Home  About us  Contact
 

Glycine-rich Loop (glycine-rich + loop)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetase

PROTEIN SCIENCE, Issue 3 2002
Keehwan Kwon
Abstract The binding of the Escherichia coli biotin holoenzyme synthetase to the two ligands, biotin and bio-5,-AMP, is coupled to disorder-to-order transitions in the protein. In the structure of the biotin complex, a "glycine-rich" loop that is disordered in the apo-enzyme is folded over the ligand. Mutations in three residues in this loop result in significant changes in the affinity of the enzyme for both biotin and bio-5,-AMP. The kinetic basis of these losses in the affinity resides primarily in changes in the unimolecular rates of dissociation of the complexes. In this work, isothermal titration calorimetry has been employed to examine the detailed thermodynamics of binding of three loop mutants to biotin and bio-5,-AMP. The energetic features of dissociation of the protein,ligand complexes also have been probed by measuring the temperature dependencies of the unimolecular dissociation rates. Analysis of the data using the Eyring formalism yielded entropic and enthalpic contributions to the energetic barrier to dissociation. The thermodynamic results coupled with the known structures of the apo-enzyme and biotin complex have been used to formulate a model for progression from the ground-state complex to the transition state in biotin dissociation. In this model, the transition-state is characterized by both partial disruption of noncovalent bonds and acquisition of some of the disorder that characterizes the glycine-rich loop in the absence of ligand. [source]

Structures of the PKC-, kinase domain in its ATP-bound and apo forms reveal defined structures of residues 533,551 in the C-terminal tail and their roles in ATP binding

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010
Tetsuo Takimura
Protein kinase C (PKC) plays an essential role in a wide range of cellular functions. Although crystal structures of the PKC-,, PKC-, and PKC-,II kinase domains have previously been determined in complexes with small-molecule inhibitors, no structure of a PKC,substrate complex has been determined. In the previously determined PKC-, complex, residues 533,551 in the C-terminal tail were disordered. In the present study, crystal structures of the PKC-, kinase domain in its ATP-bound and apo forms were determined at 2.1 and 2.0,Å resolution, respectively. In the ATP complex, the electron density of all of the C-terminal tail residues was well defined. In the structure, the side chain of Phe543 protrudes into the ATP-binding pocket to make van der Waals interactions with the adenine moiety of ATP; this is also observed in other AGC kinase structures such as binary and ternary substrate complexes of PKA and AKT. In addition to this interaction, the newly defined residues around the turn motif make multiple hydrogen bonds to glycine-rich-loop residues. These interactions reduce the flexibility of the glycine-rich loop, which is organized for ATP binding, and the resulting structure promotes an ATP conformation that is suitable for the subsequent phosphoryl transfer. In the case of the apo form, the structure and interaction mode of the C-terminal tail of PKC-, are essentially identical to those of the ATP complex. These results indicate that the protein structure is pre-organized before substrate binding to PKC-,, which is different from the case of the prototypical AGC-branch kinase PKA. [source]

Structures of human MST3 kinase in complex with adenine, ADP and Mn2+

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2010
Tzu-Ping Ko
The MST family is a subclass of mammalian serine/threonine kinases that are related to the yeast sterile-20 protein and are implicated in regulating cell growth and transformation. The MST3 protein contains a 300-residue catalytic domain and a 130-residue regulatory domain, which can be cleaved by caspase and activated by autophosphorylation, promoting apoptosis. Here, five crystal structures of the catalytic domain of MST3 are presented, including a complex with ADP and manganese, a unique cofactor preferred by the enzyme, and a complex with adenine. Similar to other protein kinases, the catalytic domain of MST3 folds into two lobes: the smaller N lobe forms the nucleotide-binding site and the larger C lobe recognizes the polypeptide substrate. The bound ADP and Mn2+ ions are covered by a glycine-rich loop and held in place by Asn149 and Asp162. A different orientation was observed for the ligand in the MST3,adenine complex. In the activation loop, the side chain of Thr178 is phosphorylated and is sandwiched by Arg143 and Arg176. Comparison of this structure with other similar kinase structures shows a 180° rotation of the loop, leading to activation of the enzyme. The well defined protein,ligand interactions also provide useful information for the design of potent inhibitors. [source]

An inhibited conformation for the protein kinase domain of the Saccharomyces cerevisiae AMPK homolog Snf1

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2010
Michael J. Rudolph
AMP-activated protein kinase (AMPK) is a master metabolic regulator for controlling cellular energy homeostasis. Its homolog in yeast, SNF1, is activated in response to glucose depletion and other stresses. The catalytic (,) subunit of AMPK/SNF1 in yeast (Snf1) contains a protein Ser/Thr kinase domain (KD), an auto-inhibitory domain (AID) and a region that mediates interactions with the two regulatory (, and ,) subunits. Here, the crystal structure of residues 41,440 of Snf1, which include the KD and AID, is reported at 2.4,Å resolution. The AID is completely disordered in the crystal. A new inhibited conformation of the KD is observed in a DFG-out conformation and with the glycine-rich loop adopting a structure that blocks ATP binding to the active site. [source]