Acta crystallographica. Section F, Structural biology communications最新文献_第4页

A first structural model for covalent dimerization of S100 proteins. S100蛋白共价二聚化的第一个结构模型。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-01 DOI: 10.1107/S2053230X26002992

Maria Demou, Laure Yatime

{"title":"A first structural model for covalent dimerization of S100 proteins.","authors":"Maria Demou, Laure Yatime","doi":"10.1107/S2053230X26002992","DOIUrl":"10.1107/S2053230X26002992","url":null,"abstract":"Extracellular S100 proteins act as alarmins and trigger pro-inflammatory signaling cascades by activating cognate cell-surface receptors such as the receptor for advanced glycation end-products (RAGE), thereby contributing to both normal and pathological inflammation depending on the physiological context. These ligand-receptor interactions occur in an oxidative environment that is known to induce post-translational modifications, notably on the cysteine residues present in S100 proteins, giving rise to disulfide-crosslinked S100 species. The fine molecular architecture of these S100 covalent assemblies and their impact on the interaction of S100 with RAGE remains poorly characterized, as most in vitro studies employ cysteine variants or reducing conditions. In this study, a thorough analysis of cysteine conservation within the whole S100 family shows an enriched presence of cysteines in the second half of helix H4, with a hotspot for cysteine occupancy at position 84. Following the introduction of a cysteine at this conserved position in S100A6, SDS-PAGE analysis under nonreducing conditions shows a noteworthy amount of covalent S100A6 Y84C dimer in solution, and the structural analysis of the resulting complex with the RAGE ectodomain reveals the formation of a covalent Cys84-Cys84 linkage between the two S100A6 protomers, thus stabilizing the dimeric conformation of RAGE-bound S100A6. Modeling of other S100 proteins that naturally bear a Cys84 in the RAGE-bound conformation suggests that this covalent S100 dimer architecture may be adopted by other members of the family previously reported to form disulfide-crosslinked species. Altogether, these findings provide a first possible model for S100 covalent homodimerization that is fully compatible with RAGE binding.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":""},"PeriodicalIF":1.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13133999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147669809","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 atomic structure of human dystrophin spectrin-like repeat 24. 人类肌营养不良蛋白谱蛋白样重复序列24的原子结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-01 DOI: 10.1107/S2053230X26003262

Oakley Streeter, Ke Shi, Hannah Bui, Hideki Aihara, James M Ervasti, Robert Evans, Joseph M Muretta

{"title":"The atomic structure of human dystrophin spectrin-like repeat 24.","authors":"Oakley Streeter, Ke Shi, Hannah Bui, Hideki Aihara, James M Ervasti, Robert Evans, Joseph M Muretta","doi":"10.1107/S2053230X26003262","DOIUrl":"10.1107/S2053230X26003262","url":null,"abstract":"The structure of spectrin-like repeat 24 of human dystrophin was determined at 2.5 Å effective resolution. The structure exhibits a three-helix bundle fold, common to all spectrin-repeat family members, and shares a high degree of homology with existing structures of spectrin-like repeat 1 from dystrophin and utrophin. The structure provides molecular details of the atomic interactions that stabilize the repeat, including hydrophobic interactions and inter-helix and intra-helix salt bridges. AlphaFold models of the repeat are in excellent agreement with the structure, showing an all-atom r.m.s.d. of 1.13 Å. Accurate modeling of SR24 supports AlphaFold modeling of all 24 of the dystrophin spectrin-like repeats and the use of these models in predicting the molecular determinants of dystrophin stability, a key aspect of its biological function as a structural protein that cross-links actin filaments to the dystrophin-glycoprotein complex to mediate a mechanical connection between the cytoskeleton and the extracellular matrix.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":""},"PeriodicalIF":1.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13133991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147759434","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 and functional characterization of an Asp49 phospholipase A₂ from the bushmaster (Lachesis muta). 大鼠Asp49磷脂酶A2的晶体结构和功能表征。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-01 DOI: 10.1107/S2053230X26002736

Noelia Erika Neyra Chama, Frey Francisco Romero Vargas, Eloy Condori Mamani, Jhon Antoni Vargas, Adriano Alves Furtado, Humberto D'Muniz Pereira, Ronald Demetrio Navarro Oviedo, Richard Charles Garratt, José Luis Javier Vega Ramírez, Diego Antonio Leonardo

{"title":"Crystal structure and functional characterization of an Asp49 phospholipase A2 from the bushmaster (Lachesis muta).","authors":"Noelia Erika Neyra Chama, Frey Francisco Romero Vargas, Eloy Condori Mamani, Jhon Antoni Vargas, Adriano Alves Furtado, Humberto D'Muniz Pereira, Ronald Demetrio Navarro Oviedo, Richard Charles Garratt, José Luis Javier Vega Ramírez, Diego Antonio Leonardo","doi":"10.1107/S2053230X26002736","DOIUrl":"10.1107/S2053230X26002736","url":null,"abstract":"Snake-venom phospholipases A2 (PLA2s) are small, structurally conserved enzymes that contribute significantly to the pathophysiology of envenomation. Here, we report the purification and crystal structure of an Asp49-PLA2 isolated from the venom of Lachesis muta, a pit viper from the Peruvian Amazon. The enzyme was purified using ion-exchange and size-exclusion chromatography and exhibited phospholipase activity in a dose- and time-dependent egg-yolk degradation assay. Pure protein crystals were obtained in space group P6222 and diffracted to 2.36 Å resolution, with two molecules in the asymmetric unit. The structure reveals the canonical fold of catalytically active group II PLA2s, with a bound Ca2+ ion and a MES molecule in the active site of one monomer. Seven disulfide bonds stabilize the structure, although one bridge typically associated with the β-hairpin is absent and is replaced by a salt bridge as in other viperid PLA2s. PISA analysis suggests a potential tetrameric assembly composed of two AB dimers generating an interface between two A subunits (A-A'). Electrostatic surface mapping reveals a notable positively charged channel at the A-A' interface, like that seen for a basic PLA2 homodimer from Crotalus durissus terrificus in which the two active sites lie accessible to the membrane. This study presents the first structural and enzymatic analysis of an Asp49-PLA2 from L. muta and provides insights into its oligomeric assembly, electrostatic landscape and potential adaptations relevant to its role in venom toxicity.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":""},"PeriodicalIF":1.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13133998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147626809","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 a cold-active arginase from Glaciozyma antarctica. 南极冰川酶冷活性精氨酸酶的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-01 DOI: 10.1107/S2053230X26003092

Doris Huai Xia Quay, Nik Yusnoraini Yusof, Mohd Anuar Jonet, Shazilah Kamaruddin, Rosli Md Illias, Nor Muhammad Mahadi, Nicholas Keep, Mohd Firdaus-Raih, Farah Diba Abu Bakar, Abdul Munir Abdul Murad

{"title":"Crystal structure of a cold-active arginase from Glaciozyma antarctica.","authors":"Doris Huai Xia Quay, Nik Yusnoraini Yusof, Mohd Anuar Jonet, Shazilah Kamaruddin, Rosli Md Illias, Nor Muhammad Mahadi, Nicholas Keep, Mohd Firdaus-Raih, Farah Diba Abu Bakar, Abdul Munir Abdul Murad","doi":"10.1107/S2053230X26003092","DOIUrl":"10.1107/S2053230X26003092","url":null,"abstract":"Arginase is a metal-dependent metalloenzyme that catalyses the hydrolysis of L-arginine to L-ornithine and urea and is widely distributed across animals, bacteria, fungi and protozoa. Here, we report the first three-dimensional crystal structure of a cold-active arginase from the psychrophilic yeast Glaciozyma antarctica (GaArg). The apo structure was solved at 2.35 Å resolution in space group H3 by molecular replacement using an AlphaFold-generated model. GaArg adopts a conserved αβα sandwich fold similar to previously characterized arginases. The crystal structure reveals four regions lacking interpretable electron density, three of which are located near the entrance to the active site. Despite conservation of the identities and the coordination geometry of metal-binding residues, the apo GaArg structure exhibits broadly conserved ligand-binding residue orientations relative to homologous arginases, with minor conformational differences and a disordered loop corresponding to a substrate-interacting region. Analytical size-exclusion chromatography and multimer prediction support the hexameric assembly of GaArg in solution. Quantitative analysis of intramolecular interactions indicates that GaArg contains fewer hydrogen bonds than mesophilic and thermophilic homologues, while its salt-bridge content is comparable to that of the mesophilic enzyme but lower than that of the thermophilic homologue. These features are consistent with a modest reduction in structural rigidity associated with cold adaptation. Ligand- and metal-bound structures will be required to establish their contributions to cold-adaptation.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":""},"PeriodicalIF":1.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13133995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147669830","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 Escherichia coli glucokinase acetylation-mimicking variants and insights into the impact of acetylation. 大肠杆菌葡萄糖激酶乙酰化模拟变异的晶体结构和对乙酰化影响的见解。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-01 DOI: 10.1107/S2053230X26002803

Joseph Andrews, Joshua Sakon, Chenguang Fan

{"title":"Crystal structures of Escherichia coli glucokinase acetylation-mimicking variants and insights into the impact of acetylation.","authors":"Joseph Andrews, Joshua Sakon, Chenguang Fan","doi":"10.1107/S2053230X26002803","DOIUrl":"10.1107/S2053230X26002803","url":null,"abstract":"In this study, we report the crystal structures of K214Q and K216Q variants of Escherichia coli glucokinase (ecGLK), each of which is bound to phosphate in the active-site cleft. The structure of the K214Q variant was determined at 2.70 Å resolution and refined with an Rwork and Rfree of 0.140 and 0.190, respectively, while that of the K216Q variant was determined at 2.44 Å resolution with an Rwork and Rfree of 0.178 and 0.225, respectively. Both variants adopt an open conformation and maintain phosphate-binding interactions similar to the wild-type ecGLK. Structural comparison of the K214Q variant revealed large backbone deviations in the 214-224 α-helix, increased disorder in the loops surrounding the glucose-binding cleft and outward shifts of Asn99, Asp100, His160 and Glu187. Our previous study demonstrated that lysine acetylation at Lys214 and Lys216 impaired the activity of ecGLK, and here we show that acetylation mimics produced domain shifts, indicating those of lysine residues that could be essential for stabilizing the glucose-binding region of ecGLK.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":""},"PeriodicalIF":1.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13133996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147626877","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}

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IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-01

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IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-04-30

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IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-04-23

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IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-04-23

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IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-04-14

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