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

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Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B 人类磷酸酶PTP1B的室温系列同步加速器结晶学
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-12-20 DOI: 10.1107/S2053230X22011645
Shivani Sharma, Ali Ebrahim, Daniel A. Keedy
{"title":"Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B","authors":"Shivani Sharma,&nbsp;Ali Ebrahim,&nbsp;Daniel A. Keedy","doi":"10.1107/S2053230X22011645","DOIUrl":"10.1107/S2053230X22011645","url":null,"abstract":"<p>Room-temperature X-ray crystallography provides unique insights into protein conformational heterogeneity, but obtaining sufficiently large protein crystals is a common hurdle. Serial synchrotron crystallography (SSX) helps to address this hurdle by allowing the use of many medium- to small-sized crystals. Here, a recently introduced serial sample-support chip system has been used to obtain the first SSX structure of a human phosphatase, specifically protein tyrosine phosphatase 1B (PTP1B) in the unliganded (apo) state. In previous apo room-temperature structures, the active site and allosteric sites adopted alternate conformations, including open and closed conformations of the active-site WPD loop and of a distal allosteric site. By contrast, in our SSX structure the active site is best fitted with a single conformation, but the distal allosteric site is best fitted with alternate conformations. This observation argues for additional nuance in interpreting the nature of allosteric coupling in this protein. Overall, our results illustrate the promise of serial methods for room-temperature crystallography, as well as future avant-garde crystallography experiments, for PTP1B and other proteins.</p>","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://www.ncbi.nlm.nih.gov/pmc/articles/PMC9813971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9751918","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: 2
The structure of a tautomerase superfamily member linked to the type VI secretion system of Acinetobacter baumannii 与鲍曼不动杆菌VI型分泌系统相关的一个互变酶超家族成员的结构
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-12-08 DOI: 10.1107/S2053230X22011414
Genady Pankov, Gabriela Mol Avelar, Grant Buchanan, Sarah J. Coulthurst, William N. Hunter
{"title":"The structure of a tautomerase superfamily member linked to the type VI secretion system of Acinetobacter baumannii","authors":"Genady Pankov,&nbsp;Gabriela Mol Avelar,&nbsp;Grant Buchanan,&nbsp;Sarah J. Coulthurst,&nbsp;William N. Hunter","doi":"10.1107/S2053230X22011414","DOIUrl":"10.1107/S2053230X22011414","url":null,"abstract":"<p>Bacteria exploit specialized secretion systems to assist in competition for resources, in collaboration and in communication. Here, a protocol for the recombinant production, purification and crystallization of a protein linked to the <i>Acinetobacter baumannii</i> type VI secretion system is provided. A high-resolution structure of this trimeric protein is reported, revealing the characteristic dual β–α–β subunit fold typical of longer subunit members of the tautomerase superfamily. The protein does not appear to be toxic to bacteria or yeast under the conditions tested. The possible biological role of this protein is discussed.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X22011414","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10559214","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
Relating protein crystal structure to ligand-binding thermodynamics. 将蛋白质晶体结构与配体结合热力学联系起来。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-12-01 DOI: 10.1107/S2053230X22011244
John R Helliwell
{"title":"Relating protein crystal structure to ligand-binding thermodynamics.","authors":"John R Helliwell","doi":"10.1107/S2053230X22011244","DOIUrl":"https://doi.org/10.1107/S2053230X22011244","url":null,"abstract":"<p><p>An important interface between biophysical chemistry and biological crystal structures involves whether it is possible to relate experimental calorimetry measurements of protein ligand binding to 3D structures. This has proved to be challenging. The probes of the structure of matter, namely X-rays, neutrons and electrons, have challenges of one type or another in their use. This article focuses on saccharide binding to lectins as a theme, yet after 25 years or so it is still a work in progress to connect 3D structure to binding energies. Whilst this study involved one type of protein (lectins) and one class of ligand (monosaccharides), i.e. it was specific, it was of general importance, as measured for instance by its wide impact. The impetus for writing this update now, as a Scientific Comment, is that a breakthrough in neutron crystal structure determinations of saccharide-bound lectins has been achieved. It is suggested here that this new research from neutron protein crystallography could improve, i.e. reduce, the errors in the estimated binding energies.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9716570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10694627","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
The structure of His-tagged Geobacillus stearothermophilus purine nucleoside phosphorylase reveals a `spanner in the works'. his标记的嗜脂嗜热地杆菌嘌呤核苷磷酸化酶的结构揭示了一个“工作中的扳手”。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-12-01 DOI: 10.1107/S2053230X22011025
Fiona M Given, Fuchsia Moran, Ashleigh S Johns, James A Titterington, Timothy M Allison, Deborah L Crittenden, Jodie M Johnston
{"title":"The structure of His-tagged Geobacillus stearothermophilus purine nucleoside phosphorylase reveals a `spanner in the works'.","authors":"Fiona M Given,&nbsp;Fuchsia Moran,&nbsp;Ashleigh S Johns,&nbsp;James A Titterington,&nbsp;Timothy M Allison,&nbsp;Deborah L Crittenden,&nbsp;Jodie M Johnston","doi":"10.1107/S2053230X22011025","DOIUrl":"https://doi.org/10.1107/S2053230X22011025","url":null,"abstract":"<p><p>The 1.72 Å resolution structure of purine nucleoside phosphorylase from Geobacillus stearothermophilus, a thermostable protein of potential interest for the biocatalytic synthesis of antiviral nucleoside compounds, is reported. The structure of the N-terminally His-tagged enzyme is a hexamer, as is typical of bacterial homologues, with a trimer-of-dimers arrangement. Unexpectedly, several residues of the recombinant tobacco etch virus protease (rTEV) cleavage site from the N-terminal tag are located in the active site of the neighbouring subunit in the dimer. Key to this interaction is a tyrosine residue, which sits where the nucleoside ring of the substrate would normally be located. Tag binding appears to be driven by a combination of enthalpic, entropic and proximity effects, which convey a particularly high affinity in the crystallized form. Attempts to cleave the tag in solution yielded only a small fraction of untagged protein, suggesting that the enzyme predominantly exists in the tag-bound form in solution, preventing rTEV from accessing the cleavage site. However, the tagged protein retained some activity in solution, suggesting that the tag does not completely block the active site, but may act as a competitive inhibitor. This serves as a warning that it is prudent to establish how affinity tags may affect protein structure and function, especially for industrial biocatalytic applications that rely on the efficiency and convenience of one-pot purifications and in cases where tag removal is difficult.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9716568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10694625","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 Sphingobacterium multivorum serine palmitoyltransferase complexed with tris(hydroxymethyl)aminomethane 多涡鞘菌丝氨酸棕榈酰转移酶与三(羟甲基)氨基甲烷络合的晶体结构
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-11-28 DOI: 10.1107/S2053230X22010937
Hiroko Ikushiro, Aya Takahashi, Taiki Murakami, Asuka Katayama, Taiki Sawai, Haruna Goto, Ikuko Miyahara, Nobuo Kamiya, Takato Yano
{"title":"Crystal structure of Sphingobacterium multivorum serine palmitoyltransferase complexed with tris(hydroxymethyl)aminomethane","authors":"Hiroko Ikushiro,&nbsp;Aya Takahashi,&nbsp;Taiki Murakami,&nbsp;Asuka Katayama,&nbsp;Taiki Sawai,&nbsp;Haruna Goto,&nbsp;Ikuko Miyahara,&nbsp;Nobuo Kamiya,&nbsp;Takato Yano","doi":"10.1107/S2053230X22010937","DOIUrl":"10.1107/S2053230X22010937","url":null,"abstract":"<p>Serine palmitoyltransferase (SPT) catalyses the first reaction in sphingolipid biosynthesis: the decarboxylative condensation of <span>l</span>-serine (<span>l</span>-Ser) and palmitoyl-CoA to form 3-ketodihydrosphingosine. SPT from <i>Sphingobacterium multivorum</i> has been isolated and its crystal structure in complex with <span>l</span>-Ser has been determined at 2.3 Å resolution (PDB entry 3a2b). However, the quality of the crystal was not good enough to judge the conformation of the cofactor molecule and the orientations of the side chains of the amino-acid residues in the enzyme active site. The crystal quality was improved by revision of the purification procedure and by optimization of both the crystallization procedure and the post-crystallization treatment conditions. Here, the crystal structure of SPT complexed with tris(hydroxymethyl)aminomethane (Tris), a buffer component, was determined at 1.65 Å resolution. The protein crystallized at 20°C and diffraction data were collected from the crystals to a resolution of 1.65 Å. The crystal belonged to the tetragonal space group <i>P</i>4<sub>1</sub>2<sub>1</sub>2, with unit-cell parameters <i>a</i> = <i>b</i> = 61.32, <i>c</i> = 208.57 Å. Analysis of the crystal structure revealed C4—C5—C5A—O4P (77°) and C5—C5A—O4P—P (–143°) torsion angles in the phosphate-group moiety of the cofactor pyridoxal 5′-phosphate (PLP) that are more reasonable than those observed in the previously reported crystal structure (14° and 151°, respectively). Furthermore, the clear electron density showing a Schiff-base linkage between PLP and the bulky artificial ligand Tris indicated exceptional flexibility of the active-site cavity of this enzyme. These findings open up the possibility for further study of the detailed mechanisms of substrate recognition and catalysis by this enzyme.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10694624","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
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-11-28
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"137719904","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
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-11-28
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"137719905","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
Crystals of SctV from different species reveal variable symmetry for the cytosolic domain of the type III secretion system export gate. 来自不同物种的 SctV 晶体显示，III 型分泌系统出口门的胞浆结构域具有不同的对称性。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-11-01 DOI: 10.1107/S2053230X22009736
Dominic Gilzer, Eileen Baum, Nele Lieske, Julia L Kowal, Hartmut H Niemann
{"title":"Crystals of SctV from different species reveal variable symmetry for the cytosolic domain of the type III secretion system export gate.","authors":"Dominic Gilzer,&nbsp;Eileen Baum,&nbsp;Nele Lieske,&nbsp;Julia L Kowal,&nbsp;Hartmut H Niemann","doi":"10.1107/S2053230X22009736","DOIUrl":"https://doi.org/10.1107/S2053230X22009736","url":null,"abstract":"<p><p>Type III secretion systems (T3SSs) are proteinaceous devices employed by Gram-negative bacteria to directly transport proteins into a host cell. Substrate recognition and secretion are strictly regulated by the export apparatus of the so-called injectisome. The export gate SctV engages chaperone-bound substrates of the T3SS in its nonameric cytoplasmic domain. Here, the purification and crystallization of the cytoplasmic domains of SctV from Photorhabdus luminescens (LscV<sub>C</sub>) and Aeromonas hydrophila (AscV<sub>C</sub>) are reported. Self-rotation functions revealed that LscV<sub>C</sub> forms oligomers with either eightfold or ninefold symmetry in two different crystal forms. Similarly, AscV<sub>C</sub> was found to exhibit tenfold rotational symmetry. These are the first instances of SctV proteins forming non-nonameric oligomers.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9629515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10493068","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 capsular polysaccharide-synthesis enzyme CapG from Staphylococcus aureus 金黄色葡萄球菌荚膜多糖合成酶CapG的晶体结构
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-10-14 DOI: 10.1107/S2053230X22008743
Ni Tien, Chien-Yi Ho, Shu-Jung Lai, Yu-Chuan Lin, Chia-Shin Yang, Yu-Chuan Wang, Wei-Chien Huang, Yeh Chen, Jui-Jen Chang
{"title":"Crystal structure of the capsular polysaccharide-synthesis enzyme CapG from Staphylococcus aureus","authors":"Ni Tien,&nbsp;Chien-Yi Ho,&nbsp;Shu-Jung Lai,&nbsp;Yu-Chuan Lin,&nbsp;Chia-Shin Yang,&nbsp;Yu-Chuan Wang,&nbsp;Wei-Chien Huang,&nbsp;Yeh Chen,&nbsp;Jui-Jen Chang","doi":"10.1107/S2053230X22008743","DOIUrl":"10.1107/S2053230X22008743","url":null,"abstract":"<p>Bacterial capsular polysaccharides provide protection against environmental stress and immune evasion from the host immune system, and are therefore considered to be attractive therapeutic targets for the development of anti-infectious reagents. Here, we focused on CapG, one of the key enzymes in the synthesis pathway of capsular polysaccharides type 5 (CP5) from the opportunistic pathogen <i>Staphylococcus aureus</i>. <i>Sa</i>CapG catalyses the 2-epimerization of UDP-<i>N</i>-acetyl-<span>d</span>-talosamine (UDP-TalNAc) to UDP-<i>N</i>-acetyl-<span>d</span>-fucosamine (UDP-FucNAc), which is one of the nucleotide-activated precursors for the synthesis of the trisaccharide repeating units of CP5. Here, the cloning, expression and purification of recombinant <i>Sa</i>CapG are reported. After extensive efforts, single crystals of <i>Sa</i>CapG were successfully obtained which belonged to space group <i>C</i>2 and exhibited unit-cell parameters <i>a</i> = 302.91, <i>b</i> = 84.34, <i>c</i> = 145.09 Å, β = 110.65°. The structure was solved by molecular replacement and was refined to 3.2 Å resolution. The asymmetric unit revealed a homohexameric assembly of <i>Sa</i>CapG, which was consistent with gel-filtration analysis. Structural comparison with UDP-<i>N</i>-acetyl-<span>d</span>-glucosamine 2-epimerase from <i>Methanocaldococcus jannaschii</i> identified α2, the α2–α3 loop and α10 as a gate-regulated switch controlling substrate entry and/or product release.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10543567","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
Ibuprofen: a weak inhibitor of carbonic anhydrase II 布洛芬:碳酸酐酶II的弱抑制剂
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2022-10-14 DOI: 10.1107/S2053230X22009761
Jacob Combs, Jacob Andring, Robert McKenna
{"title":"Ibuprofen: a weak inhibitor of carbonic anhydrase II","authors":"Jacob Combs,&nbsp;Jacob Andring,&nbsp;Robert McKenna","doi":"10.1107/S2053230X22009761","DOIUrl":"10.1107/S2053230X22009761","url":null,"abstract":"<p>Carbonic anhydrases (CAs) are drug targets for a variety of diseases. While many clinically relevant CA inhibitors are sulfonamide-based, novel CA inhibitors are being developed that incorporate alternative zinc-binding groups, such as carboxylic acid moieties, to develop CA isoform-specific inhibitors. Here, the X-ray crystal structure of human CA II (hCA II) in complex with the carboxylic acid ibuprofen [2-(4-isobutylphenyl)propanoic acid, a common over-the-counter nonsteroidal anti-inflammatory drug] is reported to 1.54 Å resolution. The binding of ibuprofen is overlaid with the structures of other carboxylic acids in complex with hCA II to compare their inhibition mechanisms by direct or indirect (via a water) binding to the active-site zinc. Additionally, enzyme-inhibition assays using ibuprofen, nicotinic acid and ferulic acid were performed with hCA II to determine their IC<sub>50</sub> values and were compared with those of other carboxylic acid binders. This study discusses the potential development of CA inhibitors utilizing the carboxylic acid moiety.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10493071","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
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