Protein Contact (protein + contact)

Distribution by Scientific Domains

Terms modified by Protein Contact

  • protein contact dermatitis

  • Selected Abstracts


    Novel mode of transcription regulation by SdiA, an Escherichia coli homologue of the quorum-sensing regulator

    MOLECULAR MICROBIOLOGY, Issue 5 2001
    Kaneyoshi Yamamoto
    SdiA, an Escherichia coli homologue of the quorum-sensing regulator, controls the expression of the ftsQAZ operon for cell division. Transcription of ftsQ is under the control of two promoters, upstream ftsQP2 and downstream ftsQP1, which are separated by 125 bp. SdiA activates transcription from ftsQP2 in vivo. Here, we demonstrate that SdiA facilitates the RNA polymerase binding to ftsQP2 and thereby stimulates transcription from P2. Gel shift and DNase I footprinting assays indicated that SdiA binds to the ftsQP2 promoter region between ,51 and ,25 with respect to the P2 promoter. Activation of ftsQP2 transcription by SdiA was observed with a mutant RNA polymerase containing a C-terminal domain (CTD)-deleted ,-subunit (,235) but not with RNA polymerase containing ,S or a CTD-deleted ,D (,D529). In good agreement with the transcription assay, no protection of P2 was observed with the RNA polymerase holoenzymes, E,S and E,D529. These observations together indicate that: (i) SdiA supports the RNA polymerase binding to ftsQP2; and (ii) this recruitment of RNA polymerase by SdiA depends on the presence of intact ,CTD. This is in contrast to the well-known mechanism of RNA polymerase recruitment by protein,protein contact between class I factors and ,CTD. In addition to the P2 activation, SdiA inhibited RNA polymerase binding to the ftsQP1 promoter and thereby repressed transcription from P1. Gel shift assays indicate weak binding of SdiA to the P1 promoter region downstream from ,13 (or +112 with respect to P2). Neither ,CTD nor ,CTD are required for this inhibition. Thus, the transcription repression of P1 by SdiA may result from its competition with the RNA polymerase in binding to this promoter. [source]


    Mobile loop mutations in an archaeal inositol monophosphatase: Modulating three-metal ion assisted catalysis and lithium inhibition

    PROTEIN SCIENCE, Issue 2 2010
    Zheng Li
    Abstract The inositol monophosphatase (IMPase) enzyme from the hyperthermophilic archaeon Methanocaldococcus jannaschii requires Mg2+ for activity and binds three to four ions tightly in the absence of ligands: KD = 0.8 ,M for one ion with a KD of 38 ,M for the other Mg2+ ions. However, the enzyme requires 5,10 mM Mg2+ for optimum catalysis, suggesting substrate alters the metal ion affinity. In crystal structures of this archaeal IMPase with products, one of the three metal ions is coordinated by only one protein contact, Asp38. The importance of this and three other acidic residues in a mobile loop that approaches the active site was probed with mutational studies. Only D38A exhibited an increased kinetic KD for Mg2+; D26A, E39A, and E41A showed no significant change in the Mg2+ requirement for optimal activity. D38A also showed an increased Km, but little effect on kcat. This behavior is consistent with this side chain coordinating the third metal ion in the substrate complex, but with sufficient flexibility in the loop such that other acidic residues could position the Mg2+ in the active site in the absence of Asp38. While lithium ion inhibition of the archaeal IMPase is very poor (IC50,250 mM), the D38A enzyme has a dramatically enhanced sensitivity to Li+ with an IC50 of 12 mM. These results constitute additional evidence for three metal ion assisted catalysis with substrate and product binding reducing affinity of the third necessary metal ion. They also suggest a specific mode of action for lithium inhibition in the IMPase superfamily. [source]


    Structure of the human p53 core domain in the absence of DNA

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2007
    Ying Wang
    The tumor suppressor protein p53 plays a key role in cell-cycle regulation by triggering DNA repair, cell-cycle arrest and apoptosis when the appropriate signal is received. p53 has the classic architecture of a transcription factor, with an amino-terminal transactivation domain, a core DNA-binding domain and carboxy-terminal tetramerization and regulatory domains. The crystal structure of the p53 core domain, which includes the amino acids from residue 96 to residue 289, has been determined in the absence of DNA to a resolution of 2.05,Å. Crystals grew in a new monoclinic space group (P21), with unit-cell parameters a = 68.91, b = 69.36, c = 84.18,Å, , = 90.11°. The structure was solved by molecular replacement and has been refined to a final R factor of 20.9% (Rfree = 24.6%). The final model contains four molecules in the asymmetric unit with four zinc ions and 389 water molecules. The non-crystallographic tetramers display different protein contacts from those in other p53 crystals, giving rise to the question of how p53 arranges as a tetramer when it binds its target DNA. [source]


    Structure of the apo form of the catabolite control protein A (CcpA) from Bacillus megaterium with a DNA-binding domain

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2007
    Rajesh Kumar Singh
    Crystal structure determination of catabolite control protein A (CcpA) at 2.6,Å resolution reveals for the first time the structure of a full-length apo-form LacI-GalR family repressor protein. In the crystal structures of these transcription regulators, the three-helix bundle of the DNA-binding domain has only been observed in cognate DNA complexes; it has not been observed in other crystal structures owing to its mobility. In the crystal packing of apo-CcpA, the protein,protein contacts between the N-terminal three-helix bundle and the core domain consisted of interactions between the homodimers that were similar to those between the corepressor protein HPr and the CcpA N-subdomain in the ternary DNA complex. In contrast to the DNA complex, the apo-CcpA structure reveals large subdomain movements in the core, resulting in a complete loss of contacts between the N-subdomains of the homodimer. [source]