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https://www.readbyqxmd.com/read/27668276/data-from-computational-analysis-of-the-peptide-linkers-in-the-mocr-bacterial-transcriptional-regulators
#1
Sebastiana Angelaccio, Teresa Milano, Angela Tramonti, Martino Luigi Di Salvo, Roberto Contestabile, Stefano Pascarella
Detailed data from statistical analyses of the structural properties of the inter-domain linker peptides of the bacterial regulators of the family MocR are herein reported. MocR regulators are a recently discovered subfamily of bacterial regulators possessing an N-terminal domain, 60 residue long on average, folded as the winged-helix-turn-helix architecture responsible for DNA recognition and binding, and a large C-terminal domain (350 residue on average) that belongs to the fold type-I pyridoxal 5'-phosphate (PLP) dependent enzymes such aspartate aminotransferase...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27446613/a-bioinformatics-analysis-reveals-a-group-of-mocr-bacterial-transcriptional-regulators-linked-to-a-family-of-genes-coding-for-membrane-proteins
#2
Teresa Milano, Sebastiana Angelaccio, Angela Tramonti, Martino Luigi Di Salvo, Roberto Contestabile, Stefano Pascarella
The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (wHTH) architecture responsible for DNA recognition and binding, linked to a large C-terminal domain (350 residues on average) that is homologous to fold type-I pyridoxal 5'-phosphate (PLP) dependent enzymes like aspartate aminotransferase (AAT). These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized...
2016: Biochemistry Research International
https://www.readbyqxmd.com/read/27403582/diverse-architectural-properties-of-sso10a-proteins-evidence-for-a-role-in-chromatin-compaction-and-organization
#3
Rosalie P C Driessen, Szu-Ning Lin, Willem-Jan Waterreus, Alson L H van der Meulen, Ramon A van der Valk, Niels Laurens, Geri F Moolenaar, Navraj S Pannu, Gijs J L Wuite, Nora Goosen, Remus T Dame
Sso10a proteins are small DNA-binding proteins expressed by the crenarchaeal model organism Sulfolobus solfataricus. Based on the structure of Sso10a1, which contains a winged helix-turn-helix motif, it is believed that Sso10a proteins function as sequence-specific transcription factors. Here we show that Sso10a1 and Sso10a2 exhibit different distinct DNA-binding modes. While the ability to bend DNA is shared between the two proteins, DNA bridging is observed only for Sso10a1 and only Sso10a2 exhibits filament formation along DNA...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27362745/conformational-dynamics-and-the-binding-of-specific-and-nonspecific-dna-by-the-autoinhibited-transcription-factor-ets-1
#4
Geneviève Desjardins, Mark Okon, Barbara J Graves, Lawrence P McIntosh
The affinity of the Ets-1 transcription factor for DNA is autoinhibited by an intrinsically disordered serine-rich region (SRR) and a helical inhibitory module (IM) appended to its winged helix-turn-helix ETS domain. Using NMR spectroscopy, we investigated how Ets-1 recognizes specific versus nonspecific DNA, with a focus on the roles of protein dynamics and autoinhibition in these processes. Upon binding either DNA, the two marginally stable N-terminal helices of the IM predominantly unfold, but still sample partially ordered conformations...
July 26, 2016: Biochemistry
https://www.readbyqxmd.com/read/27303893/structural-basis-for-dna-recognition-by-the-transcription-regulator-metr
#5
Avinash S Punekar, Jonathan Porter, Stephen B Carr, Simon E V Phillips
MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of the met genes and specifically recognizes the interrupted palindromic sequence 5'-TGAA-N5-TTCA-3'. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2...
June 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27279732/a-novel-approach-to-predict-core-residues-on-cancer-related-dna-binding-domains
#6
Ka-Chun Wong
Protein-DNA interactions are involved in different cancer pathways. In particular, the DNA-binding domains of proteins can determine where and how gene regulatory regions are bound in different cell lines at different stages. Therefore, it is essential to develop a method to predict and locate the core residues on cancer-related DNA-binding domains. In this study, we propose a computational method to predict and locate core residues on DNA-binding domains. In particular, we have selected the cancer-related DNA-binding domains for in-depth studies, namely, winged Helix Turn Helix family, homeodomain family, and basic Helix-Loop-Helix family...
2016: Cancer Informatics
https://www.readbyqxmd.com/read/27171430/structural-analysis-and-insights-into-the-oligomeric-state-of-an-arginine-dependent-transcriptional-regulator-from-bacillus-halodurans
#7
Young Woo Park, Jina Kang, Hyun Ku Yeo, Jae Young Lee
The arginine repressor (ArgR) is an arginine-dependent transcription factor that regulates the expression of genes encoding proteins involved in the arginine biosynthesis and catabolic pathways. ArgR is a functional homolog of the arginine-dependent repressor/activator AhrC from Bacillus subtilis, and belongs to the ArgR/AhrC family of transcriptional regulators. In this research, we determined the structure of the ArgR (Bh2777) from Bacillus halodurans at 2.41 Å resolution by X-ray crystallography. The ArgR from B...
2016: PloS One
https://www.readbyqxmd.com/read/27085804/molecular-insights-into-dna-binding-and-anchoring-by-the-bacillus-subtilis-sporulation-kinetochore-like-raca-protein
#8
Maria A Schumacher, Jeehyun Lee, Wenjie Zeng
During Bacillus subtilis sporulation, segregating sister chromosomes are anchored to cell poles and the chromosome is remodeled into an elongated structure called the axial filament. Data indicate that a developmentally regulated protein called RacA is involved in these functions. To gain insight into how RacA performs these diverse processes we performed a battery of structural and biochemical analyses. These studies show that RacA contains an N-terminal winged-helix-turn-helix module connected by a disordered region to a predicted coiled-coil domain...
June 20, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26953603/regulatory-pan-genome-of-an-obligate-intracellular-pathogen-in-the-pvc-superphylum
#9
Marie de Barsy, Antonio Frandi, Gaël Panis, Laurence Théraulaz, Trestan Pillonel, Gilbert Greub, Patrick H Viollier
Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold...
September 2016: ISME Journal
https://www.readbyqxmd.com/read/26943369/acetylation-of-lysine-201-inhibits-the-dna-binding-ability-of-phop-to-regulate-salmonella-virulence
#10
Jie Ren, Yu Sang, Yongcong Tan, Jing Tao, Jinjing Ni, Shuting Liu, Xia Fan, Wei Zhao, Jie Lu, Wenjuan Wu, Yu-Feng Yao
The two-component system PhoP-PhoQ is highly conserved in bacteria and regulates virulence in response to various signals for bacteria within the mammalian host. Here, we demonstrate that PhoP could be acetylated by Pat and deacetylated by deacetylase CobB enzymatically in vitro and in vivo in Salmonella Typhimurium. Specifically, the conserved lysine residue 201(K201) in winged helix-turn-helix motif at C-terminal DNA-binding domain of PhoP could be acetylated, and its acetylation level decreases dramatically when bacteria encounter low magnesium, acid stress or phagocytosis of macrophages...
March 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/26656831/the-cardiac-stress-response-factor-ms1-can-bind-to-dna-and-has-a-function-in-the-nucleus
#11
Mariola Zaleska, Claudia Fogl, Ay Lin Kho, Abdessamad Ababou, Elisabeth Ehler, Mark Pfuhl
Ms1 (also known as STARS and ABRA) has been shown to act as an early stress response gene in processes as different as hypertrophy in skeletal and cardiac muscle and growth of collateral blood vessels. It is important for cardiac development in zebrafish and is upregulated in mouse models for cardiac hypertrophy as well as in human failing hearts. Ms1 possesses actin binding sites at its C-terminus and is usually found in the cell bound to actin filaments in the cytosol or in sarcomeres. We determined the NMR structure of the only folded domain of Ms1 comprising the second actin binding site called actin binding domain 2 (ABD2, residues 294-375), and found that it is similar to the winged helix-turn-helix fold adopted mainly by DNA binding domains of transcriptional factors...
2015: PloS One
https://www.readbyqxmd.com/read/26438537/a-novel-transcriptional-regulator-of-l-arabinose-utilization-in-human-gut-bacteria
#12
Changsoo Chang, Christine Tesar, Xiaoqing Li, Youngchang Kim, Dmitry A Rodionov, Andrzej Joachimiak
Carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR...
December 2, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/26249357/structure-of-the-dna-binding-domain-of-the-response-regulator-saer-from-staphylococcus-aureus
#13
Xiaojiao Fan, Xu Zhang, Yuwei Zhu, Liwen Niu, Maikun Teng, Baolin Sun, Xu Li
The SaeR/S two-component regulatory system is essential for controlling the expression of many virulence factors in Staphylococcus aureus. SaeR, a member of the OmpR/PhoB family, is a response regulator with an N-terminal regulatory domain and a C-terminal DNA-binding domain. In order to elucidate how SaeR binds to the promoter regions of target genes, the crystal structure of the DNA-binding domain of SaeR (SaeR(DBD)) was solved at 2.5 Å resolution. The structure reveals that SaeR(DBD) exists as a monomer and has the canonical winged helix-turn-helix module...
August 2015: Acta Crystallographica. Section D, Biological Crystallography
https://www.readbyqxmd.com/read/26172911/allosteric-control-of-transcription-in-gntr-family-of-transcription-regulators-a-structural-overview
#14
REVIEW
Deepti Jain
The GntR family of transcription regulators constitutes one of the most abundant family of transcription factors. These modulators are involved in a variety of mechanisms controlling various metabolic processes. GntR family members are typically two domain proteins with a smaller N-terminus domain (NTD) with conserved architecture of winged-helix-turn-helix (wHTH) for DNA binding and a larger C-terminus domain (CTD) or the effector binding domain which is also involved in oligomerization. Interestingly, the CTD shows structural heterogeneity depending upon the type of effector molecule that it binds and displays structural homology to various classes of proteins...
July 2015: IUBMB Life
https://www.readbyqxmd.com/read/26094112/the-functional-landscape-bound-to-the-transcription-factors-of-escherichia-coli-k-12
#15
Ernesto Pérez-Rueda, Silvia Tenorio-Salgado, Alejandro Huerta-Saquero, Yalbi I Balderas-Martínez, Gabriel Moreno-Hagelsieb
Motivated by the experimental evidences accumulated in the last ten years and based on information deposited in RegulonDB, literature look up, and sequence analysis, we analyze the repertoire of 304 DNA-binding Transcription factors (TFs) in Escherichia coli K-12. These regulators were grouped in 78 evolutionary families and are regulating almost half of the total genes in this bacterium. In structural terms, 60% of TFs are composed by two-domains, 30% are monodomain, and 10% three- and four-structural domains...
October 2015: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/26057805/structure-of-the-marr-family-protein-rv0880-from-mycobacterium-tuberculosis
#16
Yun Rong Gao, Na Feng, Tao Chen, De Feng Li, Li Jun Bi
Rv0880 from the pathogen Mycobacterium tuberculosis is classified as a MarR family protein in the Pfam database. It consists of 143 amino acids and has an isoelectric point of 10.9. Crystals of Rv0880 belonged to space group P1, with unit-cell parameters a = 54.97, b = 69.60, c = 70.32 Å, α = 103.71, β = 111.06, γ = 105.83°. The structure of the MarR family transcription regulator Rv0880 was solved at a resolution of 2.0 Å with an R(cryst) and R(free) of 21.2 and 24.9%, respectively. The dimeric structure resembles that of other MarR proteins, with each subunit comprising a winged helix-turn-helix domain connected to an α-helical dimerization domain...
June 2015: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/25979249/structural-and-functional-analysis-of-the-signal-transducing-linker-in-the-ph-responsive-one-component-system-cadc-of-escherichia-coli
#17
Sophie Buchner, Andreas Schlundt, Jürgen Lassak, Michael Sattler, Kirsten Jung
The pH-responsive one-component signaling system CadC in Escherichia coli belongs to the family of ToxR-like proteins, whose members share a conserved modular structure, with an N-terminal cytoplasmic winged helix-turn-helix DNA-binding domain being followed by a single transmembrane helix and a C-terminal periplasmic pH-sensing domain. In E. coli CadC, a cytoplasmic linker comprising approximately 50 amino acids is essential for transmission of the signal from the sensor to the DNA-binding domain. However, the mechanism of transduction is poorly understood...
July 31, 2015: Journal of Molecular Biology
https://www.readbyqxmd.com/read/25605793/identification-of-the-target-dna-sequence-and-characterization-of-dna-binding-features-of-hlyu-and-suggestion-of-a-redox-switch-for-hlya-expression-in-the-human-pathogen-vibrio-cholerae-from-in-silico-studies
#18
Debadrita Mukherjee, Aritrika Pal, Devlina Chakravarty, Pinak Chakrabarti
HlyU, a transcriptional regulator common in many Vibrio species, activates the hemolysin gene hlyA in Vibrio cholerae, the rtxA1 operon in Vibrio vulnificus and the genes of plp-vah1 and rtxACHBDE gene clusters in Vibrio anguillarum. The protein is also proposed to be a potential global virulence regulator for V. cholerae and V. vulnificus. Mechanisms of gene control by HlyU in V. vulnificus and V. anguillarum are reported. However, detailed elucidation of the interaction of HlyU in V. cholerae with its target DNA at the molecular level is not available...
February 18, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25550425/structural-basis-of-dna-recognition-by-pcg2-reveals-a-novel-dna-binding-mode-for-winged-helix-turn-helix-domains
#19
Junfeng Liu, Jinguang Huang, Yanxiang Zhao, Huaian Liu, Dawei Wang, Jun Yang, Wensheng Zhao, Ian A Taylor, You-Liang Peng
The MBP1 family proteins are the DNA binding subunits of MBF cell-cycle transcription factor complexes and contain an N terminal winged helix-turn-helix (wHTH) DNA binding domain (DBD). Although the DNA binding mechanism of MBP1 from Saccharomyces cerevisiae has been extensively studied, the structural framework and the DNA binding mode of other MBP1 family proteins remains to be disclosed. Here, we determined the crystal structure of the DBD of PCG2, the Magnaporthe oryzae orthologue of MBP1, bound to MCB-DNA...
January 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25543962/genetics-of-critical-contacts-and-clashes-in-the-dna-packaging-specificities-of-bacteriophages-%C3%AE-and-21
#20
COMPARATIVE STUDY
Jean Sippy, Priyal Patel, Nicole Vahanian, Rachel Sippy, Michael Feiss
The cos sites in λ and 21 chromosomes contain binding sites that recruit terminase to initiate DNA packaging. The small subunits of terminase, gpNu1 (λ) and gp1 (21), have winged helix-turn-helix DNA binding domains, where the recognition helixes differ in four of nine residues. To initiate packaging, the small subunit binds three R sequences in the cosB subsite. λ and 21 cannot package each other׳s DNA, due to recognition helix and R sequence differences. In λ and 21 cosBs, two bp, tri1 and tri2, are conserved in the R sequences yet differ between the phages; they are proposed to play a role in phage-specific packaging by λ and 21...
February 2015: Virology
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