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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Crystallographic study of mechanism of ribonuclease T1-catalysed specific RNA hydrolysis.
Udo Heinemann,Wolfram Saenger +1 more
TL;DR: X-Ray analysis provided insight in the geometry of the active site and in the parts of the enzyme involved in the recognition of guanosine, showing that Glu58, His92 and Arg77 are active in phosphodiester hydrolysis.
Journal ArticleDOI
Amplification of signaling via cellular allosteric relay and protein disorder
Buyong Ma,Ruth Nussinov +1 more
TL;DR: In this issue of PNAS, Popovych et al. found that without cAMP binding, the CAP apo form loses 3 helical turns and the DNA binding domain rotates, shifting from its DNA binding-ready state.
Journal ArticleDOI
Determination of the Conformations of cAMP Receptor Protein and Its T127L,S128A Mutant with and without cAMP from Small Angle Neutron Scattering Measurements
Susan Krueger,Inna Gorshkova,James E. Brown,Joel Hoskins,Keith McKenney,Frederick P. Schwarz +5 more
TL;DR: It appears that CRP undergoes a conformational change from the open form to the closed form in solution upon ligation with cAMP, and there is very little structural difference between the two species of CRP*.
Journal ArticleDOI
Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches.
Shuichi Hirono,Peter A. Kollman +1 more
TL;DR: The analyses suggest that the mutation from Glu46 to Gln may lead to a preference of RNase T1 for adenine in contrast to the guanine preference of the wild-type enzyme, and the molecular dynamics/free energy perturbation method will be useful for both energetic and structural analysis of protein-ligand interactions.
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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