Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 Å

Davies, G.J.; Gamblin, S.J.; Littlechild, J.A.; Dauter, Z.; Wilson, K.S.; Watson, Herman C.

doi:10.1107/s0907444993011138

Cited by 80 publications

(153 citation statements)

References 20 publications

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“…2C). This conformation is very similar to previously observed crystal structures of open forms of PGK from various species (8,9,39). Comparison of the structures of these half-open binary complexes with the open structure of apo-PGK shows how binding of 3PG prepares the enzyme for catalysis.…”

Section: Solution Structure Of Apo-pgk and Domain Movements Insupporting

confidence: 69%

A Spring-loaded Release Mechanism Regulates Domain Movement and Catalysis in Phosphoglycerate Kinase

Zerrad

Merli

Schröder

et al. 2011

Journal of Biological Chemistry

105

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Phosphoglycerate kinase (PGK) is the enzyme responsible for the first ATP-generating step of glycolysis and has been implicated extensively in oncogenesis and its development. Solution small angle x-ray scattering (SAXS) data, in combination with crystal structures of the enzyme in complex with substrate and product analogues, reveal a new conformation for the resting state of the enzyme and demonstrate the role of substrate binding in the preparation of the enzyme for domain closure. Comparison of the x-ray scattering curves of the enzyme in different states with crystal structures has allowed the complete reaction cycle to be resolved both structurally and temporally. The enzyme appears to spend most of its time in a fully open conformation with short periods of closure and catalysis, thereby allowing the rapid diffusion of substrates and products in and out of the binding sites. Analysis of the open apoenzyme structure, defined through deformable elastic network refinement against the SAXS data, suggests that interactions in a mostly buried hydrophobic region may favor the open conformation. This patch is exposed on domain closure, making the open conformation more thermodynamically stable. Ionic interactions act to maintain the closed conformation to allow catalysis. The short time PGK spends in the closed conformation and its strong tendency to rest in an open conformation imply a springloaded release mechanism to regulate domain movement, catalysis, and efficient product release. Phosphoglycerate kinase (PGK)2 catalyzes the transfer of phosphate from 1,3-bisphosphoglycerate (1,3BPG) to ADP in the first ATP-generating step of the glycolytic pathway. As a major controller of flux through the pathway, PGK is a viable target for drugs against anaerobic pathogens, such as Trypanosoma and Plasmodium species, which depend solely on glycolysis for energy metabolism (1). In addition to its metabolic role, the phosphoryl transfer activity of PGK is important in the processing of antiretroviral prodrugs that take the form of L-nucleoside analogues (2). The rate-limiting step in the in vivo activation of such compounds has been demonstrated to be the addition of a third phosphate by PGK (3). A third activity of PGK is as a signaling molecule in chordates. It is integral in the response to hypoxia, when it is secreted from the cell and inhibits angiogenesis through a disulfide reductase activity that activates plasminogen autoproteolytic activity, producing angiostatin (4). This activity apparently uses the same mechanism as the normal metabolic reaction and can be inhibited competitively by 3-phosphoglycerate (3PG) or ADP (5). Consequently, PGK has a crucial role in oncogenesis and its development.PGK is composed of two similarly sized domains, both with Rossmann fold topology, termed the N-terminal domain, which binds the phosphoglycerate species 3PG and 1,3BPG, and the C-terminal domain, which binds the nucleotides ADP and ATP. In early crystal structures of PGK (6 -9), it was apparent that this state of the enzyme ...

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Section: Solution Structure Of Apo-pgk and Domain Movements Insupporting

confidence: 69%

A Spring-loaded Release Mechanism Regulates Domain Movement and Catalysis in Phosphoglycerate Kinase

Zerrad

Merli

Schröder

et al. 2011

Journal of Biological Chemistry

105

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“…Molecular Modeling of Cold-active PGK-The Pseudomonas PGK structural model was based on the three-dimensional structures of PGK from yeast (15), B. stearothermophilus (10), T. maritima (18), and T. brucei (17). Such a strategy offers the advantage of minimizing the number of loops that are generated.…”

Section: Methodsmentioning

confidence: 99%

“…Most of the conserved residues lie in the active site cleft, the substratebinding sites and the hinge region. As shown by crystallographic studies, the triose substrate binds to a basic patch in the N-terminal domain (9) whereas the nucleotide substrate binds to the C-terminal domain (10). Six three-dimensional structures have been solved by x-ray crystallography: the PGK from horse muscle (11)(12)(13), yeast (14,15), pig muscle (9,16), Bacillus stearothermophilus (10), Trypanosoma brucei (17), and Thermotoga maritima (18).…”

mentioning

confidence: 99%

Structural, Kinetic, and Calorimetric Characterization of the Cold-active Phosphoglycerate Kinase from the AntarcticPseudomonas sp. TACII18

Bentahir

Feller

Aittaleb

et al. 2000

Journal of Biological Chemistry

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The gene encoding the phosphoglycerate kinase (PGK) from the Antarctic Pseudomonas sp. TACII18 has been cloned and found to be inserted between the genes encoding for glyceraldhyde-3-phosphate dehydrogenase and fructose aldolase. The His-tagged and the native recombinant PGK from the psychrophilic Pseudomonas were expressed in Escherichia coli. The wild-type and the native recombinant enzymes displayed identical properties, such as a decreased thermostability and a 2-fold higher catalytic efficiency at 25°C when compared with the mesophilic PGK from yeast. These properties, which reflect typical features of cold-adapted enzymes, were strongly altered in the His-tagged recombinant PGK. The structural model of the psychrophilic PGK indicated that a key determinant of its low stability is the reduced number of salt bridges, surface charges, and aromatic interactions when compared with mesophilic and thermophilic PGK. Differential scanning calorimetry of the psychrophilic PGK revealed unusual variations in its conformational stability for the free and substrate-bound forms. In the free form, a heatlabile and a thermostable domain unfold independently. It is proposed that the heat-labile domain acts as a destabilizing domain, providing the required flexibility around the active site for catalysis at low temperatures.

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“…The data-collection and processing statistics are given in Table 1. The structure was solved using the molecular-replacement method with the MOLREP program (Vagin & Teplyakov, 1997) within the CCP4 package (Winn et al, 2011) using PGK from Bacillus stearothermophilus (PDB entry 1php; sequence identity 52%; Davies et al, 1994) as a model. A promising solution has been obtained.…”

mentioning

confidence: 99%

Expression, purification, crystallization and preliminary X-ray diffraction studies of phosphoglycerate kinase from methicillin-resistantStaphylococcus aureusMRSA252

2011

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Phosphoglycerate kinase (PGK) from methicillin-resistant Staphylococcus aureus MRSA252 has been cloned in pQE30 expression vector, overexpressed in Escherichia coli SG13009 (pREP4) cells and purified to homogeneity. The protein was crystallized from 0.15 M CaCl 2 , 0.1 M HEPES-NaOH pH 6.8, 20%(w/v) polyethylene glycol 2000 at 298 K by the hanging-drop vapourdiffusion method. The crystals belonged to space group P2 1 , with unit-cell parameters a = 45.14, b = 74.75, c = 58.67 Å , = 95.72. X-ray diffraction data have been collected and processed to a maximum resolution of 2.3 Å . The presence of one molecule in the asymmetric unit gives a Matthews coefficient (V M ) of 2.26 Å 3 Da À1 with a solvent content of 46%. The structure has been solved by molecular replacement and structure refinement is now in progress.

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Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 Å

Cited by 80 publications

References 20 publications

A Spring-loaded Release Mechanism Regulates Domain Movement and Catalysis in Phosphoglycerate Kinase

A Spring-loaded Release Mechanism Regulates Domain Movement and Catalysis in Phosphoglycerate Kinase

Structural, Kinetic, and Calorimetric Characterization of the Cold-active Phosphoglycerate Kinase from the AntarcticPseudomonas sp. TACII18

Expression, purification, crystallization and preliminary X-ray diffraction studies of phosphoglycerate kinase from methicillin-resistantStaphylococcus aureusMRSA252

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