首页 > 最新文献

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

英文 中文
Online carbohydrate 3D structure validation with the Privateer web app. 利用 Privateer 网络应用程序在线验证碳水化合物的三维结构。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-02-01 Epub Date: 2024-01-24 DOI: 10.1107/S2053230X24000359
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Paul S Bond, Filomeno Sánchez Rodríguez, Stuart J McNicholas, Jon Agirre

Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to date and available to be used online (https://privateer.york.ac.uk) without installation. This self-updating tool, which runs locally on the user's machine, will allow structural biologists to simply and quickly analyse carbohydrate ligands and protein glycosylation from a web browser whilst retaining all confidential information on their devices.

由于与碳水化合物相关的工作困难重重,在将聚糖三维结构存入蛋白质数据库之前对其进行验证已成为结构解析管道的主要工作。Privateer 软件提供了验证、分析、完善和以图形表示聚糖三维原子结构的综合方法,既可作为配体,也可作为蛋白质修饰物。虽然 Privateer 是免费软件,但它要求用户安装任何支持它的结构生物学软件套件,或从源代码中构建它。这里介绍的 Privateer 网络应用程序始终是最新的,无需安装即可在线使用(https://privateer.york.ac.uk)。这种在用户机器上本地运行的自我更新工具,将使结构生物学家能够通过网络浏览器简单快速地分析碳水化合物配体和蛋白质糖基化,同时将所有机密信息保留在他们的设备上。
{"title":"Online carbohydrate 3D structure validation with the Privateer web app.","authors":"Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Paul S Bond, Filomeno Sánchez Rodríguez, Stuart J McNicholas, Jon Agirre","doi":"10.1107/S2053230X24000359","DOIUrl":"10.1107/S2053230X24000359","url":null,"abstract":"<p><p>Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to date and available to be used online (https://privateer.york.ac.uk) without installation. This self-updating tool, which runs locally on the user's machine, will allow structural biologists to simply and quickly analyse carbohydrate ligands and protein glycosylation from a web browser whilst retaining all confidential information on their devices.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"30-35"},"PeriodicalIF":0.9,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10836424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139541238","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
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-25
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 2","pages":"36-42"},"PeriodicalIF":0.9,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139676785","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
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-24
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 2","pages":"30-35"},"PeriodicalIF":0.9,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139676784","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
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-11
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 1","pages":"22-27"},"PeriodicalIF":0.9,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139435001","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
Biochemical and structural characterization of a class A β-lactamase from Nocardia cyriacigeorgica 来自 Nocardia cyriacigeorgica 的 A 类 β-内酰胺酶的生物化学和结构特征。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-03 DOI: 10.1107/S2053230X23010671
Jérôme Feuillard, Julie Couston, Yvonne Benito, Elisabeth Hodille, Oana Dumitrescu, Mickaël Blaise

Nocardia are Gram-positive bacteria from the Actinobacteria phylum. Some Nocardia species can infect humans and are usually considered to be opportunist pathogens, as they often infect immunocompromised patients. Although their clinical incidence is low, many Nocardia species are now considered to be emerging pathogens. Primary sites of infection by Nocardia are the skin or the lungs, but dissemination to other body parts is very frequent. These disseminated infections are very difficult to treat and thus are tackled with multiple classes of antibiotics, in addition to the traditional treatment targeting the folate pathway. β-Lactams are often included in the regimen, but many Nocardia species present moderate or strong resistance to some members of this drug class. Genomic, microbiological and biochemical studies have reported the presence of class A β-lactamases (ABLs) in a handful of Nocardia species, but no structural investigation of Nocardia β-lactamases has yet been performed. In this study, the expression, purification and preliminary biochemical characterization of an ABL from an N. cyriacigeorgica (NCY-1) clinical strain are reported. The crystallization and the very high resolution crystal structure of NCY-1 are also described. The sequence and structural analysis of the protein demonstrate that NCY-1 belongs to the class A1 β-lactamases and show its very high conservation with ABLs from other human-pathogenic Nocardia. In addition, the presence of one molecule of citrate tightly bound in the catalytic site of the enzyme is described. This structure may provide a solid basis for future drug development to specifically target Nocardia spp. β-lactamases.

诺卡氏菌是放线菌门的革兰氏阳性细菌。一些诺卡氏菌可感染人类,通常被认为是机会性病原体,因为它们经常感染免疫力低下的患者。虽然它们的临床发病率很低,但许多诺卡氏菌现在被认为是新出现的病原体。诺卡氏菌的主要感染部位是皮肤或肺部,但传播到身体其他部位的情况也很常见。这些播散性感染非常难以治疗,因此除了针对叶酸途径的传统治疗方法外,还需要使用多种抗生素。β-内酰胺类药物通常被纳入治疗方案,但许多诺卡氏菌对该类药物的某些成分具有中度或较强的耐药性。基因组学、微生物学和生物化学研究报告称,在少数诺卡氏菌中存在 A 类 β-内酰胺酶(ABLs),但尚未对诺卡氏菌 β-内酰胺酶进行结构研究。本研究报告了一种来自 N. cyriacigeorgica(NCY-1)临床菌株的 ABL 的表达、纯化和初步生化鉴定。研究还描述了 NCY-1 的结晶和高分辨率晶体结构。对该蛋白的序列和结构分析表明,NCY-1 属于 A1 类 β-内酰胺酶,并表明它与其他人类致病性诺卡氏菌的 ABL 有很高的一致性。此外,还描述了在该酶的催化位点存在一分子紧密结合的柠檬酸盐。该结构可为今后开发专门针对诺卡氏菌属β-内酰胺酶的药物奠定坚实的基础。
{"title":"Biochemical and structural characterization of a class A β-lactamase from Nocardia cyriacigeorgica","authors":"Jérôme Feuillard,&nbsp;Julie Couston,&nbsp;Yvonne Benito,&nbsp;Elisabeth Hodille,&nbsp;Oana Dumitrescu,&nbsp;Mickaël Blaise","doi":"10.1107/S2053230X23010671","DOIUrl":"10.1107/S2053230X23010671","url":null,"abstract":"<p><i>Nocardia</i> are Gram-positive bacteria from the Actinobacteria phylum. Some <i>Nocardia</i> species can infect humans and are usually considered to be opportunist pathogens, as they often infect immunocompromised patients. Although their clinical incidence is low, many <i>Nocardia</i> species are now considered to be emerging pathogens. Primary sites of infection by <i>Nocardia</i> are the skin or the lungs, but dissemination to other body parts is very frequent. These disseminated infections are very difficult to treat and thus are tackled with multiple classes of antibiotics, in addition to the traditional treatment targeting the folate pathway. β-Lactams are often included in the regimen, but many <i>Nocardia</i> species present moderate or strong resistance to some members of this drug class. Genomic, microbiological and biochemical studies have reported the presence of class A β-lactamases (ABLs) in a handful of <i>Nocardia</i> species, but no structural investigation of <i>Nocardia</i> β-lactamases has yet been performed. In this study, the expression, purification and preliminary biochemical characterization of an ABL from an <i>N. cyriacigeorgica</i> (NCY-1) clinical strain are reported. The crystallization and the very high resolution crystal structure of NCY-1 are also described. The sequence and structural analysis of the protein demonstrate that NCY-1 belongs to the class A1 β-lactamases and show its very high conservation with ABLs from other human-pathogenic <i>Nocardia</i>. In addition, the presence of one molecule of citrate tightly bound in the catalytic site of the enzyme is described. This structure may provide a solid basis for future drug development to specifically target <i>Nocardia</i> spp. β-lactamases.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 1","pages":"13-21"},"PeriodicalIF":0.9,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139085405","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
High-resolution double vision of the allosteric phosphatase PTP1B. 异位磷酸酶 PTP1B 的高分辨率双重视觉。
IF 1.1 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 DOI: 10.1107/S2053230X23010749
Shivani Sharma, Tamar Skaist Mehlman, Reddy Sudheer Sagabala, Benoit Boivin, Daniel A Keedy

Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments, including diabetes, obesity and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between data sets, including non-isomorphism. Here, the highest resolution crystal structure of apo wild-type (WT) PTP1B to date is presented out of a total of ∼350 PTP1B structures in the PDB. This structure is in a crystal form that is rare for PTP1B, with two unique copies of the protein that exhibit distinct patterns of conformational heterogeneity, allowing a controlled comparison of local disorder across the two chains within the same asymmetric unit. The conformational differences between these chains are interrogated in the apo structure and between several recently reported high-resolution ligand-bound structures. Electron-density maps in a high-resolution structure of a recently reported activating double mutant are also examined, and unmodeled alternate conformations in the mutant structure are discovered that coincide with regions of enhanced conformational heterogeneity in the new WT structure. These results validate the notion that these mutations operate by enhancing local dynamics, and suggest a latent susceptibility to such changes in the WT enzyme. Together, these new data and analysis provide a detailed view of the conformational ensemble of PTP1B and highlight the utility of high-resolution crystallography for elucidating conformational heterogeneity with potential relevance for function.

蛋白酪氨酸磷酸酶 1B(PTP1B)在细胞稳态中发挥着重要作用,是糖尿病、肥胖症和乳腺癌等多种人类疾病的高度有效的治疗靶点。然而,关于构象变化如何通过 PTP1B 的结构传递信息,从而实现配体的异位调节或对突变的功能反应,还有很多问题有待了解。高分辨率 X 射线晶体学可为了解蛋白质构象组合提供独特的窗口,但即使是高分辨率结构的比较也往往因数据集之间的差异(包括非同构性)而变得复杂。在这里,我们展示了迄今为止 PDB 中总计 350 个 PTP1B 结构中分辨率最高的 apo 野生型(WT)PTP1B 晶体结构。该结构采用了 PTP1B 少见的晶体形式,具有两个独特的蛋白质拷贝,它们表现出不同的构象异质性模式,从而可以对同一不对称单元中两条链的局部无序性进行有控制的比较。这些链之间的构象差异是在apo结构和最近报道的几种高分辨率配体结合结构之间进行研究的。此外,还研究了最近报道的活化双突变体高分辨率结构中的电子密度图,发现突变体结构中未建模的替代构象与新 WT 结构中构象异质性增强的区域相吻合。这些结果验证了这些突变通过增强局部动力学来发挥作用的观点,并表明 WT 酶对这种变化具有潜在的敏感性。总之,这些新数据和分析提供了 PTP1B 构象组合的详细视图,并突出了高分辨率晶体学在阐明与功能潜在相关的构象异质性方面的效用。
{"title":"High-resolution double vision of the allosteric phosphatase PTP1B.","authors":"Shivani Sharma, Tamar Skaist Mehlman, Reddy Sudheer Sagabala, Benoit Boivin, Daniel A Keedy","doi":"10.1107/S2053230X23010749","DOIUrl":"10.1107/S2053230X23010749","url":null,"abstract":"<p><p>Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments, including diabetes, obesity and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between data sets, including non-isomorphism. Here, the highest resolution crystal structure of apo wild-type (WT) PTP1B to date is presented out of a total of ∼350 PTP1B structures in the PDB. This structure is in a crystal form that is rare for PTP1B, with two unique copies of the protein that exhibit distinct patterns of conformational heterogeneity, allowing a controlled comparison of local disorder across the two chains within the same asymmetric unit. The conformational differences between these chains are interrogated in the apo structure and between several recently reported high-resolution ligand-bound structures. Electron-density maps in a high-resolution structure of a recently reported activating double mutant are also examined, and unmodeled alternate conformations in the mutant structure are discovered that coincide with regions of enhanced conformational heterogeneity in the new WT structure. These results validate the notion that these mutations operate by enhancing local dynamics, and suggest a latent susceptibility to such changes in the WT enzyme. Together, these new data and analysis provide a detailed view of the conformational ensemble of PTP1B and highlight the utility of high-resolution crystallography for elucidating conformational heterogeneity with potential relevance for function.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"1-12"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138827635","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 outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae. 侵袭性病原体肺炎克雷伯氏菌外膜孔蛋白 OmpW 的结构。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 DOI: 10.1107/S2053230X23010579
Chloe Seddon, Gad Frankel, Konstantinos Beis

Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraNα in the donor and OmpW in the recipient. Here, the crystal structure of K. pneumoniae OmpW (OmpWKP) is reported at 3.2 Å resolution. OmpWKP forms an eight-stranded β-barrel flanked by extracellular loops. The structures of E. coli OmpW (OmpWEC) and OmpWKP show high conservation despite sequence variability in the extracellular loops.

共轭是质粒(包括携带抗生素基因的质粒)从一种细菌(供体)转移到另一种细菌(受体)的过程。类 IncF 质粒的共轭效率依赖于供体(质粒编码的 TraN 异构体)和受体细菌的外膜蛋白之间通过亲密的相互作用形成配对稳定。R100-1 质粒与大肠埃希菌和肺炎克雷伯菌(KP)受体的共轭依赖于供体中质粒编码的 TraNα 与受体中的 OmpW 之间的配对。本文以 3.2 Å 的分辨率报告了肺炎克雷伯菌 OmpW(OmpWKP)的晶体结构。OmpWKP 形成一个八链的 β 管,两侧有胞外环。大肠杆菌 OmpW(OmpWEC)和 OmpWKP 的结构显示出高度的一致性,尽管胞外环的序列存在变异。
{"title":"Structure of the outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae.","authors":"Chloe Seddon, Gad Frankel, Konstantinos Beis","doi":"10.1107/S2053230X23010579","DOIUrl":"10.1107/S2053230X23010579","url":null,"abstract":"<p><p>Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraNα in the donor and OmpW in the recipient. Here, the crystal structure of K. pneumoniae OmpW (OmpW<sub>KP</sub>) is reported at 3.2 Å resolution. OmpW<sub>KP</sub> forms an eight-stranded β-barrel flanked by extracellular loops. The structures of E. coli OmpW (OmpW<sub>EC</sub>) and OmpW<sub>KP</sub> show high conservation despite sequence variability in the extracellular loops.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 Pt 1","pages":"22-27"},"PeriodicalIF":0.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139416013","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
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-12-22
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 1","pages":"1-12"},"PeriodicalIF":0.9,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139435110","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
Direct relationship between dimeric form and activity in the acidic copper–zinc superoxide dismutase from lemon 柠檬中酸性铜锌超氧化物歧化酶的二聚体形式与活性之间的直接关系
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-12-18 DOI: 10.1107/S2053230X23010646
Ratna A. Utami, Hiromi Yoshida, Lydia H. Kartadinata, Virgi A. Abdillah, Cut R. Faratilla, Debbie S. Retnoningrum, Wangsa T. Ismaya

The copper–zinc superoxide dismutase (CuZnSOD) from lemon (SOD_CL) is active in an acidic environment and resists proteolytic degradation. The enzyme occurs as a dimer, which has an indirect effect on the enzyme activity as the monomer retains only ∼35% of the activity. Here, the crystal structure of SOD_CL at 1.86 Å resolution is reported that may explain this peculiarity. The crystal belonged to space group P21, with unit-cell parameters a = 61.11, b = 74.55, c = 61.69 Å, β = 106.86°, and contained four molecules in the asymmetric unit. The overall structure of SOD_CL resembles that of CuZnSOD from plants. The structure of SOD_CL shows a unique arrangement of surface loop IV that connects the dimer interface and the active site, which is located away from the dimer-interface region. This arrangement allows direct interaction between the residues residing in the dimer interface and those in the active site. The arrangement also includes Leu62 and Gln164, which are conserved in cytoplasmic CuZnSOD. This supports the classification of SOD_CL as a cytoplasmic CuZnSOD despite sharing the highest amino-acid sequence homology with CuZnSODs from spinach and tomato, which are chloroplastic.

柠檬中的铜锌超氧化物歧化酶(CuZnSOD)(SOD_CL)在酸性环境中具有活性,并能抵抗蛋白水解。该酶以二聚体形式存在,由于单体只保留了 ∼ 35% 的活性,因此间接影响了酶的活性。本文报告了分辨率为 1.86 Å 的 SOD_CL 晶体结构,或许可以解释这种特殊性。该晶体属于空间群 P21,单位晶胞参数为 a = 61.11,b = 74.55,c = 61.69 Å,β = 106.86°,不对称单元中包含四个分子。SOD_CL 的整体结构与植物中的 CuZnSOD 相似。SOD_CL 的结构显示了连接二聚体界面和活性位点的表面环 IV 的独特排列,而活性位点位于远离二聚体界面的区域。这种排列方式使得二聚体界面上的残基与活性位点上的残基能够直接相互作用。这种排列还包括在细胞质 CuZnSOD 中保守的 Leu62 和 Gln164。这支持将 SOD_CL 归类为细胞质 CuZnSOD,尽管它与菠菜和番茄中的 CuZnSOD 具有最高的氨基酸序列同源性,而后者是叶绿体 CuZnSOD。
{"title":"Direct relationship between dimeric form and activity in the acidic copper–zinc superoxide dismutase from lemon","authors":"Ratna A. Utami,&nbsp;Hiromi Yoshida,&nbsp;Lydia H. Kartadinata,&nbsp;Virgi A. Abdillah,&nbsp;Cut R. Faratilla,&nbsp;Debbie S. Retnoningrum,&nbsp;Wangsa T. Ismaya","doi":"10.1107/S2053230X23010646","DOIUrl":"10.1107/S2053230X23010646","url":null,"abstract":"<p>The copper–zinc superoxide dismutase (CuZnSOD) from lemon (SOD_CL) is active in an acidic environment and resists proteolytic degradation. The enzyme occurs as a dimer, which has an indirect effect on the enzyme activity as the monomer retains only ∼35% of the activity. Here, the crystal structure of SOD_CL at 1.86 Å resolution is reported that may explain this peculiarity. The crystal belonged to space group <i>P</i>2<sub>1</sub>, with unit-cell parameters <i>a</i> = 61.11, <i>b</i> = 74.55, <i>c</i> = 61.69 Å, β = 106.86°, and contained four molecules in the asymmetric unit. The overall structure of SOD_CL resembles that of CuZnSOD from plants. The structure of SOD_CL shows a unique arrangement of surface loop IV that connects the dimer interface and the active site, which is located away from the dimer-interface region. This arrangement allows direct interaction between the residues residing in the dimer interface and those in the active site. The arrangement also includes Leu62 and Gln164, which are conserved in cytoplasmic CuZnSOD. This supports the classification of SOD_CL as a cytoplasmic CuZnSOD despite sharing the highest amino-acid sequence homology with CuZnSODs from spinach and tomato, which are chloroplastic.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 12","pages":"301-307"},"PeriodicalIF":0.9,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138717613","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
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-12-18
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"79 12","pages":"295-300"},"PeriodicalIF":0.9,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139042002","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
期刊
Acta crystallographica. Section F, Structural biology communications
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1