2p5l › Citations

Structure and function of the arginine repressor-operator complex from Bacillus subtilis.

Garnett JA, Marincs F, Baumberg S, Stockley PG, Phillips SE
J Mol Biol 379 284-98 (2008)
Cited: 24 times
EuropePMC logo PMID: 18455186

Abstract

In many bacteria, the concentration of L-arginine is controlled by a transcriptional regulator, the arginine repressor. In Bacillus subtilis this transcription factor is called AhrC and has roles in both the repression and activation of the genes involved in arginine metabolism. It interacts with 18 bp ARG boxes in the promoters of arginine biosynthetic and catabolic operons. AhrC is a hexamer and each subunit has two domains. The C-terminal domains form the core, mediating inter-subunit interactions and L-arginine binding, while the N-terminal domains contain a winged helix-turn-helix DNA-binding motif and are arranged around the periphery. Upon binding of the co-repressor L-arginine there is a approximately 15 degrees relative rotation between core C-terminal trimers. Here, we report the X-ray crystal structure of a dimer of the N-terminal domains of AhrC (NAhrC) in complex with an 18 bp DNA ARG box operator, refined to 2.85 A resolution. Comparison of the N-terminal domains within this complex with those of the free domain reveals that the flexible beta-wings of the DNA-binding motif in the free domain form a stable dimer interface in the protein-DNA complex, favouring correct orientation of the recognition helices. These are then positioned to insert into adjacent turns of the major groove of the ARG box, whilst the wings contact the minor groove. There are extensive contacts between the protein and the DNA phosphodiester backbone, as well as a number of direct hydrogen bonds between conserved amino acid side chains and bases. Combining this structure with other crystal structures of other AhrC components, we have constructed a model of the repression complex of AhrC at the B. subtilis biosynthetic argC operator and, along with transcriptome data, analysed the origins of sequence specificity and arginine activation.

Articles - 2p5l mentioned but not cited (4)

  1. Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance. McMahon SA, Roberts GA, Johnson KA, Cooper LP, Liu H, White JH, Carter LG, Sanghvi B, Oke M, Walkinshaw MD, Blakely GW, Naismith JH, Dryden DT. Nucleic Acids Res 37 4887-4897 (2009)
  2. Local conformational changes in the DNA interfaces of proteins. Sunami T, Kono H. PLoS One 8 e56080 (2013)
  3. Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex. Chaix D, Ferguson ML, Atmanene C, Van Dorsselaer A, Sanglier-Cianférani S, Royer CA, Declerck N. Nucleic Acids Res 38 5944-5957 (2010)
  4. Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors. Pandey SK, Melichercik M, Řeha D, Ettrich RH, Carey J. Molecules 25 E2247 (2020)


Articles citing this publication (20)

  1. Structure of the LexA-DNA complex and implications for SOS box measurement. Zhang AP, Pigli YZ, Rice PA. Nature 466 883-886 (2010)
  2. ArgR is an essential local transcriptional regulator of the arcABC operon in Streptococcus suis and is crucial for biological fitness in an acidic environment. Fulde M, Willenborg J, de Greeff A, Benga L, Smith HE, Valentin-Weigand P, Goethe R. Microbiology (Reading) 157 572-582 (2011)
  3. Crystal structure of ArgP from Mycobacterium tuberculosis confirms two distinct conformations of full-length LysR transcriptional regulators and reveals its function in DNA binding and transcriptional regulation. Zhou X, Lou Z, Fu S, Yang A, Shen H, Li Z, Feng Y, Bartlam M, Wang H, Rao Z. J Mol Biol 396 1012-1024 (2010)
  4. Insight into the induction mechanism of the GntR/HutC bacterial transcription regulator YvoA. Resch M, Schiltz E, Titgemeyer F, Muller YA. Nucleic Acids Res 38 2485-2497 (2010)
  5. Regulation of the arginine deiminase system by ArgR2 interferes with arginine metabolism and fitness of Streptococcus pneumoniae. Schulz C, Gierok P, Petruschka L, Lalk M, Mäder U, Hammerschmidt S. mBio 5 e01858-14 (2014)
  6. Identification of protein candidates for the serodiagnosis of Q fever endocarditis by an immunoproteomic approach. Sekeyová Z, Kowalczewska M, Decloquement P, Pelletier N, Spitalská E, Raoult D. Eur J Clin Microbiol Infect Dis 28 287-295 (2009)
  7. ArgR of Streptomyces coelicolor is a versatile regulator. Pérez-Redondo R, Rodríguez-García A, Botas A, Santamarta I, Martín JF, Liras P. PLoS One 7 e32697 (2012)
  8. Listeria monocytogenes 10403S Arginine Repressor ArgR Finely Tunes Arginine Metabolism Regulation under Acidic Conditions. Cheng C, Dong Z, Han X, Sun J, Wang H, Jiang L, Yang Y, Ma T, Chen Z, Yu J, Fang W, Song H. Front Microbiol 8 145 (2017)
  9. Solution structure and DNA-binding properties of the winged helix domain of the meiotic recombination HOP2 protein. Moktan H, Guiraldelli MF, Eyster CA, Zhao W, Lee CY, Mather T, Camerini-Otero RD, Sung P, Zhou DH, Pezza RJ. J Biol Chem 289 14682-14691 (2014)
  10. Mutational activation of the RocR activator and of a cryptic rocDEF promoter bypass loss of the initial steps of proline biosynthesis in Bacillus subtilis. Zaprasis A, Hoffmann T, Wünsche G, Flórez LA, Stülke J, Bremer E. Environ Microbiol 16 701-717 (2014)
  11. The structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and Co-repressor, L-arginine. Cherney LT, Cherney MM, Garen CR, James MN. J Mol Biol 388 85-97 (2009)
  12. Crystal structure of the arginine repressor protein in complex with the DNA operator from Mycobacterium tuberculosis. Cherney LT, Cherney MM, Garen CR, Lu GJ, James MN. J Mol Biol 384 1330-1340 (2008)
  13. Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. Malhotra S, Sowdhamini R. BMC Bioinformatics 13 165 (2012)
  14. Crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression. Cherney LT, Cherney MM, Garen CR, James MN. J Mol Biol 399 240-254 (2010)
  15. Catabolic Ornithine Carbamoyltransferase Activity Facilitates Growth of Staphylococcus aureus in Defined Medium Lacking Glucose and Arginine. Reslane I, Halsey CR, Stastny A, Cabrera BJ, Ahn J, Shinde D, Galac MR, Sladek MF, Razvi F, Lehman MK, Bayles KW, Thomas VC, Handke LD, Fey PD. mBio 13 e0039522 (2022)
  16. Crystallization and preliminary X-ray diffraction analysis of the arginine repressor ArgR from Bacillus halodurans. Kang J, Park YW, Yeo HK, Lee JY. Acta Crystallogr F Struct Biol Commun 71 291-294 (2015)
  17. L-Proline Synthesis Mutants of Bacillus subtilis Overcome Osmotic Sensitivity by Genetically Adapting L-Arginine Metabolism. Stecker D, Hoffmann T, Link H, Commichau FM, Bremer E. Front Microbiol 13 908304 (2022)
  18. Structural Analysis and Insights into the Oligomeric State of an Arginine-Dependent Transcriptional Regulator from Bacillus halodurans. Park YW, Kang J, Yeo HK, Lee JY. PLoS One 11 e0155396 (2016)
  19. In Silico Analysis of Changes in Predicted Metabolic Capabilities of Intestinal Microbiota after Fecal Microbial Transplantation for Treatment of Recurrent Clostridioides difficile Infection. Dahiya M, Jovel J, Monaghan T, Wong K, Elhenawy W, Chui L, McAlister F, Kao D. Microorganisms 11 1078 (2023)
  20. Tyrosine binding and promiscuity in the arginine repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis. Mariutti RB, Ullah A, Araujo GC, Murakami MT, Arni RK. Biochem Biophys Res Commun 475 350-355 (2016)


Quick links