Biochemical Journal最新文献_第4页

Mechanistic insights into acetylated histone recognition by the CECR2 bromodomain. CECR2溴结构域对乙酰化组蛋白识别的机制研究。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2026-07-03 DOI: 10.1042/bcj20260182

Soumyajit Chakraborty,Anirban Roy,Smrutimayee Prusty,Snehasudha Sahoo,Babu Sudhamalla

{"title":"Mechanistic insights into acetylated histone recognition by the CECR2 bromodomain.","authors":"Soumyajit Chakraborty,Anirban Roy,Smrutimayee Prusty,Snehasudha Sahoo,Babu Sudhamalla","doi":"10.1042/bcj20260182","DOIUrl":"https://doi.org/10.1042/bcj20260182","url":null,"abstract":"Chromatin remodeling regulator CECR2 plays critical roles in neurulation, spermatogenesis, DNA damage response, and cancer metastasis, yet the structural determinants underlying its recognition of acetylated histones remain poorly understood. Here, we characterize the histone-binding specificity and structural determinants of the CECR2 bromodomain using isothermal titration calorimetry, biochemical assays, and structure-guided computational modeling. The CECR2 bromodomain recognizes multiple monoacetylated histone H4 peptides, including H4K5ac, H4K8ac, H4K12ac, and H4K16ac, demonstrating engagement across the H4 N-terminal tail. Combinatorial acetylation differentially modulates binding: while H4K5acK8ac exhibits reduced affinity, H4K5acK12ac and H4K8acK12ac maintain binding comparable to monoacetylated peptides. The bromodomain also recognizes acetylated peptides from other histones, including H3K23ac and H2AK5ac. Mutational analysis identifies conserved pocket residues essential for acetyllysine recognition. Molecular docking suggests that a single acetyllysine occupies the canonical bromodomain pocket, while additional modifications extend along the protein surface, providing a structural basis for selective recognition of combinatorial marks. Comparative analysis with the BET family bromodomain BRD4-BD1 highlights differences in pocket architecture and ligand accommodation, with CECR2 displaying a more permissive binding environment that can accommodate larger acyllysine modifications. Together, these findings provide biochemical and modeled structural insight into histone recognition by the CECR2 bromodomain and establish a foundation for understanding how it contributes to chromatin engagement.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"19 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148372630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Alternative Splicing of Rice Chloroplastic CuZn Superoxide Dismutase, OsCSD2: Impact on expression and protein characteristics. 水稻叶绿体CuZn超氧化物歧化酶（OsCSD2）的选择性剪接：对表达和蛋白特性的影响

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2026-06-25 DOI: 10.1042/bcj20260119

Ravi Prakash Sanyal,Vishal Prashar,Ramanjulu Sunkar,Ajay Saini

{"title":"Alternative Splicing of Rice Chloroplastic CuZn Superoxide Dismutase, OsCSD2: Impact on expression and protein characteristics.","authors":"Ravi Prakash Sanyal,Vishal Prashar,Ramanjulu Sunkar,Ajay Saini","doi":"10.1042/bcj20260119","DOIUrl":"https://doi.org/10.1042/bcj20260119","url":null,"abstract":"Superoxide dismutases (SODs) are involved in cellular reactive oxygen species (ROS) homeostasis under diverse conditions. Among different plant SODs, CuZnSODs (CSDs) are most abundant and localized to multiple compartments, including chloroplast. Rice (Oryza sativa) genome encodes a chloroplastic CuZnSOD (OsCSD2, LOC_Os08g44770), which undergoes alternative splicing (AS), generating two splice variants (SVs), OsCSD2-SV1 (constitutive) and OsCSD2-SV2 (alternative). The AS-event remove 12 nucleotides in OsCSD2-SV2, causing loss of four amino acids (29GPTT32) in OsCSD2-SV2. The two OsCSD2 isoforms were analyzed at RNA and protein levels. The OsCSD2-SV1 and OsCSD2-SV2 transcripts showed comparable stability but differed in expression pattern in certain tissues and stress conditions. For assessment of 'GPTT loss', OsCSD2 isoforms were over-expressed in E. coli, purified, and compared for biochemical-biophysical characteristics. Both isoforms were found to be homodimers (subunit molecular weight: ~19 kDa), and enzymatically active; however, OsCSD2-SV2 (lacking GPTT) showed substantially lower SOD activity than OsCSD2-SV1. Both isoforms showed comparable pH optima, but differed in SOD activity and stability at higher pH and temperature (OsCSD2-SV1 > OsCSD2-SV2), sensitivity to H2O2 (OsCSD2-SV1 > OsCSD2-SV2), and Cu cofactor content. Circular dichroism (CD) showed discernible differences between the isoforms, while differential scanning fluorimetry (DSF) revealed lower thermostability of OsCSD2-SV2, likely due to reduced H-bonds/other interactions. OsCSD2 isoforms showed heteromeric interaction with each other and with the SOD-specific chaperone. Analysis of purified homo/heterodimers indicated that heteromeric interaction reduces the SOD activity of OsCSD2. The study showed several new insights into AS-mediated modulation of rice OsCSD2, which might be important for its chloroplastic functions.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"130 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148313656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

VDR/RXR antagonizes calcineurin-activated NFAT1, an essential regulator of Coronin-1A expression and Mycobacterial persistence. VDR/RXR可拮抗钙调磷酸酶激活的NFAT1，后者是冠状蛋白1a表达和分枝杆菌持久性的重要调节因子。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2026-06-24 DOI: 10.1042/bcj20260025

Sayantani Datta,Arnab Hazra,Payel Das,Sadhana Roy,Debayan Das,Arjun Sankhla,Somdeb BoseDasgupta

{"title":"VDR/RXR antagonizes calcineurin-activated NFAT1, an essential regulator of Coronin-1A expression and Mycobacterial persistence.","authors":"Sayantani Datta,Arnab Hazra,Payel Das,Sadhana Roy,Debayan Das,Arjun Sankhla,Somdeb BoseDasgupta","doi":"10.1042/bcj20260025","DOIUrl":"https://doi.org/10.1042/bcj20260025","url":null,"abstract":"Coronin-1A (CORO1A), a conserved WD-repeat protein enriched in immune cells, plays a pivotal role in host-pathogen interactions and immune regulation, yet the mechanisms controlling its expression have remained elusive. We identify Vitamin D3 (VitD3) and Retinoic acid (RA) as potent repressors of CORO1A transcription via a novel competitive displacement mechanism, wherein soluble VDR/RXR heterodimers outcompete NFAT1 at its binding site on the CORO1A promoter. Luciferase reporter assays, Chromatin immunoprecipitation and Electrophoretic Mobility Shift Assays pinpoint NFAT1 as the dominant transcriptional driver of CORO1A in the myeloid lineage, with NFAT1/NFAT2 jointly controlling its expression in lymphoid cells. Strikingly, perturbation of the calcineurin-NFAT1 axis sharply reduces CORO1A levels, markedly enhancing macrophage-mediated mycobacterial clearance. This work uncovers previously unrecognized lineage-specific transcriptional circuitry for CORO1A regulation and positions the calcineurin-NFAT1 pathway as a compelling therapeutic target for immune modulation and host-directed interventions against infectious disease.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"21 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148305033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Bioinformatic assessment of the potential amyloidogenicity of the human and evolutionarily more ancient proteomes. 人类和进化上更古老的蛋白质组潜在淀粉样变性的生物信息学评估。

IF 4.1 3区生物学

Biochemical Journal Pub Date : 2026-06-22 DOI: 10.1042/bcj20250336

Douglas B Kell,Ivayla Roberts,Xiaomian Tan,J Bernadette Moore,Etheresia Pretorius

{"title":"Bioinformatic assessment of the potential amyloidogenicity of the human and evolutionarily more ancient proteomes.","authors":"Douglas B Kell,Ivayla Roberts,Xiaomian Tan,J Bernadette Moore,Etheresia Pretorius","doi":"10.1042/bcj20250336","DOIUrl":"https://doi.org/10.1042/bcj20250336","url":null,"abstract":"AmyloGram is a computer program that uses n-gram encoding and a random forest classifier to produce a numerical score between 0 and 1 for the predicted amyloidogenicity of a given protein sequence. In a variety of recent studies we have used AmyloGram to obtain an overall amyloidogenicity score for members of the human proteome. Of 83,567 full-length canonical human polypeptides, 79.2% had a score exceeding 0.7 (the median was 0.813), consistent with the view that most natural protein sequences contain elements that are in fact potentially amyloidogenic. Here we first asked whether this operational threshold is supported by orthogonal predictors and curated amyloid proteins, and then whether similarly high scores are also observed in evolutionarily ancient proteomes. For the human proteome, PASTA2 values correlated positively with AmyloGram scores (r² = 0.374 for minimum free energy and 0.321 for average free energy), and proteins with AmyloGram scores ≥0.7 were significantly enriched for strongly negative PASTA2 values (for average free energy < -10 PEU: 4,724/66,190 versus 75/17,377; c² p = 2.4 × 10-250). In AmyPro, 117 curated amyloid proteins had substantially higher median AmyloGram scores than did the eight curated non-amyloids, although the imbalance of this dataset demands caution. AMYPred-FRL showed only a weak and partly discordant relationship with AmyloGram in the archaeal test proteome examined. We then computed AmyloGram score distributions for the proteomes of 130 other organisms, including archaea, Gram-negative bacteria, Gram-positive bacteria and viruses, representing 475,999 proteins in total.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"30 1","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148299339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Regulation between LRRK2 and PP2A signaling in cellular models of Parkinson's disease. 帕金森病细胞模型中LRRK2和PP2A信号的调控

IF 3.9 3区生物学

Biochemical Journal Pub Date : 2026-06-03 DOI: 10.1042/BCJ20260194

Panagiotis S Athanasopoulos, Anna Memou, Franz Y Ho, Ahmed Soliman, Henderikus Pots, Vassiliki Papadopoulou, Felix von Zweydorf, Saiganesh Sriraman, Alexander Marc Thouin, Laurine Vandewynckel, William Sibran, Marie-Christine Chartier-Harlin, R Jeremy Nichols, Elisa Greggio, Jean-Marc Taymans, Christian Johannes Gloeckner, Hardy J Rideout, Arjan Kortholt

{"title":"Regulation between LRRK2 and PP2A signaling in cellular models of Parkinson's disease.","authors":"Panagiotis S Athanasopoulos, Anna Memou, Franz Y Ho, Ahmed Soliman, Henderikus Pots, Vassiliki Papadopoulou, Felix von Zweydorf, Saiganesh Sriraman, Alexander Marc Thouin, Laurine Vandewynckel, William Sibran, Marie-Christine Chartier-Harlin, R Jeremy Nichols, Elisa Greggio, Jean-Marc Taymans, Christian Johannes Gloeckner, Hardy J Rideout, Arjan Kortholt","doi":"10.1042/BCJ20260194","DOIUrl":"10.1042/BCJ20260194","url":null,"abstract":"Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of late-onset familial and idiopathic Parkinson's disease (PD), known to date. Importantly, recent data from postmortem tissue as well as biomarker studies suggest that independent of mutations, increased kinase activity of LRRK2 plays an essential role in idiopathic PD pathogenesis. Despite extensive research on LRRK2, its activation mechanism(s) and how the various mutations result in increased kinase activity and neuronal death are still not completely understood. Accumulating evidence points to LRRK2 phosphoregulation, both autophosphorylation and phosphorylation by other kinases, as one potential molecular trigger of its activation. LRRK2 activation and localization are regulated by phosphatases such as protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A); however, the exact mechanism of this phosphoregulation is not known. Our data reveal that in vitro PP2A dephosphorylates sites within the RocCOR-GTPase domain of LRRK2 and, as a result, destabilizes LRRK2 dimers, with consequent reduction of its kinase activity. Strikingly, our data further highlight that LRRK2 in turn phosphorylates the catalytic subunit of the PP2A holoenzyme PPP2CA at its critical residue T304. Furthermore, LRRK2-mediated phosphorylation of PP2CA T304 alters the methylation of the C-terminus, which is crucial for both holoenzyme formation and catalytic activity. Importantly, expression of WT-PPP2CA protects from LRRK2-G2019S-induced neuronal cell death, while the PPP2CA-T304A mutant fails to do so, suggesting that impaired PP2A holoenzyme formation might be detrimental for LRRK2-PD.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":"1097-1114"},"PeriodicalIF":3.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13212363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147939994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Computational modelling of cell identity. 细胞身份的计算模型。

IF 3.9 3区生物学

Biochemical Journal Pub Date : 2026-06-03 DOI: 10.1042/BCJ20250132

Woo Jun Shim, Chris Siu Yeung Chow, Shaine Chenxin Bao, Qiongyi Zhao, Nathan J Palpant

{"title":"Computational modelling of cell identity.","authors":"Woo Jun Shim, Chris Siu Yeung Chow, Shaine Chenxin Bao, Qiongyi Zhao, Nathan J Palpant","doi":"10.1042/BCJ20250132","DOIUrl":"10.1042/BCJ20250132","url":null,"abstract":"Deciphering cell identity remains a central challenge in biology, as experimental profiling can only capture a fraction of the molecular diversity across human cell states. Computational modelling fills this gap by offering scalable predictions beyond what experimental assays can measure. These models play key roles in classifying cell type, discovering previously unknown states, interpreting perturbation responses, and generating hypotheses for contexts that are experimentally inaccessible. The rapid expansion of consortium-level data has enabled models to learn generalisable genomic features of cell identity. In the present review, we examine 43 representative computational methods utilising information extracted from genomic regulatory elements, marker genes, or reference atlases and traditional machine learning or transformer-based approaches for cell identity inference. By outlining biological rationales, applications, and limitations of these methods in a minimally technical tone, the review serves as a practical guide for biologists to choose appropriate methods for their specific analytical needs.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"483 6","pages":"1049-1071"},"PeriodicalIF":3.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13199844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147986475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Deep learning insights into β-lactamase dynamics and resistance evolution. β-内酰胺酶动力学和耐药性进化的深度学习见解。

IF 3.9 3区生物学

Biochemical Journal Pub Date : 2026-06-03 DOI: 10.1042/BCJ20260196

Jing Gu, Lin Gao, Shuang Chen, Manming Xu, Jassi Goyal, Rida Haider, Fedaa Attana, Othman R A Alzahrani, Robert A Bonomo, Shozeb Haider

{"title":"Deep learning insights into β-lactamase dynamics and resistance evolution.","authors":"Jing Gu, Lin Gao, Shuang Chen, Manming Xu, Jassi Goyal, Rida Haider, Fedaa Attana, Othman R A Alzahrani, Robert A Bonomo, Shozeb Haider","doi":"10.1042/BCJ20260196","DOIUrl":"10.1042/BCJ20260196","url":null,"abstract":"The rapid global expansion of β-lactamase-mediated antimicrobial resistance demands mechanistic approaches capable of resolving the dynamics of enzyme adaptation. Although β-lactamase evolution often involves subtle rearrangements rather than large structural shifts, traditional structural and simulation analyses struggle to capture the conformational heterogeneity that underlies shifts in substrate specificity and inhibitor susceptibility. Here, we review recent advances in applying deep learning to probe the conformational dynamics of β-lactamases across classes A-D. We highlight how convolutional variational autoencoders (CVAEs) reconstruct nonlinear conformational manifolds from molecular dynamics simulations, exposing metastable states, cryptic pockets, and catalytic intermediates. DiffNets integrate supervised objectives to identify structural determinants of biochemical phenotypes, while BindSiteS-CNN and geometric deep learning methods provide high-resolution insight into active-site remodelling and local pocket plasticity. Additionally, graph neural networks trained on dynamics-informed descriptors capture long-range allosteric couplings and accurately predict mutational fitness and epistasis. The deep learning-enabled analysis of protein dynamics offers a unified and predictive framework for understanding β-lactamase adaptation.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"483 6","pages":"861-879"},"PeriodicalIF":3.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13161196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Illuminating compartmentalized AMPK signaling in single cells. 阐明单细胞中区隔化的AMPK信号。

IF 3.9 3区生物学

Biochemical Journal Pub Date : 2026-06-03 DOI: 10.1042/BCJ20250267

Arnav Jhawar, Kasey Parks, Danielle L Schmitt

{"title":"Illuminating compartmentalized AMPK signaling in single cells.","authors":"Arnav Jhawar, Kasey Parks, Danielle L Schmitt","doi":"10.1042/BCJ20250267","DOIUrl":"10.1042/BCJ20250267","url":null,"abstract":"AMP-activated protein kinase (AMPK) is a crucial regulator of cellular energy balance, affecting numerous downstream targets across various subcellular locations. Under cellular energy stress, AMPK becomes fully activated when it binds AMP and is phosphorylated by upstream kinases, including liver kinase B1 and calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2), and works to restore metabolic equilibrium. Additionally, CaMKK2 can activate AMPK independent of AMP in response to calcium signaling. In the present review, we summarize how genetically encoded kinase activity reporters for measuring AMPK activity have evolved for a comprehensive measurement of spatial and temporal AMPK activity in single cells. These reporters have provided important insights into AMPK activity dependent upon upstream kinases, location, and signaling cues. We also discuss the use of genetic actuators such as the AMPK inhibitory peptide that can be targeted to suppress AMPK activity at specific compartments. Together, these advances have established AMPK as a key regulator of metabolism with distinct spatial and temporal signaling patterns, suggesting compartmentalization of AMPK activity in the cell.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":"483 6","pages":"849-860"},"PeriodicalIF":3.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13161187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Heparan sulfate promotes autoactivation of procathepsin K by destabilizing the propeptide-catalytic domain interaction. 硫酸乙酰肝素通过破坏前肽-催化结构域相互作用来促进前组织蛋白酶K的自激活。

IF 3.9 3区生物学

Biochemical Journal Pub Date : 2026-06-03 DOI: 10.1042/BCJ20260109

Huanmeng Hao, Xiaoxiao Zhang, Jian Liu, Ding Xu

{"title":"Heparan sulfate promotes autoactivation of procathepsin K by destabilizing the propeptide-catalytic domain interaction.","authors":"Huanmeng Hao, Xiaoxiao Zhang, Jian Liu, Ding Xu","doi":"10.1042/BCJ20260109","DOIUrl":"10.1042/BCJ20260109","url":null,"abstract":"Procathepsin K (pro-CtsK) is the zymogen of cathepsin K (CtsK), a collagenase that is essential for bone resorption. Pro-CtsK is known to bind heparan sulfate (HS), but the biological significance of the interaction remains unclear. Here, we report that HS accelerates the autoprocessing of pro-CtsK in a manner dependent on both sulfation pattern and oligosaccharide length. We discovered a previously unknown electrostatic interaction between the propeptide and the catalytic domain, which stabilizes the conformation of the propeptide and prevents it from intermolecular proteolytic activation. HS accelerates autoprocessing of pro-CtsK by disrupting this critical electrostatic interaction. Mechanistically, HS competes with two glutamic acids in the propeptide for binding to three basic residues on the catalytic domain, thereby substantially altering the conformation of the propeptide and making it more labile for autoprocessing. We further discovered that HS is highly enriched in secretory lysosomes of osteoclasts and might be directly involved in autoactivation of CtsK.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":"967-980"},"PeriodicalIF":3.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13296955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147962015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 backside β-turn is a key structural element of Rad6-family E2 ubiquitin-conjugating enzymes. 背面转β是rad6家族E2泛素偶联酶的关键结构元件。

IF 3.9 3区生物学

Biochemical Journal Pub Date : 2026-06-03 DOI: 10.1042/BCJ20260108

Prakash K Shukla, Andrew M Leng, Hui-Hsuan Chen, Rajarshi Ganguly, Nicholas Newell, Mahesh B Chandrasekharan

{"title":"The backside β-turn is a key structural element of Rad6-family E2 ubiquitin-conjugating enzymes.","authors":"Prakash K Shukla, Andrew M Leng, Hui-Hsuan Chen, Rajarshi Ganguly, Nicholas Newell, Mahesh B Chandrasekharan","doi":"10.1042/BCJ20260108","DOIUrl":"10.1042/BCJ20260108","url":null,"abstract":"Protein ubiquitination regulates diverse cellular processes, and its dysregulation contributes to human disease, including cancer. E2 ubiquitin-conjugating enzymes share a conserved UBC fold in which surface loops fine-tune catalysis and partner interactions, yet the roles of individual loops remain incompletely defined. Here, we identify loop 3-a component of the \"backside\" β2-β3 hairpin-as a conserved structural and allosteric element in Rad6-family E2s. Structural and bioinformatic analyses of yeast Rad6 and its human homologs (UBE2A/UBE2B) reveal that loop 3 forms an overlapping triple β-turns, with variable first turn and a highly conserved second/third turn that links catalytic regulation to E3 ligase engagement. Systematic mutagenesis of the yeast Rad6 backside β-turn (residues 42-51) shows that this element is required in vivo for Bre1-dependent histone H2B Lys123 monoubiquitination, Rad18-dependent PCNA monoubiquitination, and Ubr1/Ubr2-dependent polyubiquitination and degradation of Sml1 and N-end rule substrates, and related biological processes. Charge-reversal mutations at backside β-turn Glu49 and Asp50 disrupt E3 binding, whereas cancer-relevant substitutions in kink-inducing prolines (Pro43/Pro47) impair mono- and polyubiquitination without abolishing E3 interactions. Certain backside β-turn mutations, including cancer-relevant variants, compromise steady-state levels following DNA damage, revealing them as conditional null or loss-of-function alleles. Nuclear magnetic resonance spectroscopy demonstrates that Pro43/Pro47 mutations induce long-range structural perturbations from backside β-turn into the front-face catalytic pocket, correlating with reduced in vitro ubiquitination activity. Deletion or alanine replacement of the β-turn destabilizes yeast Rad6 and human UBE2A/UBE2B. Together, these findings establish the loop 3/backside β-turn as a critical structural element of Rad6-family enzymes.","PeriodicalId":8825,"journal":{"name":"Biochemical Journal","volume":" ","pages":"1007-1027"},"PeriodicalIF":3.9,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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