Pub Date : 2023-08-26DOI: 10.1007/s12104-023-10147-1
Julia A. Brom, Sasiprapa Samsri, Ruta G. Petrikis, Stuart Parnham, Gary J. Pielak
Adenylate kinase reversibly catalyzes the conversion of ATP plus AMP to two ADPs. This essential catalyst is present in every cell, and the Escherichia coli protein is often employed as a model enzyme. Our aim is to use the E. coli enzyme to understand dry protein structure and protection. Here, we report the expression, purification, steady-state assay, NMR conditions and 1H, 13C, 15N backbone resonance NMR assignments of its C77S variant. These data will also help others utilize this prototypical enzyme.
{"title":"1H, 13C, 15N backbone resonance assignment of Escherichia coli adenylate kinase","authors":"Julia A. Brom, Sasiprapa Samsri, Ruta G. Petrikis, Stuart Parnham, Gary J. Pielak","doi":"10.1007/s12104-023-10147-1","DOIUrl":"10.1007/s12104-023-10147-1","url":null,"abstract":"<div><p>Adenylate kinase reversibly catalyzes the conversion of ATP plus AMP to two ADPs. This essential catalyst is present in every cell, and the <i>Escherichia coli</i> protein is often employed as a model enzyme. Our aim is to use the <i>E. coli</i> enzyme to understand dry protein structure and protection. Here, we report the expression, purification, steady-state assay, NMR conditions and <sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N backbone resonance NMR assignments of its C77S variant. These data will also help others utilize this prototypical enzyme.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71910623","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}
Pub Date : 2023-08-17DOI: 10.1007/s12104-023-10148-0
Carolina O. Matos, Glaucia M.S. Pinheiro, Carlos H. I. Ramos, Fabio C. L. Almeida
Molecular chaperones aid proteins to fold and assemble without modifying their final structure, requiring, in several folding processes, the interplay between members of the Hsp70 and Hsp40 families. Here, we report the NMR chemical shift assignments for 1 H, 15 N, and 13 C nuclei of the backbone and side chains of the J-domain of the class B Hsp40 from Saccharomyces cerevisiae, Sis1, complexed with the C-terminal EEVD motif of Hsp70. The data revealed information on the structure and backbone dynamics that add significantly to the understanding of the J-domain-Hsp70-EEVD mechanism of interaction.
{"title":"Backbone and sidechain NMR assignments of residues 1–81 from yeast Sis1 in complex with an Hsp70 C-terminal EEVD peptide","authors":"Carolina O. Matos, Glaucia M.S. Pinheiro, Carlos H. I. Ramos, Fabio C. L. Almeida","doi":"10.1007/s12104-023-10148-0","DOIUrl":"10.1007/s12104-023-10148-0","url":null,"abstract":"<div><p>Molecular chaperones aid proteins to fold and assemble without modifying their final structure, requiring, in several folding processes, the interplay between members of the Hsp70 and Hsp40 families. Here, we report the NMR chemical shift assignments for <sup>1</sup> H, <sup>15</sup> N, and <sup>13</sup> C nuclei of the backbone and side chains of the J-domain of the class B Hsp40 from <i>Saccharomyces cerevisiae</i>, Sis1, complexed with the C-terminal EEVD motif of Hsp70. The data revealed information on the structure and backbone dynamics that add significantly to the understanding of the J-domain-Hsp70-EEVD mechanism of interaction.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10005545","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}
The InterPro family IPR007621 TPM_phosphatase is a widely conserved family of protein domains found in prokaryotes, plants and invertebrates. Despite similar predicted protein folding, members of this family are involved in different cellular processes. In recent years, the structural and biochemical characterization of evolutionarily divergent TPM domains has shown their ability to hydrolyze phosphate groups of different substrates. However, there are still inaccurate functional annotations and uncertain relationships between the structure and function of this domain family. We here report the 1H, 13C, and 15N backbone and sidechain resonances of the TPM domain of a predicted TPM domain-containing protein of the thermophilic bacterium Rhodothermus marinus. These data will lay the groundwork for future NMR-based investigations, contributing to a thorough comprehension of the intricate aspects governing the interplay between structure and function of TPM domains. Additionally, they will unlock opportunities to explore dynamic structural changes, providing valuable insights into the molecular mechanisms underlying the evolutionary adaptations to extreme environmental conditions within this protein family.
{"title":"1H, 15N and 13C backbone and side chain solution NMR assignments of the TPM domain-containing protein of the thermophilic bacterium Rhodothermus marinus","authors":"Leonardo Pellizza, Lila Ramis, Ignacio Argañaraz Araoz, Martín Aran","doi":"10.1007/s12104-023-10146-2","DOIUrl":"10.1007/s12104-023-10146-2","url":null,"abstract":"<div><p>The InterPro family IPR007621 TPM_phosphatase is a widely conserved family of protein domains found in prokaryotes, plants and invertebrates. Despite similar predicted protein folding, members of this family are involved in different cellular processes. In recent years, the structural and biochemical characterization of evolutionarily divergent TPM domains has shown their ability to hydrolyze phosphate groups of different substrates. However, there are still inaccurate functional annotations and uncertain relationships between the structure and function of this domain family. We here report the <sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N backbone and sidechain resonances of the TPM domain of a predicted TPM domain-containing protein of the thermophilic bacterium <i>Rhodothermus marinus</i>. These data will lay the groundwork for future NMR-based investigations, contributing to a thorough comprehension of the intricate aspects governing the interplay between structure and function of TPM domains. Additionally, they will unlock opportunities to explore dynamic structural changes, providing valuable insights into the molecular mechanisms underlying the evolutionary adaptations to extreme environmental conditions within this protein family.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71909141","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}
Pub Date : 2023-07-27DOI: 10.1007/s12104-023-10145-3
Omar Al-Danoon, Smita Mohanty
Ostrinia nubilalis, also known as European Corn Borer (ECB), is a serious pest in Europe and North America, as well as in Central Asia and Northern Africa. It damages a variety of agricultural crops such as corn, oats, buckwheat, millet, and soybeans. causing annually at least one billion dollars in loss. The Ostrinia nubilalis pheromone-binding protein3 (OnubPBP3), preferentially expressed in the male moth antenna, has been implicated in the detection of the female-secreted pheromone blend during the mating process. Understanding the structure of and function of OnubPBP3, including the mechanism of pheromone binding and its release at the dendritic olfactory neuron (ORN), is essential if integrated pest management through sensory inhibition is to be achieved. We report here the backbone and side-chain resonance assignments of OnubPBP3 at pH 6.5 using various triple resonance NMR experiments on a 13C, 15N-labeled protein sample. The secondary structure of OnubPBP3 consists of six α-helices and an unstructured C-terminus based on backbone chemical shifts.
{"title":"Backbone and side chain NMR assignments and secondary structure calculation of the pheromone binding protein3 of Ostrinia nubilalis, an agricultural pest","authors":"Omar Al-Danoon, Smita Mohanty","doi":"10.1007/s12104-023-10145-3","DOIUrl":"10.1007/s12104-023-10145-3","url":null,"abstract":"<div><p><i>Ostrinia nubilalis</i>, also known as European Corn Borer (ECB), is a serious pest in Europe and North America, as well as in Central Asia and Northern Africa. It damages a variety of agricultural crops such as corn, oats, buckwheat, millet, and soybeans. causing annually at least one billion dollars in loss. The <i>Ostrinia nubilalis</i> pheromone-binding protein3 (OnubPBP3), preferentially expressed in the male moth antenna, has been implicated in the detection of the female-secreted pheromone blend during the mating process. Understanding the structure of and function of OnubPBP3, including the mechanism of pheromone binding and its release at the dendritic olfactory neuron (ORN), is essential if integrated pest management through sensory inhibition is to be achieved. We report here the backbone and side-chain resonance assignments of OnubPBP3 at pH 6.5 using various triple resonance NMR experiments on a <sup>13</sup>C, <sup>15</sup>N-labeled protein sample. The secondary structure of OnubPBP3 consists of six α-helices and an unstructured C-terminus based on backbone chemical shifts.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9879801","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}
Pub Date : 2023-07-15DOI: 10.1007/s12104-023-10144-4
Assia Mouhand, Joana Pissarra, Stéphane Delbecq, Christian Roumestand, Philippe Barthe
Human babesiosis is a vector-borne zoonotic infection caused mostly by the Apicomplexan parasite Babesia microti, distributed worldwide. The infection can result in severe symptoms such as hemolytic anemia, especially in immunodeficient patients. Also, asymptomatic patients continue transmission as unscreened blood donors, and represent a risk for Public Health. Early host-parasite interactions are mediated by BmSA1, the major surface antigen of Babesia microti, crucial for invasion and immune escape. Hence, a structural and functional characterization of the BmSA1 protein constitutes a first strategic milestone toward the development of innovative tools to control infection. Knowledge of the 3D structure of such an important antigen is crucial for the development of vaccines or new diagnostic tests. Here, we report the 1H, 15N and 13C NMR resonance assignment of ∆∆BmSA1, a truncated recombinant version of BmSA1 without the N-terminal signal peptide and the hydrophobic C-terminal GPI-anchor. Secondary structure prediction using CSI.3 and TALOS-N demonstrates a high content of alpha-helical structure. This preliminary study provides foundations for further structural characterization of BMSA1.
{"title":"1H, 13C and 15N backbone and side-chain resonance assignments of ∆∆BmSA1, the surface antigen of Babesia microti","authors":"Assia Mouhand, Joana Pissarra, Stéphane Delbecq, Christian Roumestand, Philippe Barthe","doi":"10.1007/s12104-023-10144-4","DOIUrl":"10.1007/s12104-023-10144-4","url":null,"abstract":"<div><p>Human babesiosis is a vector-borne zoonotic infection caused mostly by the Apicomplexan parasite <i>Babesia microti</i>, distributed worldwide. The infection can result in severe symptoms such as hemolytic anemia, especially in immunodeficient patients. Also, asymptomatic patients continue transmission as unscreened blood donors, and represent a risk for Public Health. Early host-parasite interactions are mediated by BmSA1, the major surface antigen of <i>Babesia microti</i>, crucial for invasion and immune escape. Hence, a structural and functional characterization of the BmSA1 protein constitutes a first strategic milestone toward the development of innovative tools to control infection. Knowledge of the 3D structure of such an important antigen is crucial for the development of vaccines or new diagnostic tests. Here, we report the <sup>1</sup>H, <sup>15</sup>N and <sup>13</sup>C NMR resonance assignment of ∆∆BmSA1, a truncated recombinant version of BmSA1 without the N-terminal signal peptide and the hydrophobic C-terminal GPI-anchor. Secondary structure prediction using CSI.3 and TALOS-N demonstrates a high content of alpha-helical structure. This preliminary study provides foundations for further structural characterization of BMSA1.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71909559","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}
Pub Date : 2023-07-08DOI: 10.1007/s12104-023-10138-2
Madison Rizzo, Eric Baggs, Abu Sayeed Chowdhury, Rajesh Nagarajan, Lisa Rose Warner
The N-acyl-L-homoserine lactone (AHL) quorum sensing regulates virulence in the opportunistic pathogen, Pseudomonas aeruginosa. The LasI and RhlI AHL synthases use acyl carrier protein substrates to synthesize, respectively, the 3-oxododecanoyl-L-homoserine lactone (3-oxoC12-HSL) and butyryl-L-homoserine lactone (C4-HSL) QS signals for this bacterium. Although P. aeruginosa genome contains three open reading frames to encode three acyl carrier proteins, namely the ACP1, ACP2 and ACP3, microarray and gene replacement studies show that only the ACP1 carrier protein is under quorum sensing regulation. In this study, we isotopically enriched one of the acyl carrier proteins, ACP1 from P. aeruginosa and describe the backbone resonance assignments for this protein to delineate the structural and molecular basis of ACP1 recognition in P. aeruginosa AHL quorum sensing signal synthesis.
{"title":"Backbone 1H, 13C and 15N assignments of the apo-acyl carrier protein (ACP1) of Pseudomonas aeruginosa","authors":"Madison Rizzo, Eric Baggs, Abu Sayeed Chowdhury, Rajesh Nagarajan, Lisa Rose Warner","doi":"10.1007/s12104-023-10138-2","DOIUrl":"10.1007/s12104-023-10138-2","url":null,"abstract":"<div><p>The N-acyl-L-homoserine lactone (AHL) quorum sensing regulates virulence in the opportunistic pathogen, <i>Pseudomonas aeruginosa</i>. The LasI and RhlI AHL synthases use acyl carrier protein substrates to synthesize, respectively, the 3-oxododecanoyl-L-homoserine lactone (3-oxoC12-HSL) and butyryl-L-homoserine lactone (C4-HSL) QS signals for this bacterium. Although <i>P. aeruginosa</i> genome contains three open reading frames to encode three acyl carrier proteins, namely the ACP<sub>1</sub>, ACP<sub>2</sub> and ACP<sub>3</sub>, microarray and gene replacement studies show that only the ACP<sub>1</sub> carrier protein is under quorum sensing regulation. In this study, we isotopically enriched one of the acyl carrier proteins, ACP<sub>1</sub> from <i>P. aeruginosa</i> and describe the backbone resonance assignments for this protein to delineate the structural and molecular basis of ACP<sub>1</sub> recognition in <i>P. aeruginosa</i> AHL quorum sensing signal synthesis.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71909381","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}
Pub Date : 2023-07-05DOI: 10.1007/s12104-023-10143-5
Ramdas Aute, Mandar V. Deshmukh
In the model organism Drosophila melanogaster, one of the Dicer homologs, Dcr-2, initiates the RNA interference pathway by cleaving long double-stranded RNA into small interfering RNA (siRNA). The Dcr-2:R2D2 heterodimer subsequently binds to the 21-nucleotide siRNA to form the R2D2:Dcr-2 Initiator (RDI) complex, which is critical for initiating the assembly of the RNA-induced silencing complex containing guide siRNA strand. During RDI complex formation, R2D2 senses the stability of the 5′ end of the siRNA and a 5′-phosphate group, although the underlying mechanism of siRNA asymmetry sensing and 5′-phosphate recognition by R2D2 is elusive. In this study, we present nearly complete chemical shift assignments of the backbone and the side chain of a construct that comprises the N-terminus dsRBD1 and linker of R2D2 (~ 10.3 kDa; henceforth: R2D2D1L). Our study would further aid in the structural and functional characterization of R2D2.
{"title":"Chemical shift assignments of dsRBD1 and linker region of R2D2, a siRNA binding protein in the Drosophila RNAi pathway","authors":"Ramdas Aute, Mandar V. Deshmukh","doi":"10.1007/s12104-023-10143-5","DOIUrl":"10.1007/s12104-023-10143-5","url":null,"abstract":"<div><p>In the model organism <i>Drosophila melanogaster</i>, one of the Dicer homologs, Dcr-2, initiates the RNA interference pathway by cleaving long double-stranded RNA into small interfering RNA (siRNA). The Dcr-2:R2D2 heterodimer subsequently binds to the 21-nucleotide siRNA to form the R2D2:Dcr-2 Initiator (RDI) complex, which is critical for initiating the assembly of the RNA-induced silencing complex containing guide siRNA strand. During RDI complex formation, R2D2 senses the stability of the 5′ end of the siRNA and a 5′-phosphate group, although the underlying mechanism of siRNA asymmetry sensing and 5′-phosphate recognition by R2D2 is elusive. In this study, we present nearly complete chemical shift assignments of the backbone and the side chain of a construct that comprises the N-terminus dsRBD1 and linker of R2D2 (~ 10.3 kDa; henceforth: R2D2D1L). Our study would further aid in the structural and functional characterization of R2D2.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10110774","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}
Pub Date : 2023-07-05DOI: 10.1007/s12104-023-10142-6
Qingxin Li, Hui Qi Ng, Ying Ru Loh, CongBao Kang
Dengue virus is an important human pathogen affecting people especially in tropical and subtropical regions. Its genome encodes seven non-structural proteins that are important for viral assembly and replication. Dengue NS2B is a membrane protein containing four transmembrane helices and involved in protein-protein interactions. Its transmembrane helices are critical for location of NS2B on the cell membrane while one cytoplasmic region composed of approximately 40 amino acids serves as a cofactor of viral NS3 protease by forming a tight complex with the N-terminal region of NS3. Here, we report the backbone resonance assignments for a dengue NS2B construct referred to as mini-NS2B containing only the transmembrane regions without NS3 cofactor region in detergent micelles. Mini-NS2B exhibits well-dispersed cross-peaks in the 1H-15N-HSQC spectrum and contains four helices in solution. The available mini-NS2B and its assignment will be useful for determining the structure of NS2B and identifying small molecules binding to the transmembrane regions.
{"title":"Backbone 1H, 15N and 13C resonance assignments for dengue NS2B without the NS3 protease cofactor region in detergent micelles","authors":"Qingxin Li, Hui Qi Ng, Ying Ru Loh, CongBao Kang","doi":"10.1007/s12104-023-10142-6","DOIUrl":"10.1007/s12104-023-10142-6","url":null,"abstract":"<div><p>Dengue virus is an important human pathogen affecting people especially in tropical and subtropical regions. Its genome encodes seven non-structural proteins that are important for viral assembly and replication. Dengue NS2B is a membrane protein containing four transmembrane helices and involved in protein-protein interactions. Its transmembrane helices are critical for location of NS2B on the cell membrane while one cytoplasmic region composed of approximately 40 amino acids serves as a cofactor of viral NS3 protease by forming a tight complex with the N-terminal region of NS3. Here, we report the backbone resonance assignments for a dengue NS2B construct referred to as mini-NS2B containing only the transmembrane regions without NS3 cofactor region in detergent micelles. Mini-NS2B exhibits well-dispersed cross-peaks in the <sup>1</sup>H-<sup>15</sup>N-HSQC spectrum and contains four helices in solution. The available mini-NS2B and its assignment will be useful for determining the structure of NS2B and identifying small molecules binding to the transmembrane regions.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71908985","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}
Pub Date : 2023-07-05DOI: 10.1007/s12104-023-10140-8
Dihong Fu, Bo Duan, Xianzhi Dong, Bin Xia
SarA is a global transcription regulator in S. aureus which regulates the expression of over 120 genes related to quorum sensing, biofilm synthesis, drug resistance and many other important physiological processes during host infection. SarA can bind to the promoter region of agr and other target genes to activate or repress the transcription. The crystal structure of SarA uncovered a MarR protein-like conformation with two symmetrical winged helix domains, while its DNA binding mechanism is still unknown. We have constructed a monomeric DNA binding domain of SarA (SarAΔN19) for the study of the interaction between SarA and DNA with NMR spectroscopy. Here, we report the 1H, 13C and 15N NMR assignment of SarAΔN19/DNA complex which is the first step towards further structure and function analysis.
{"title":"1H, 13C, and 15N resonance assignments of SarA monomer from Staphylococcus aureus in complex with DNA","authors":"Dihong Fu, Bo Duan, Xianzhi Dong, Bin Xia","doi":"10.1007/s12104-023-10140-8","DOIUrl":"10.1007/s12104-023-10140-8","url":null,"abstract":"<div><p>SarA is a global transcription regulator in <i>S. aureus</i> which regulates the expression of over 120 genes related to quorum sensing, biofilm synthesis, drug resistance and many other important physiological processes during host infection. SarA can bind to the promoter region of <i>agr</i> and other target genes to activate or repress the transcription. The crystal structure of SarA uncovered a MarR protein-like conformation with two symmetrical winged helix domains, while its DNA binding mechanism is still unknown. We have constructed a monomeric DNA binding domain of SarA (SarA<sup>ΔN19</sup>) for the study of the interaction between SarA and DNA with NMR spectroscopy. Here, we report the <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N NMR assignment of SarA<sup>ΔN19</sup>/DNA complex which is the first step towards further structure and function analysis.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71908986","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}
E3 ubiquitin protein ligase RNF31 is present in human proteins and is involved in linear ubiquitin chain assembly complex (LUBAC) activity and cell growth. RNF31 is involved in ubiquitination, which is the post-translational modification of proteins. Ubiquitin molecules connect with amino acid residues of target proteins under the action of ubiquitin-activating enzyme E1, ubiquitin binding enzyme E2 and ubiquitin ligase E3, so as to achieve certain physiological functions. The abnormal expression of ubiquitination promotes the formation of cancer. In studies of breast cancer, RNF31 mRNA levels were found to be higher in cancer cells than in other tissues. The PUB domain of RNF31 is the binding site of the ubiquitin thioesterase otulin. Here, we report the backbone and side-chain resonance assignments of the PUB domain of RNF31 and study the backbone relaxation of the domain. These studies will contribute to further understanding of the structural and functional relationship of RNF31 protein, which may also be a target for drug research.
{"title":"Resonance assignments of the PUB domain of the RNF31 protein","authors":"Lanlan Song, Fumei Zhong, Xiaoming Tu, Jiahai Zhang","doi":"10.1007/s12104-023-10139-1","DOIUrl":"10.1007/s12104-023-10139-1","url":null,"abstract":"<div><p>E3 ubiquitin protein ligase RNF31 is present in human proteins and is involved in linear ubiquitin chain assembly complex (LUBAC) activity and cell growth. RNF31 is involved in ubiquitination, which is the post-translational modification of proteins. Ubiquitin molecules connect with amino acid residues of target proteins under the action of ubiquitin-activating enzyme E1, ubiquitin binding enzyme E2 and ubiquitin ligase E3, so as to achieve certain physiological functions. The abnormal expression of ubiquitination promotes the formation of cancer. In studies of breast cancer, RNF31 mRNA levels were found to be higher in cancer cells than in other tissues. The PUB domain of RNF31 is the binding site of the ubiquitin thioesterase otulin. Here, we report the backbone and side-chain resonance assignments of the PUB domain of RNF31 and study the backbone relaxation of the domain. These studies will contribute to further understanding of the structural and functional relationship of RNF31 protein, which may also be a target for drug research.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2023-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9731209","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}