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

{"title":"Serendipitous crystal structure of mJuniper, a rationally designed cyan fluorescent protein","authors":"Alpay Aydin,&nbsp;Nathan Fraikin,&nbsp;Priscillia Lagoutte,&nbsp;Christian Lesterlin,&nbsp;Laurent Terradot","doi":"10.1107/S2053230X26009052","DOIUrl":"10.1107/S2053230X26009052","url":null,"abstract":"<p>mJuniper is a recently developed monomeric cyan fluorescent protein (CFP) optimized for bacterial imaging, distinguished by the fastest maturation kinetics recorded for a CFP. mJuniper shows significant promise for time-lapse microscopy, but was used here to improve the solubility of a target protein. Here, we report the high-resolution X-ray structure of mJuniper, obtained serendipitously during an attempted structural characterization of CagG, an essential component of the <i>Helicobacter pylori</i> Cag type IV secretion system. The structure reveals a classical β-barrel scaffold, as well as a chromophore with two rotameric states, resulting from specific radiation damage occurring in its vicinity.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 10","pages":"356-361"},"PeriodicalIF":1.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148987814","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}

{"title":"Structure of recombinant Thermoascus aurantiacus xylanase TaXyn10 with an authentic N-terminal pyroglutamate.","authors":"Jelena Mijatovic, Uwe Mueller, Manfred S Weiss, Frank Lennartz","doi":"10.1107/S2053230X26009155","DOIUrl":"10.1107/S2053230X26009155","url":null,"abstract":"<p><p>The thermostable GH10 xylanase from Thermoascus aurantiacus (TaXyn10) is an industrially relevant enzyme whose native structure contains an N-terminal pyroglutamate (PCA) modification. Recombinant production of proteins containing an N-terminal PCA is often hindered by purification strategies that disrupt the authentic N-terminus. Here, we report the 1.1 Å resolution crystal structure of TaXyn10 recombinantly produced in Escherichia coli and purified using a split-intein-based system. The structure closely resembles that of the native protein. Electron-density maps support the presence of an intact N-terminal PCA, with partial occupancy consistent with spontaneous cyclization of the exposed N-terminal glutamine after intein cleavage. These results demonstrate that split-intein-based purification enables recovery of the native mature state of TaXyn10 and can preserve physiologically relevant N-terminal PCA formation in recombinant protein produced in E. coli.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"329-335"},"PeriodicalIF":1.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13629641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015145","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}

{"title":"Structural insights into a putative BLF1-like deamidase from Methylomonas sp. Kb3","authors":"Nur Afiqah Shalihin Muhamad Ismail,&nbsp;Amirul Adli Abd Aziz,&nbsp;Atsushi Nakagawa,&nbsp;Farah Diba Abu Bakar,&nbsp;Abdul Munir Abdul Murad,&nbsp;Sheila Nathan,&nbsp;Mohd Firdaus Mohd Raih,&nbsp;Doris Huai Xia Quay,&nbsp;David Rice","doi":"10.1107/S2053230X2600868X","DOIUrl":"10.1107/S2053230X2600868X","url":null,"abstract":"<p>Bacteria that act as eukaryotic pathogens are known to express enzyme toxins that interfere with critical pathways in their targets. Among these are deamidases that modify conserved glutamine residues such as those found in eukaryotic initiation factor 4A (eIF4A) or in the small GTPases Rho, Rac and Cdc42, converting them to glutamic acid and thereby disrupting the function of the target proteins. Structural and biochemical studies have shown that deamidases from <i>Burkholderia</i>, <i>Burkholderia</i> lethal factor 1 (BLF1), and from <i>Escherichia coli</i>, cytotoxic necrotizing factor (CNF1), share a similar fold in their deamidase domains with similar mechanisms for deamidase chemistry. The active site of these toxins contains an apparently conserved LSGC motif as part of a cysteine–histidine catalytic dyad which catalyses the site-specific deamidation. Sequence searches in bacterial databases have suggested that deamidases with this fold are more widespread in nature and that the LSGC motif varies substantially. Using crystals grown in magnesium sulfate, we determined the 1.95 Å resolution crystal structure of a putative deamidase from <i>Methylomonas</i> sp. Kb3, CWO84_RS12955, which shows limited sequence identity to BLF1. The structure reveals that CWO84_RS12955 adopts a similar fold to that of BLF1, albeit with significant differences at the periphery due to sequence insertions and deletions, and that it conserves the catalytic dyad but replaces the LSGC motif with MDGC. However, compared with BLF1, none of the residues that interact with eIF4A are conserved. These structural features suggest that the <i>Methylomonas</i> protein that we have identified may act as a BLF1-like deamidase but against a currently unknown target, and that other bacterial proteins with similar sequence fingerprints could play important roles in broader bacterial biology.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 10","pages":"336-347"},"PeriodicalIF":1.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148975339","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}

{"title":"Crystal structures of the sweet-tasting protein honey truffle active component from Mattirolomyces terfezioides","authors":"Tyler T. Pitkanen,&nbsp;Anne Cooper,&nbsp;Phillip Vo,&nbsp;Chase T. McFarland,&nbsp;Ranjan Patnaik,&nbsp;Scott Lovell,&nbsp;Daniel E. Connors","doi":"10.1107/S2053230X26008745","DOIUrl":"10.1107/S2053230X26008745","url":null,"abstract":"<p>Crystal structures of honey truffle active component (HT-AC) originally derived from the fungus <i>Mattirolomyces terfezioides</i> are reported for the first time. HT-AC is a 13 kDa protein and is one of a small class of unrelated proteins that interact with an allosteric site on the human T1R2/R3 sweet taste receptor. These proteins can be used as sweeteners, and result in sweet taste perception at lower concentrations than sugar (the orthosteric receptor target) or many other high-intensity small-molecule sweeteners. Orthorhombic (space group <i>P</i>2₁2₁2₁) and monoclinic (space group <i>P</i>2₁) crystal structures of HT-AC are reported at resolutions ranging from 1.23 to 1.70 Å.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 10","pages":"348-355"},"PeriodicalIF":1.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148966093","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}

{"title":"Sulfate-compatible density marks an intratrimeric junction in the Escherichia coli dihydrolipoamide succinyltransferase catalytic domain.","authors":"Bison Lim, Eunji Kim, Jungeun Byun, Minjeong Kim, Hyo Jung Kim","doi":"10.1107/S2053230X2600909X","DOIUrl":"10.1107/S2053230X2600909X","url":null,"abstract":"<p><p>The catalytic domain of Escherichia coli dihydrolipoamide succinyltransferase (EcDSCD), the E2 component of the 2-oxoglutarate dehydrogenase complex, forms the oligomeric core of the multi-enzyme assembly. Here, we report the crystal structure of EcDSCD determined in space group F432. The F432 crystal symmetry captures a compact trimeric building block and a symmetry-expanded 24-subunit assembly consistent with the octahedral architecture of the E2 catalytic core. Structural analysis revealed sulfate-compatible electron density near Lys196 at a crystallographic threefold intratrimeric junction. Comparison with previously reported EcDSCD structures suggests that this density marks a structurally relevant oxyanion-sensitive hotspot at the intratrimeric junction. Notably, the α1-helix is positioned adjacent to the Lys196-centered junction and extends towards the active-site pocket, where it adopts a shifted orientation relative to other EcDSCD crystal forms. These observations link sulfate-compatible density, the intratrimeric junction and α1-helix positioning within the EcDSCD 24-mer, providing a structural framework for understanding local oxyanion-sensitive features in the E2 catalytic core.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"362-368"},"PeriodicalIF":1.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13629643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148987762","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}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 10","pages":"329-335"},"PeriodicalIF":1.1,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149100557","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}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 10","pages":"362-368"},"PeriodicalIF":1.1,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149100249","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}

{"title":"Diverse DTPA-chelated lanthanides with relevance for nuclear medicine bound to an engineered lipocalin reveal conserved ligand geometry.","authors":"Alina Mirwald, Andreas Eichinger, Arne Skerra","doi":"10.1107/S2053230X26007624","DOIUrl":"10.1107/S2053230X26007624","url":null,"abstract":"<p><p>The Anticalin CL31d, an engineered lipocalin protein previously designed to specifically bind rare-earth and related metal ions as chelate complexes with p-NH₂-Bn-CHX-A″-DTPA (DTPA-NH₂), was subjected to structural and binding studies with a series of 11 different M^III·DTPA-NH₂ complexes. These complexes include various lanthanide and main-group metal(III) ions whose radioisotopes are useful in nuclear medicine, with ionic radii ranging from 0.62 to 1.03 Å. Binding activities of the Anticalin for the M^III·DTPA-NH₂ complexes were quantified by fluorescence titration (probing the intrinsic Tyr/Trp emission), revealing K_d values of 0.8-2.4 nM for most of the lanthanide ions investigated (r_ion = 0.75-0.96 Å), but showing markedly reduced affinities towards the small and large main-group metal ions Ga³⁺ (K_d = 15.3 nM) and Bi³⁺ (K_d = 47.8 nM), respectively. The crystal structures of six representative M^III·DTPA-NH₂ complexes bound to the Anticalin were solved at high resolution (1.5-1.8 Å) using synchrotron X-ray diffraction. Superposition onto the previously described Anticalin CL31 with bound Y³⁺·DTPA-SCN indicated an essentially invariant conformation both for the binding protein and its metal-chelate ligands, including conserved hydrogen bonds, and a surprisingly uniform ninefold metal coordination via five carboxylate groups, three N atoms and one water molecule. However, there were two exceptions: the small Sc³⁺ ion appeared to be coordinated only eightfold with the DTPA-NH₂ chelator but lacking the water ligand, whereas no metal electron density was observed for the Ga³⁺ ion, in line with its known noncanonical DTPA complex geometry. Interestingly, in this case a water molecule was detected at the expected position of the central metal ion within the protein-bound DTPA-NH₂ chelator. Our investigation of the influence of chelate geometry on complex stability establishes the Anticalin CL31d as a small and robust universal binding protein for medically relevant M^III·DTPA complexes with surprisingly broad tolerance towards varying ionic radii, thus enabling flexible radionuclide-targeting strategies in nuclear medicine.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"301-311"},"PeriodicalIF":1.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13523712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148758240","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}

{"title":"Molecular insights into NLRP1 Gly/N-degron recognition by CRL2ZER1","authors":"Bing Zhang,&nbsp;Tao Wang,&nbsp;Liuyu Wang,&nbsp;Junlin Li,&nbsp;Quanyan Liu,&nbsp;Cheng Dong","doi":"10.1107/S2053230X26007715","DOIUrl":"10.1107/S2053230X26007715","url":null,"abstract":"<p>The Gly/N-degron pathway is a branch of the proteasomal degradation pathway that specifically targets proteins initiated with an N-terminal glycine. The E3 ligase substrate adaptors ZYG11B and ZER1 have been identified as being responsible for recognizing the target proteins of the Gly/N-degron pathway. Previously, it has been shown that the Gly/N-degron pathway activates the human NLRP1 inflammasome by degrading the autoinhibitory N-terminal fragment of NLRP1 after cleavage by the enteroviral 3C protease. However, the recognition of the NLRP1 Gly/N-degron is not yet fully understood. Here, we determined the X-ray crystal structure of ZER1 bound to the NLRP1 Gly/N-degron at a resolution of 2.2 Å. The structural information revealed that ZER1 uses its ARM repeats to form a conserved cavity that engages the N-terminal glycine (G1) through hydrogen bonds to Asp556, Asn597 and Glu600. Structural comparisons show a shared recognition mode for Gly/N-degrons despite subtle differences in side-chain interactions. However, ZER1 exhibits weaker affinity for the NLRP1 Gly/N-degron than ZYG11B, likely due to distinct local environments surrounding position 3. This study elucidates the molecular basis of NLRP1 recognition by ZER1 and provides insights into targeting this pathway in inflammatory diseases.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 9","pages":"312-319"},"PeriodicalIF":1.1,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148760474","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}

{"title":"Crystal structure of rice l-galactose dehydrogenase","authors":"Zui Fujimoto,&nbsp;Mitsuru Momma,&nbsp;Nobuhiro Suzuki","doi":"10.1107/S2053230X26007430","DOIUrl":"10.1107/S2053230X26007430","url":null,"abstract":"<p><span>l</span>-Galactose dehydrogenase plays a key role in the biosynthesis of <span>l</span>-ascorbic acid (vitamin C) in plants. Here, we report crystal structures of rice (<i>Oryza sativa</i>) <span>l</span>-galactose dehydrogenase in both apo and NAD⁺-bound forms at 1.2 and 1.8 Å resolution, respectively. Rice <span>l</span>-galactose dehydrogenase adopts a conserved (β/α)₈-barrel fold with a well preserved NAD⁺-binding cleft, as in other plant <span>l</span>-galactose dehydrogenases. Structural comparisons revealed conformational flexibility in the first and second loop regions, which form the lid and side wall of the NAD⁺-binding site. These loops undergo significant rearrangement upon NAD⁺ binding, likely facilitating cofactor and substrate uptake. These findings suggest a flexible loop-mediated regulation of cofactor and substrate access.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"82 9","pages":"289-294"},"PeriodicalIF":1.1,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148672830","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}