A Folded Excited State of Ligand-Free Nuclear Coactivator Binding Domain (NCBD) Underlies Plasticity in Ligand Recognition

Biochemistry ◽  
2013 ◽  
Vol 52 (10) ◽  
pp. 1686-1693 ◽  
Author(s):  
Magnus Kjaergaard ◽  
Lisbeth Andersen ◽  
Lau Dalby Nielsen ◽  
Kaare Teilum
Keyword(s):  
Excited State ◽  
Binding Domain ◽  
Ligand Recognition ◽  
Ligand Free

An enzyme captured in two conformational states: crystal structure ofS-adenosyl-L-homocysteine hydrolase fromBradyrhizobium elkanii

2015 ◽  
Vol 71 (12) ◽  
pp. 2422-2432 ◽  
Author(s):  
Tomasz Manszewski ◽  
Kriti Singh ◽  
Barbara Imiolczyk ◽  
Mariusz Jaskolski
Keyword(s):  
Crystal Structure ◽  
Enzymatic Reaction ◽  
Binding Domain ◽  
Dimerization Domain ◽  
Biologically Relevant ◽  
Cofactor Binding ◽  
Enzymatic Regulation ◽  
Ligand Free ◽  
Substrate Binding Domain ◽  
Methyl Group Transfer

S-Adenosyl-L-homocysteine hydrolase (SAHase) is involved in the enzymatic regulation ofS-adenosyl-L-methionine (SAM)-dependent methylation reactions. After methyl-group transfer from SAM,S-adenosyl-L-homocysteine (SAH) is formed as a byproduct, which in turn is hydrolyzed to adenosine (Ado) and homocysteine (Hcy) by SAHase. The crystal structure of BeSAHase, an SAHase fromBradyrhizobium elkanii, which is a nitrogen-fixing bacterial symbiont of legume plants, was determined at 1.7 Å resolution, showing the domain organization (substrate-binding domain, NAD+cofactor-binding domain and dimerization domain) of the subunits. The protein crystallized in its biologically relevant tetrameric form, with three subunits in a closed conformation enforced by complex formation with the Ado product of the enzymatic reaction. The fourth subunit is ligand-free and has an open conformation. The BeSAHase structure therefore provides a unique snapshot of the domain movement of the enzyme induced by the binding of its natural ligands.

Structure and ligand recognition of the phosphotyrosine binding domain of Shc

Nature ◽  
1995 ◽  
Vol 378 (6557) ◽  
pp. 584-592 ◽  
Author(s):  
Ming-Ming Zhou ◽  
Kodimangalam S. Ravichandran ◽  
Edward T. Olejniczak ◽  
Andrew M. Petros ◽  
Robert P. Meadows ◽  
...  
Keyword(s):  
Binding Domain ◽  
Ligand Recognition ◽  
Phosphotyrosine Binding Domain

scholarly journals Ligand recognition by A‐class Eph receptors: crystal structures of the EphA2 ligand‐binding domain and the EphA2/ephrin‐A1 complex

EMBO Reports ◽  
2009 ◽  
Vol 10 (7) ◽  
pp. 722-728 ◽  
Author(s):  
Juha P Himanen ◽  
Yehuda Goldgur ◽  
Hui Miao ◽  
Eugene Myshkin ◽  
Hong Guo ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Crystal Structures ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Ligand Recognition ◽  
Eph Receptors

scholarly journals Biochemical mapping of a ligand-binding domain within Arabidopsis BAM1 reveals diversified ligand recognition mechanisms of plant LRR-RKs

2012 ◽  
Vol 70 (5) ◽  
pp. 845-854 ◽  
Author(s):  
Hidefumi Shinohara ◽  
Yuji Moriyama ◽  
Kentaro Ohyama ◽  
Yoshikatsu Matsubayashi
Keyword(s):  
Ligand Binding ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Ligand Recognition

Resonance assignment of the ligand-free cyclic nucleotide-binding domain from the murine ion channel HCN2

2014 ◽  
Vol 9 (2) ◽  
pp. 243-246
Author(s):  
Claudia Börger ◽  
Sven Schünke ◽  
Justin Lecher ◽  
Matthias Stoldt ◽  
Friederike Winkhaus ◽  
...  
Keyword(s):  
Ion Channel ◽  
Resonance Assignment ◽  
Cyclic Nucleotide ◽  
Nucleotide Binding ◽  
Binding Domain ◽  
Nucleotide Binding Domain ◽  
Cyclic Nucleotide Binding ◽  
Ligand Free ◽  
Cyclic Nucleotide Binding Domain

scholarly journals Structural Studies of the 3′,3′-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation

2018 ◽  
Vol 19 (11) ◽  
pp. 3527 ◽  
Author(s):  
Chaoqun Li ◽  
Xiaojia Zhao ◽  
Xiaomin Zhu ◽  
Pengtao Xie ◽  
Guangju Chen
Keyword(s):  
Molecular Dynamics ◽  
Bound States ◽  
Binding Pocket ◽  
Bound State ◽  
Structural Features ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Ligand Recognition ◽  
Compact Structure ◽  
Ligand Free

Riboswtich RNAs can control gene expression through the structural change induced by the corresponding small-molecule ligands. Molecular dynamics simulations and free energy calculations on the aptamer domain of the 3′,3′-cGAMP riboswitch in the ligand-free, cognate-bound and noncognate-bound states were performed to investigate the structural features of the 3′,3′-cGAMP riboswitch induced by the 3′,3′-cGAMP ligand and the specificity of ligand recognition. The results revealed that the aptamer of the 3′,3′-cGAMP riboswitch in the ligand-free state has a smaller binding pocket and a relatively compact structure versus that in the 3′,3′-cGAMP-bound state. The binding of the 3′,3′-cGAMP molecule to the 3′,3′-cGAMP riboswitch induces the rotation of P1 helix through the allosteric communication from the binding sites pocket containing the J1/2, J1/3 and J2/3 junction to the P1 helix. Simultaneously, these simulations also revealed that the preferential binding of the 3′,3′-cGAMP riboswitch to its cognate ligand, 3′,3′-cGAMP, over its noncognate ligand, c-di-GMP and c-di-AMP. The J1/2 junction in the 3′,3′-cGAMP riboswitch contributing to the specificity of ligand recognition have also been found.

scholarly journals Structural basis of ligand recognition by PABC, a highly specific peptide-binding domain found in poly(A)-binding protein and a HECT ubiquitin ligase

2003 ◽  
Vol 23 (2) ◽  
pp. 272-281 ◽  
Author(s):  
Guennadi Kozlov ◽  
Gregory De Crescenzo ◽  
Nadia S Lim ◽  
Nadeem Siddiqui ◽  
Daniel Fantus ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Binding Protein ◽  
Peptide Binding ◽  
Binding Domain ◽  
Structural Basis ◽  
Ligand Recognition ◽  
Specific Peptide

LIGAND RECOGNITION IN GLUTAMATE RECEPTORS: INSIGHTS FROM MUTAGENESIS OF THE SOLUBLE AMPA-BINDING DOMAIN OF GLUR-D

1997 ◽  
Vol 25 (3) ◽  
pp. 535S-535S
Author(s):  
K. Keinänen ◽  
M. Arvola ◽  
A. Kuusinen ◽  
M. Johnson
Keyword(s):  
Glutamate Receptors ◽  
Binding Domain ◽  
Ligand Recognition

Renilla Bioluminescence: A Morphologic Approach to the Location of Photocytes

1974 ◽  
Vol 32 ◽  
pp. 208-209
Author(s):  
Ben O. Spurlock ◽  
Milton J. Cormier
Keyword(s):  
Excited State ◽  
Ground State ◽  
Molecular Basis ◽  
Light Emission ◽  
Chemical Basis ◽  
Electronic Excited State ◽  
Colonial Form ◽  
The Common ◽  
Eighteenth And Nineteenth Centuries ◽  
Catalyzed Oxidation

The phenomenon of bioluminescence has fascinated layman and scientist alike for many centuries. During the eighteenth and nineteenth centuries a number of observations were reported on the physiology of bioluminescence in Renilla, the common sea pansy. More recently biochemists have directed their attention to the molecular basis of luminosity in this colonial form. These studies have centered primarily on defining the chemical basis for bioluminescence and its control. It is now established that bioluminescence in Renilla arises due to the luciferase-catalyzed oxidation of luciferin. This results in the creation of a product (oxyluciferin) in an electronic excited state. The transition of oxyluciferin from its excited state to the ground state leads to light emission.

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