Journal ArticleDOI
Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA
David B. McKay,Thomas A. Steitz +1 more
TLDR
The 2.9 Å resolution crystal structure of Escherichia coli catabolite gene activator protein (CAP) completed with cyclic AMP reveals two distinct structural domains separated by a cleft, suggesting that the CAP conversion of right- to left-handed DNA in a closed supercoil, is what activates transcription by RNA polymerase.Abstract:
The 2.9 A resolution crystal structure of Escherichia coli catabolite gene activator protein (CAP) complexed with cyclic AMP reveals two distinct structural domains separated by a cleft. The smaller carboxy-terminal domain is presumed to bind DNA while the amino-terminal domain is seen to bind cyclic AMP. Model building studies suggest that CAP binds to left-handed B-type DNA, contracting its major groove via two alpha-helices. It is possible that the CAP conversion of right- to left-handed DNA in a closed supercoil, is what activates transcription by RNA polymerase.read more
Citations
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Ligand-linked structural changes in the Escherichia coli biotin repressor: the significance of surface loops for binding and allostery.
TL;DR: Results implicate the C-terminal domain of BirA, for which no function has previously been known, in small ligand and site-specific DNA binding and highlight the significance of surface loops, some of which are disordered in the apoBirA structure, for ligand binding and transmission of allosteric information in the protein.
Journal ArticleDOI
The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium.
TL;DR: The dimerization of the O2 sensor FNR is regulated by extremely fine-tuned interactions, mediated by two salt bridges near the amino-terminal cluster-binding domain and an “imperfect” coiled-coil dimer interface.
Journal ArticleDOI
Crystal structure of CO-sensing transcription activator CooA bound to exogenous ligand imidazole.
Hirofumi Komori,Sayaka Inagaki,Sayaka Inagaki,Shiro Yoshioka,Shigetoshi Aono,Yoshiki Higuchi +5 more
TL;DR: The results indicate that the release of the N terminus resulting from imidazole binding is not sufficient to activate CooA, and the structure provides new insights into the structural changes required to achieve activation.
Journal ArticleDOI
Possible molecular detent in the DNA structure at regulatory sequences.
TL;DR: A common feature that appears in a number of DNA sites where proteins interact is the sequence GTG/CAC, which leads to a region with a higher imino proton exchange rate well below the optical melting temperature.
Journal ArticleDOI
Identification of the DNA binding domain of the phage lambda cII transcriptional activator and the direct correlation of cII protein stability with its oligomeric forms.
TL;DR: The bacteriophage lambda transcriptional activator protein cII is a DNA-binding protein that coordinately regulates transcription from phage promoters important for lysogenic growth and an Escherichia coli HtpR- strain has been identified that greatly stabilizes these highly unstable cII mutants.
References
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Journal ArticleDOI
Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution.
TL;DR: The haemagglutinin glycoprotein of influenza virus is a trimer comprising two structurally distinct regions: a triple-stranded coiled-coil of α-helices extends 76 Å from the membrane and a globular region of antiparallel β-sheet is positioned on top of this stem.
Journal ArticleDOI
Molecular structure of a left-handed double helical DNA fragment at atomic resolution
Andrew H.-J. Wang,Gary J. Quigley,F. Kolpak,J.L. Crawford,J. H. Van Boom,G. A. Van Der Marel,Alexander Rich +6 more
TL;DR: The DNA fragment d(CpGpCpC pGp CpG pG) crystallises as a left-handed double helical molecule with Watson–Crick base pairs and an antiparallel organisation of the sugar phosphate chains.
Journal ArticleDOI
Optimised parameters for A-DNA and B-DNA
TL;DR: The molecular structures presented have the most probable values of bond-lengths, bond-angles and furanose ring conformations as defined by accurate X-ray crystallographic analyses of relevant monomers.
Journal ArticleDOI
Three-Dimensional Structure of Immunoglobulins
L M Amzel,Roberto J. Poljak +1 more
TL;DR: This chapter discusses a study analyzing the three-dimensional structure of immunoglobulins, in which the periodicity of the crystal was used to reduce the background noise and reveal the molecular outline.
Journal ArticleDOI
Tomato bushy stunt virus at 2.9 A resolution.
Stephen C. Harrison,Arthur J. Olson,Clarence E. Schutt,Clarence E. Schutt,Frank Winkler,Frank Winkler,Gérard Bricogne +6 more
TL;DR: The polypeptide chain of a TBSV subunit folds into two domains, connected by a hinge, and a flexibly-linked N-terminal arm, and RNA is also not uniquely fixed to sites on the major domains.
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