@article {1588, title = {Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.}, journal = {Nucleic Acids Research}, volume = {34}, year = {2006}, month = {2006 Mar 9}, pages = {1439-49}, abstract = {

The Lrp/AsnC family of transcriptional regulatory proteins is found in both archaea and bacteria. Members of the family influence cellular metabolism in both a global (Lrp) and specific (AsnC) manner, often in response to exogenous amino acid effectors. In the present study we have determined both the first bacterial and the highest resolution structures for members of the family. Escherichia coli AsnC is a specific gene regulator whose activity is triggered by asparagine binding. Bacillus subtilis LrpC is a global regulator involved in chromosome condensation. Our AsnC-asparagine structure is the first for a regulator-effector complex and is revealed as an octameric disc. Key ligand recognition residues are identified together with a route for ligand access. The LrpC structure reveals a stable octamer supportive of a topological role in dynamic DNA packaging. The structures yield significant clues to the functionality of Lrp/AsnC-type regulators with respect to ligand binding and oligomerization states as well as to their role in specific and global DNA regulation.

}, keywords = {Amino Acid Sequence, Asparagine, Bacillus subtilis, Bacterial, Bacterial Proteins, Escherichia coli Proteins, Gene Expression Regulation, Genetic, Ligands, Models, Molecular, Molecular Sequence Data, Sequence Alignment, Trans-Activators, Transcription, Transcription Factors}, issn = {1362-4962}, doi = {10.1093/nar/gkl009}, author = {Thaw, Paul and Sedelnikova, Svetlana E and Muranova, Tatyana and Wiese, Sebastian and Ayora, Sylvia and Alonso, Juan C and Brinkman, Arie B and Akerboom, Jasper and van der Oost, John and Rafferty, John B} } @article {1590, title = {The structures of inhibitor complexes of Pyrococcus furiosus phosphoglucose isomerase provide insights into substrate binding and catalysis.}, journal = {Journal of Molecular Biology}, volume = {343}, year = {2004}, month = {2004 Oct 22}, pages = {649-57}, abstract = {

Pyrococcus furiosus phosphoglucose isomerase (PfPGI) is a metal-containing enzyme that catalyses the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). The recent structure of PfPGI has confirmed the hypothesis that the enzyme belongs to the cupin superfamily and identified the position of the active site. This fold is distinct from the alphabetaalpha sandwich fold commonly seen in phosphoglucose isomerases (PGIs) that are found in bacteria, eukaryotes and some archaea. Whilst the mechanism of the latter family is thought to proceed through a cis-enediol intermediate, analysis of the structure of PfPGI in the presence of inhibitors has led to the suggestion that the mechanism of this enzyme involves the metal-dependent direct transfer of a hydride between C1 and C2 atoms of the substrate. To gain further insight in the reaction mechanism of PfPGI, the structures of the free enzyme and the complexes with the inhibitor, 5-phospho-d-arabinonate (5PAA) in the presence and absence of metal have been determined. Comparison of these structures with those of equivalent complexes of the eukaryotic PGIs reveals similarities at the active site in the disposition of possible catalytic residues. These include the presence of a glutamic acid residue, Glu97 in PfPGI, which occupies the same position relative to the inhibitor as that of the glutamate that is thought to function as the catalytic base in the eukaryal-type PGIs. These similarities suggest that aspects of the catalytic mechanisms of these two structurally unrelated PGIs may be similar and based on an enediol intermediate.

}, keywords = {Archaeal Proteins, Binding Sites, Catalysis, Crystallography, Dimerization, Fructosephosphates, Glucose-6-Phosphate, Glucose-6-Phosphate Isomerase, Manganese, Models, Molecular, Molecular Structure, Pentosephosphates, Protein Binding, Protein Conformation, Pyrococcus furiosus, X-Ray}, issn = {0022-2836}, doi = {10.1016/j.jmb.2004.08.061}, author = {Berrisford, John M and Akerboom, Jasper and Brouns, Stan and Sedelnikova, Svetlana E and Turnbull, Andrew P and van der Oost, John and Salmon, Laurent and Hardr{\'e}, Renaud and Murray, Iain A and Blackburn, G Michael and Rice, David W and Baker, Patrick J} } @article {1592, title = {Crystal structure of Pyrococcus furiosus phosphoglucose isomerase. Implications for substrate binding and catalysis.}, journal = {The Journal of Biological Chemistry}, volume = {278}, year = {2003}, month = {2003 Aug 29}, pages = {33290-7}, abstract = {

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization between d-fructose 6-phosphate and d-glucose 6-phosphate as part of the glycolytic pathway. PGI from the Archaea Pyrococcus furiosus (Pfu) was crystallized, and its structure was determined by x-ray diffraction to a 2-A resolution. Structural comparison of this archaeal PGI with the previously solved structures of bacterial and eukaryotic PGIs reveals a completely different structure. Each subunit of the homodimeric Pfu PGI consists of a cupin domain, for which the overall structure is similar to other cupin domain-containing proteins, and includes a conserved transition metal-binding site. Biochemical data on the recombinant enzyme suggests that Fe2+ is bound to Pfu PGI. However, as catalytic activity is not strongly influenced either by the replacement of Fe2+ by a range of transition metals or by the presence or absence of the bound metal ion, we suggest that the metal may not be directly involved in catalysis but rather may be implicated in substrate recognition.

}, keywords = {Amino Acid, Amino Acid Sequence, Binding Sites, Chemical, Crystallography, Dimerization, Fructosephosphates, Glucose-6-Phosphate, Glucose-6-Phosphate Isomerase, Ions, Iron, Metals, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Structure, Pyrococcus furiosus, Secondary, Selenomethionine, Sequence Homology, Substrate Specificity, Temperature, Tertiary, X-Ray, X-Ray Diffraction}, issn = {0021-9258}, doi = {10.1074/jbc.M305170200}, author = {Berrisford, John M and Akerboom, Jasper and Turnbull, Andrew P and de Geus, Daniel and Sedelnikova, Svetlana E and Staton, Ian and McLeod, Cameron W and Verhees, Corn{\'e} H and van der Oost, John and Rice, David W and Baker, Patrick J} } @article {1591, title = {Purification, crystallization and preliminary crystallographic analysis of phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus.}, journal = {Acta Crystallographica. Section D, Biological Crystallography}, volume = {59}, year = {2003}, month = {2003 Oct 19}, pages = {1822-3}, abstract = {

The glycolytic enzyme phosphoglucose isomerase catalyses the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus, which shows no sequence similarity to any known bacterial or eukaryotic phosphoglucose isomerase, has been cloned and overexpressed in Escherichia coli, purified and subsequently crystallized by the hanging-drop method of vapour diffusion using 1.6 M sodium citrate as the precipitant at pH 6.5. Multiple-wavelength anomalous dispersive X-ray data have been collected to a maximum resolution of 1.92 A on a single selenomethionine-incorporated crystal. This crystal belongs to space group C2, with approximate unit-cell parameters a = 84.7

}, keywords = {Crystallization, Crystallography, Escherichia coli, Glucose-6-Phosphate Isomerase, Protein Conformation, Pyrococcus furiosus, Recombinant Proteins, Selenomethionine, X-Ray}, issn = {0907-4449}, author = {Akerboom, Jasper and Turnbull, Andrew P and Hargreaves, David and Fisher, Martin and de Geus, Daniel and Sedelnikova, Svetlana E and Berrisford, John M and Baker, Patrick J and Verhees, Corn{\'e} H and van der Oost, John and Rice, David W} }