scholarly journals Functional and structural analysis of catabolite control protein C that responds to citrate

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei Liu ◽  
Jinli Chen ◽  
Liming Jin ◽  
Zi-Yong Liu ◽  
Ming Lu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein C ◽  
Functional Divergence ◽  
Tca Cycle ◽  
Structural Basis ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Interactions ◽  
Genes Encoding ◽  
Control Protein ◽  
Catabolite Control

AbstractCatabolite control protein C (CcpC) belongs to the LysR-type transcriptional regulator (LTTR) family, which regulates the transcription of genes encoding the tricarboxylic acid branch enzymes of the TCA cycle by responding to a pathway-specific metabolite, citrate. The biological function of CcpC has been characterized several times, but the structural basis for the molecular function of CcpC remains elusive. Here, we report the characterization of a full-length CcpC from Bacillus amyloliquefaciens (BaCcpC-FL) and a crystal structure of the C-terminal inducer-binding domain (IBD) complexed with citrate. BaCcpC required both dyad symmetric regions I and II to recognize the citB promoter, and the presence of citrate reduced citB promoter binding. The crystal structure of CcpC-IBD shows two subdomains, IBD-I and IBD-II, and a citrate molecule buried between them. Ile100, two arginines (Arg147 and Arg260), and three serines (Ser129, Ser189, and Ser191) exhibit strong hydrogen-bond interactions with citrate molecules. A structural comparison of BaCcpC-IBD with its homologues showed that they share the same tail-to-tail dimer alignment, but the dimeric interface and the rotation between these molecules exhibit significant differences. Taken together, our results provide a framework for understanding the mechanism underlying the functional divergence of the CcpC protein.

scholarly journals Functional and structural analysis of a catabolite control protein C that responds to citrate

2021 ◽  
Author(s):  
Wei Liu ◽  
Jinli Chen ◽  
Liming Jin ◽  
Zi-Yong Liu ◽  
Ming Lu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein C ◽  
Functional Divergence ◽  
Tca Cycle ◽  
Structural Basis ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Interactions ◽  
Genes Encoding ◽  
Control Protein ◽  
Catabolite Control

Abstract Catabolite control protein C (CcpC) belongs to the LysR-type transcriptional regulator (LTTR) family that regulates the transcription of genes encoding the tricarboxylic acid branch enzymes of the TCA cycle by responding to a pathway-specific metabolite, citrate. The biological function of CcpC has been characterized several times, but the structural basis for the molecular function of CcpC remains elusive. Here, we report characterization of a full-length CcpC from Bacillus amyloliquefaciens (BaCcpC-FL) and a crystal structure of the C-terminal inducer-binding domain (IBD) complexed with citrate. BaCcpC required both dyad symmetric regions I and II to recognize the citB promoter, and the presence of citrate reduced citB promoter binding. The crystal structure of CcpC-IBD shows two subdomains, IBD-I and IBD-II, and a citrate molecule buried between them. Ile100, two arginines (Arg147 and Arg260), and three serines (Ser129, Ser189, and Ser191) have strong hydrogen-bond interactions with citrate molecules. A structural comparison of BaCcpC-IBD with its homologues shows that they share the same tail-to-tail dimer alignment, but the dimeric interface and the rotation between these molecules exhibit significant differences. In addition, citrate can convert large BaCcpC-FL oligomers to monomers in solution. Taken together, our results provide a framework for understanding the mechanism underlying the functional divergence of the CcpC protein.

scholarly journals Crystal structure of human angiogenin reveals the structural basis for its functional divergence from ribonuclease.

1994 ◽  
Vol 91 (8) ◽  
pp. 2915-2919 ◽  
Author(s):  
K. R. Acharya ◽  
R. Shapiro ◽  
S. C. Allen ◽  
J. F. Riordan ◽  
B. L. Vallee
Keyword(s):  
Crystal Structure ◽  
Functional Divergence ◽  
Structural Basis

scholarly journals Analysis of Catabolite Control Protein A-Dependent Repression inStaphylococcus xylosus by a Genomic Reporter Gene System

2001 ◽  
Vol 183 (2) ◽  
pp. 580-586 ◽  
Author(s):  
Ivana Jankovic ◽  
Oliver Egeter ◽  
Reinhold Brückner
Keyword(s):  
Glucose Uptake ◽  
Reporter Gene ◽  
Protein A ◽  
Single Copy ◽  
Reporter System ◽  
Promoter Regions ◽  
Genes Encoding ◽  
Glucose Kinase ◽  
Control Protein ◽  
Catabolite Control

ABSTRACT A single-copy reporter system for Staphylococcus xylosus has been developed, that uses a promoterless version of the endogenous β-galactosidase gene lacH as a reporter gene and that allows integration of promoters cloned in front oflacH into the lactose utilization gene cluster by homologous recombination. The system was applied to analyze carbon catabolite repression of S. xylosus promoters by the catabolite control protein CcpA. To test if lacHis a suitable reporter gene, β-galactosidase activities directed by two promoters known to be subject to CcpA regulation were measured. In these experiments, repression of the malRAmaltose utilization operon promoter and autoregulation of theccpA promoters were confirmed, proving the applicability of the system. Subsequently, putative CcpA operators, termed catabolite-responsive elements (cres), from promoter regions of several S. xylosus genes were tested for their ability to confer CcpA regulation upon a constitutive promoter, P vegII. For that purpose, cresequences were placed at position +3 or +4 within the transcribed region of P vegII. Measurements of β-galactosidase activities in the presence or absence of glucose yielded repression ratios between two- and eightfold. Inactivation of ccpA completely abolished glucose-dependent regulation. Therefore, the tested cres functioned as operator sites for CcpA. With promoters exclusively regulated by CcpA, signal transduction leading to CcpA activation in S. xylosus was examined. Glucose-dependent regulation was measured in a set of isogenic mutants showing defects in genes encoding glucose kinase GlkA, glucose uptake protein GlcU, and HPr kinase HPrK. GlkA and GlcU deficiency diminished glucose-dependent CcpA-mediated repression, but loss of HPr kinase activity abolished regulation. These results clearly show that HPr kinase provides the essential signal to activate CcpA in S. xylosus. Glucose uptake protein GlcU and glucose kinase GlkA participate in activation, but they are not able to trigger CcpA-mediated regulation independently from HPr kinase.

scholarly journals Crystal Growth and Characterization of the Non-Centrosymmetric Hydrated Co-hexaborate templated by racemic 2-methylpiperazinium (C5H14N2){Co[B6O7(OH)6]2}.2H2O

2014 ◽  
Vol 10 (3) ◽  
pp. 2377-2387 ◽  
Author(s):  
Samah Akriche ◽  
Aymen Tliba ◽  
Mohamed Rzaigui
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Organic Cation ◽  
Strong Hydrogen Bond ◽  
Single Crystal Xrd ◽  
Photoluminescent Property ◽  
Gap Energy ◽  
Hydrogen Bond Interactions ◽  
Semiconductor Behavior

Large single crystals of the non-centrosymmetric hydrated Co-hexaborate (C5H14N2){Co[B6O7(OH)6]2}.2H2O were grown from aqueous solution and characterized by powder and single-crystal XRD methods, IR, UV-Vis and photoluminescence spectroscopy measurements. Single-crystal XRD analyses show that the reported compound crystallizes in the orthorhombic non-centrosymmetric space group Fdd2 and its crystal structure consists of anionic molecular Co-hexaborate units arranged into 3D-supramolecular honey-comb like structure network with the organic cation and water of crystallization occupying large tunnels voids along [110] through strong hydrogen bond interactions. In addition, Its electronic properties have also been investigated showing a considerable important gap energy well proving the semiconductor behavior and the photoluminescent property of reported material.

Crystal structure of tamsulosin hydrochloride, C20H29N2O5SCl

2021 ◽  
pp. 1-7
Author(s):  
Nilan V. Patel ◽  
Joseph T. Golab ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Atom ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbon Chain ◽  
Strong Hydrogen Bond ◽  
Powder Diffraction File ◽  
Ether Oxygen ◽  
Sulfonamide Group

The crystal structure of tamsulosin hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Tamsulosin hydrochloride crystallizes in space group P21 (#4) with a = 7.62988(2), b = 9.27652(2), c = 31.84996(12) Å, β = 93.2221(2)°, V = 2250.734(7) Å3, and Z = 4. In the crystal structure, two arene rings are connected by a carbon chain oriented roughly parallel to the c-axis. The crystal structure is characterized by two slabs of tamsulosin hydrochloride molecules perpendicular to the c-axis. As expected, each of the hydrogens on the protonated nitrogen atoms makes a strong hydrogen bond to one of the chloride anions. The result is to link the cations and anions into columns along the b-axis. One hydrogen atom of each sulfonamide group also makes a hydrogen bond to a chloride anion. The other hydrogen atom of each sulfonamide group forms bifurcated hydrogen bonds to two ether oxygen atoms. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1415.

scholarly journals Structural basis of Naa20 activity towards a canonical NatB substrate

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Dominik Layer ◽  
Jürgen Kopp ◽  
Miriam Fontanillo ◽  
Maja Köhn ◽  
Karine Lapouge ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Drug Development ◽  
Catalytic Mechanism ◽  
Peptide Binding ◽  
Competitive Inhibitor ◽  
Structural Basis ◽  
Substrate Affinity ◽  
Protein Homeostasis ◽  
Auxiliary Subunit

AbstractN-terminal acetylation is one of the most common protein modifications in eukaryotes and is carried out by N-terminal acetyltransferases (NATs). It plays important roles in protein homeostasis, localization, and interactions and is linked to various human diseases. NatB, one of the major co-translationally active NATs, is composed of the catalytic subunit Naa20 and the auxiliary subunit Naa25, and acetylates about 20% of the proteome. Here we show that NatB substrate specificity and catalytic mechanism are conserved among eukaryotes, and that Naa20 alone is able to acetylate NatB substrates in vitro. We show that Naa25 increases the Naa20 substrate affinity, and identify residues important for peptide binding and acetylation activity. We present the first Naa20 crystal structure in complex with the competitive inhibitor CoA-Ac-MDEL. Our findings demonstrate how Naa20 binds its substrates in the absence of Naa25 and support prospective endeavors to derive specific NAT inhibitors for drug development.

scholarly journals Production of succinate by engineered strains of Synechocystis PCC 6803 overexpressing phosphoenolpyruvate carboxylase and a glyoxylate shunt

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Claudia Durall ◽  
Kateryna Kukil ◽  
Jeffrey A. Hawkes ◽  
Alessia Albergati ◽  
Peter Lindblad ◽  
...  
Keyword(s):  
Phosphoenolpyruvate Carboxylase ◽  
Isocitrate Lyase ◽  
Tricarboxylic Acid Cycle ◽  
Cell Metabolism ◽  
Tca Cycle ◽  
Malate Synthase ◽  
Glyoxylate Shunt ◽  
Control Strain ◽  
Genes Encoding ◽  
Pcc 6803

Abstract Background Cyanobacteria are promising hosts for the production of various industrially important compounds such as succinate. This study focuses on introduction of the glyoxylate shunt, which is naturally present in only a few cyanobacteria, into Synechocystis PCC 6803. In order to test its impact on cell metabolism, engineered strains were evaluated for succinate accumulation under conditions of light, darkness and anoxic darkness. Each condition was complemented by treatments with 2-thenoyltrifluoroacetone, an inhibitor of succinate dehydrogenase enzyme, and acetate, both in nitrogen replete and deplete medium. Results We were able to introduce genes encoding the glyoxylate shunt, aceA and aceB, encoding isocitrate lyase and malate synthase respectively, into a strain of Synechocystis PCC 6803 engineered to overexpress phosphoenolpyruvate carboxylase. Our results show that complete expression of the glyoxylate shunt results in higher extracellular succinate accumulation compared to the wild type control strain after incubation of cells in darkness and anoxic darkness in the presence of nitrate. Addition of the inhibitor 2-thenoyltrifluoroacetone increased succinate titers in all the conditions tested when nitrate was available. Addition of acetate in the presence of the inhibitor further increased the succinate accumulation, resulting in high levels when phosphoenolpyruvate carboxylase was overexpressed, compared to control strain. However, the highest succinate titer was obtained after dark incubation of an engineered strain with a partial glyoxylate shunt overexpressing isocitrate lyase in addition to phosphoenolpyruvate carboxylase, with only 2-thenoyltrifluoroacetone supplementation to the medium. Conclusions Heterologous expression of the glyoxylate shunt with its central link to the tricarboxylic acid cycle (TCA) for acetate assimilation provides insight on the coordination of the carbon metabolism in the cell. Phosphoenolpyruvate carboxylase plays an important role in directing carbon flux towards the TCA cycle.

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