Acta Crystallographica Section F-structural Biology and Crystallization Communications最新文献_第8页

Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7 Å resolution. 在1.7 Å分辨率下，雪梨纤维蛋白与天然结合的s -腺苷- l-蛋氨酸复合物的结构。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-08-01 Epub Date: 2012-07-26 DOI: 10.1107/S1744309112026528

Udesh de Silva, Zhaoli Zhou, Bernard A Brown

{"title":"Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7 Å resolution.","authors":"Udesh de Silva, Zhaoli Zhou, Bernard A Brown","doi":"10.1107/S1744309112026528","DOIUrl":"https://doi.org/10.1107/S1744309112026528","url":null,"abstract":"Fibrillarin is the key methyltransferase associated with the C/D class of small nuclear ribonucleoproteins (snRNPs) and participates in the preliminary step of pre-ribosomal rRNA processing. This molecule is found in the fibrillar regions of the eukaryotic nucleolus and is involved in methylation of the 2'-O atom of ribose in rRNA. Human fibrillarin contains an N-terminal GAR domain, a central RNA-binding domain comprising an RNP-2-like superfamily consensus sequence and a catalytic C-terminal helical domain. Here, Aeropyrum pernix fibrillarin is described, which is homologous to the C-terminal domain of human fibrillarin. The protein was crystallized with an S-adenosyl-L-methionine (SAM) ligand bound in the active site. The molecular structure of this complex was solved using X-ray crystallography at a resolution of 1.7 Å using molecular replacement with fibrillarin structural homologs. The structure shows the atomic details of SAM and its active-site interactions; there are a number of conserved residues that interact directly with the cofactor. Notably, the adenine ring of SAM is stabilized by π-π interactions with the conserved residue Phe110 and by electrostatic interactions with the Asp134, Ala135 and Gln157 residues. The π-π interaction appears to play a critical role in stabilizing the association of SAM with fibrillarin. Furthermore, comparison of A. pernix fibrillarin with homologous structures revealed different orientations of Phe110 and changes in α-helix 6 of fibrillarin and suggests key differences in its interactions with the adenine ring of SAM in the active site and with the C/D RNA. These differences may play a key role in orienting the SAM ligand for catalysis as well as in the assembly of other ribonucleoproteins and in the interactions with C/D RNA.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"68 Pt 8","pages":"854-9"},"PeriodicalIF":0.9,"publicationDate":"2012-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1744309112026528","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30815444","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: 5

Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor. Pim-1 激酶 P 环的灵活性：观察与抑制剂相互作用诱导的新构象。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-08-01 Epub Date: 2012-07-31 DOI: 10.1107/S1744309112027108

Lorien J Parker, Hisami Watanabe, Keiko Tsuganezawa, Yuri Tomabechi, Noriko Handa, Mikako Shirouzu, Hitomi Yuki, Teruki Honma, Naoko Ogawa, Tetsuo Nagano, Shigeyuki Yokoyama, Akiko Tanaka

{"title":"Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor.","authors":"Lorien J Parker, Hisami Watanabe, Keiko Tsuganezawa, Yuri Tomabechi, Noriko Handa, Mikako Shirouzu, Hitomi Yuki, Teruki Honma, Naoko Ogawa, Tetsuo Nagano, Shigeyuki Yokoyama, Akiko Tanaka","doi":"10.1107/S1744309112027108","DOIUrl":"10.1107/S1744309112027108","url":null,"abstract":"The serine/threonine kinase Pim-1 is emerging as a promising target for cancer therapeutics. Much attention has recently been focused on identifying potential Pim-1 inhibitor candidates for the treatment of haematopoietic malignancies. The outcome of a rational drug-design project has recently been reported [Nakano et al. (2012), J. Med. Chem. 55, 5151-5156]. The report described the process of optimization of the structure-activity relationship and detailed from a medicinal chemistry perspective the development of a low-potency and nonselective compound initially identified from in silico screening into a potent, selective and metabolically stable Pim-1 inhibitor. Here, the structures of the initial in silico hits are reported and the noteworthy features of the Pim-1 complex structures are described. A particular focus was placed on the rearrangement of the glycine-rich P-loop region that was observed for one of the initial compounds, (Z)-7-(azepan-1-ylmethyl)-2-[(1H-indol-3-yl)methylidene]-6-hydroxy-1-benzofuran-3(2H)-one (compound 1), and was also found in all further derivatives. This novel P-loop conformation, which appears to be stabilized by an additional interaction with the β3 strand located above the binding site, is not usually observed in Pim-1 structures.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"68 Pt 8","pages":"860-6"},"PeriodicalIF":0.9,"publicationDate":"2012-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412761/pdf/f-68-00860.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30815445","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 a fluorescent protein from Aequorea victoria bearing the obligate-monomer mutation A206K. 带有强制性单体突变 A206K 的 Aequorea victoria 荧光蛋白的结构。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-08-01 Epub Date: 2012-07-26 DOI: 10.1107/S1744309112028667

David von Stetten, Marjolaine Noirclerc-Savoye, Joachim Goedhart, Theodorus W J Gadella, Antoine Royant

{"title":"Structure of a fluorescent protein from Aequorea victoria bearing the obligate-monomer mutation A206K.","authors":"David von Stetten, Marjolaine Noirclerc-Savoye, Joachim Goedhart, Theodorus W J Gadella, Antoine Royant","doi":"10.1107/S1744309112028667","DOIUrl":"10.1107/S1744309112028667","url":null,"abstract":"The green fluorescent protein (GFP) from the jellyfish Aequoria victoria has been shown to dimerize at high concentrations, which could lead to artefacts in imaging experiments. To ensure a truly monomeric state, an A206K mutation has been introduced into most of its widely used variants, with minimal effect on the spectroscopic properties. Here, the first structure of one of these variants, the cyan fluorescent protein mTurquoise, is presented and compared with that of its dimeric version mTurquoise-K206A. No significant structural change is detected in the chromophore cavity, reinforcing the notion that this mutation is spectroscopically silent and validating that the structural analysis performed on dimeric mutants also applies to monomeric versions. Finally, it is explained why cyan versions of GFP containing the Y66W and N146I mutations do not require the A206K mutation to prevent dimerization at high concentrations.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"68 Pt 8","pages":"878-82"},"PeriodicalIF":0.9,"publicationDate":"2012-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3412764/pdf/f-68-00878.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30814865","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

Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6. 一种新型嗜热氢杆菌TK-6磷酸丝氨酸磷酸酶的结晶和初步x射线衍射分析。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-08-01 Epub Date: 2012-07-31 DOI: 10.1107/S1744309112025213

Yoko Chiba, Shoichiro Horita, Jun Ohtsuka, Hiroyuki Arai, Koji Nagata, Yasuo Igarashi, Masaru Tanokura, Masaharu Ishii

{"title":"Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6.","authors":"Yoko Chiba, Shoichiro Horita, Jun Ohtsuka, Hiroyuki Arai, Koji Nagata, Yasuo Igarashi, Masaru Tanokura, Masaharu Ishii","doi":"10.1107/S1744309112025213","DOIUrl":"https://doi.org/10.1107/S1744309112025213","url":null,"abstract":"Two novel-type phosphoserine phosphatases (PSPs) with unique substrate specificity from the thermophilic and hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6 have previously been identified. Here, one of the PSPs (iPSP1) was heterologously expressed in Escherichia coli, purified and crystallized. Diffraction-quality crystals were obtained by the sitting-drop vapour-diffusion method using PEG 4000 as the precipitant. Two diffraction data sets with resolution ranges of 45.0-2.50 and 45.0-1.50 Å were collected from a single crystal and were merged to give a highly complete data set. The space group of the crystal was identified as primitive orthorhombic P2(1)2(1)2(1), with unit-cell parameters a = 49.8, b = 73.6, c = 124.3 Å. The calculated Matthews coefficient (V(M) = 2.32 Å(3) Da(-1)) indicated that the crystal contained one iPSP1 complex per asymmetric unit.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"68 Pt 8","pages":"911-3"},"PeriodicalIF":0.9,"publicationDate":"2012-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1744309112025213","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30815942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Structure of human Rack1 protein at a resolution of 2.45 Å. 分辨率为 2.45 Å 的人类 Rack1 蛋白结构。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-08-01 Epub Date: 2012-07-26 DOI: 10.1107/S1744309112027480

David Ruiz Carrillo, Ramya Chandrasekaran, Martina Nilsson, Tobias Cornvik, Chong Wai Liew, Suet Mien Tan, Julien Lescar

引用次数: 0

Two crystal forms of a helix-rich fatty acid- and retinol-binding protein, Na-FAR-1, from the parasitic nematode Necator americanus. 寄生线虫 Necator americanus 中富含螺旋的脂肪酸和视黄醇结合蛋白 Na-FAR-1 的两种晶体形态。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-07-01 Epub Date: 2012-06-28 DOI: 10.1107/S1744309112023597

Mads Gabrielsen, M Florencia Rey-Burusco, Kate Griffiths, Andrew J Roe, Alan Cooper, Brian O Smith, Malcolm W Kennedy, Betina Corsico

引用次数: 0

Structure of Leishmania major cysteine synthase. 利什曼原虫主要半胱氨酸合酶的结构。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-07-01 Epub Date: 2012-06-22 DOI: 10.1107/S1744309112019124

Paul K Fyfe, Gareth D Westrop, Tania Ramos, Sylke Müller, Graham H Coombs, William N Hunter

{"title":"Structure of Leishmania major cysteine synthase.","authors":"Paul K Fyfe, Gareth D Westrop, Tania Ramos, Sylke Müller, Graham H Coombs, William N Hunter","doi":"10.1107/S1744309112019124","DOIUrl":"https://doi.org/10.1107/S1744309112019124","url":null,"abstract":"Cysteine biosynthesis is a potential target for drug development against parasitic Leishmania species; these protozoa are responsible for a range of serious diseases. To improve understanding of this aspect of Leishmania biology, a crystallographic and biochemical study of L. major cysteine synthase has been undertaken, seeking to understand its structure, enzyme activity and modes of inhibition. Active enzyme was purified, assayed and crystallized in an orthorhombic form with a dimer in the asymmetric unit. Diffraction data extending to 1.8 Å resolution were measured and the structure was solved by molecular replacement. A fragment of γ-poly-D-glutamic acid, a constituent of the crystallization mixture, was bound in the enzyme active site. Although a D-glutamate tetrapeptide had insignificant inhibitory activity, the enzyme was competitively inhibited (K(i) = 4 µM) by DYVI, a peptide based on the C-terminus of the partner serine acetyltransferase with which the enzyme forms a complex. The structure surprisingly revealed that the cofactor pyridoxal phosphate had been lost during crystallization.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"68 Pt 7","pages":"738-43"},"PeriodicalIF":0.9,"publicationDate":"2012-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1744309112019124","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30731651","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: 17

Crystallization of SHARPIN using an automated two-dimensional grid screen for optimization. 利用自动二维网格筛对 SHARPIN 结晶进行优化。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-07-01 Epub Date: 2012-06-28 DOI: 10.1107/S1744309112022208

Benjamin Stieglitz, Katrin Rittinger, Lesley F Haire

引用次数: 0

Expression, purification, crystallization and preliminary X-ray diffraction analysis of the apo form of InsP5 2-K from Arabidopsis thaliana. 拟南芥中 InsP5 2-K 的表达、纯化、结晶和初步 X 射线衍射分析。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-06-01 Epub Date: 2012-05-23 DOI: 10.1107/S1744309112017307

Jose Ignacio Baños-Sanz, Julia Sanz-Aparicio, Charles A Brearley, Beatriz González

{"title":"Expression, purification, crystallization and preliminary X-ray diffraction analysis of the apo form of InsP5 2-K from Arabidopsis thaliana.","authors":"Jose Ignacio Baños-Sanz, Julia Sanz-Aparicio, Charles A Brearley, Beatriz González","doi":"10.1107/S1744309112017307","DOIUrl":"10.1107/S1744309112017307","url":null,"abstract":"Inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IP(5) 2-K) is a key enzyme that catalyzes the synthesis of phytic acid (IP(6)) from inositol 1,3,4,5,6-pentakisphosphate (IP(5)) and ATP. The first structure of IP(5) 2-K, that from Arabidopsis thaliana, has been solved previously; it only crystallized in the presence of inositol, either the substrate IP(5) or the product IP(6), and failed to crystallize in its free state (without inositol). Based on structural analysis, a point mutation of IP(5) 2-K (W129A) has been produced in order to overcome this limitation and obtain information about protein conformational changes upon substrate binding. Here, the production and crystallization of W129A IP(5) 2-K in its free state and with bound nucleotide is described. These crystals differed from the native crystals and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 66.00, b = 68.23, c = 105.80 Å and a = 63.06, b = 71.80, c = 100.23 Å, respectively. The crystals diffracted to resolutions of 2.22 Å (apo) and 2.05 Å (nucleotide bound) using synchrotron radiation and contained one molecule per asymmetric unit. The structures have been determined using the molecular-replacement method and refinement is being undertaken.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":" ","pages":"701-4"},"PeriodicalIF":0.9,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370915/pdf/f-68-00701.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30679383","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

Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of a cyclophilin A-like protein from Piriformospora indica. 从 Piriformospora indica 中克隆、纯化、结晶和初步 X 射线晶体学分析一种类似于 cyclophilin A 的蛋白质。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-06-01 Epub Date: 2012-05-24 DOI: 10.1107/S1744309112018131

Harshesh Bhatt, Dipesh Kumar Trivedi, Ravi Kant Pal, Atul Kumar Johri, Narendra Tuteja, Neel Sarovar Bhavesh

引用次数: 0