package based on robust statistical analysis for serial crystallography data processing.","authors":"Marjan Hadian-Jazi, Alireza Sadri","doi":"10.1107/S2059798323005855","DOIUrl":"10.1107/S2059798323005855","url":null,"abstract":"The term robustness in statistics refers to methods that are generally insensitive to deviations from model assumptions. In other words, robust methods are able to preserve their accuracy even when the data do not perfectly fit the statistical models. Robust statistical analyses are particularly effective when analysing mixtures of probability distributions. Therefore, these methods enable the discretization of X-ray serial crystallography data into two probability distributions: a group comprising true data points (for example the background intensities) and another group comprising outliers (for example Bragg peaks or bad pixels on an X-ray detector). These characteristics of robust statistical analysis are beneficial for the ever-increasing volume of serial crystallography (SX) data sets produced at synchrotron and X-ray free-electron laser (XFEL) sources. The key advantage of the use of robust statistics for some applications in SX data analysis is that it requires minimal parameter tuning because of its insensitivity to the input parameters. In this paper, a software package called Robust Gaussian Fitting library (RGFlib) is introduced that is based on the concept of robust statistics. Two methods are presented based on the concept of robust statistics and RGFlib for two SX data-analysis tasks: (i) a robust peak-finding algorithm and (ii) an automated robust method to detect bad pixels on X-ray pixel detectors.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 9","pages":"820-829"},"PeriodicalIF":2.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10521367","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 basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin. 基因毒素可乐菌素生物合成的核心氨酶 ClbL 的结构基础。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-09-01 Epub Date: 2023-08-10 DOI: 10.1107/S2059798323005703

Prabhanshu Tripathi, Jarrod J Mousa, Naga Sandhya Guntaka, Steven D Bruner

{"title":"Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin.","authors":"Prabhanshu Tripathi, Jarrod J Mousa, Naga Sandhya Guntaka, Steven D Bruner","doi":"10.1107/S2059798323005703","DOIUrl":"10.1107/S2059798323005703","url":null,"abstract":"Colibactin is a genotoxic natural product produced by select commensal bacteria in the human gut microbiota. The compound is a bis-electrophile that is predicted to form interstrand DNA cross-links in target cells, leading to double-strand DNA breaks. The biosynthesis of colibactin is carried out by a mixed NRPS-PKS assembly line with several noncanonical features. An amidase, ClbL, plays a key role in the pathway, catalyzing the final step in the formation of the pseudodimeric scaffold. ClbL couples α-aminoketone and β-ketothioester intermediates attached to separate carrier domains on the NRPS-PKS assembly. Here, the 1.9 Å resolution structure of ClbL is reported, providing a structural basis for this key step in the colibactin biosynthetic pathway. The structure reveals an open hydrophobic active site surrounded by flexible loops, and comparison with homologous amidases supports its unusual function and predicts macromolecular interactions with pathway carrier-protein substrates. Modeling protein-protein interactions supports a predicted molecular basis for enzyme-carrier domain interactions. Overall, the work provides structural insight into this unique enzyme that is central to the biosynthesis of colibactin.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 9","pages":"830-836"},"PeriodicalIF":2.6,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10478638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10539163","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