Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation

Lee, Jun Hyuck; Im, Young Jun; Bae, Jungdon; Kim, Doo-Il; Kim, Mun-Kyoung; Kang, Gil Bu; Lee, Dae-Sil; Eom, Soo Hyun

doi:10.1016/j.bbrc.2006.09.151

Cited by 11 publications

(12 citation statements)

References 18 publications

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“…Spot 22 was identified as an enolase, known to be involved in glycolysis‐related machinery. Phosphoglycerate kinase was another key glycolytic enzyme to be identified (Spot 146): it catalyzes the reversible transfer of a phosphate from 1,3‐bisphosphoglycerate to ADP to form 3‐phosphoglycerate and ATP in the presence of magnesium (Lee et al , 2006). This protein has also been associated with metal stress in Rhodobacter capsulatus (Mohamed Fahmy Gad El‐Rab et al , 2006).…”

Section: Resultsmentioning

confidence: 99%

In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea

Andrade

Silva

Pereira³

et al. 2008

FEMS Microbiology Letters

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The genus Xanthomonas is composed of several species that cause severe crop losses around the world. In Latin America, one of the most relevant species is Xanthomonas campestris pv. campestris, which is responsible for black rot in cruciferous plants. This pathogen causes yield losses in several cultures, including cabbage, cauliflower and broccoli. Although the complete structural genome of X. campestris pv. campestris has been elucidated, little is known about the protein expression of this pathogen in close interaction with the host plant. Recently, a method for in vivo analysis of Xanthomonas axonopodis pv. citri was developed. In the present study, this technique was employed for the characterization of the protein expression of X. campestris pv. campestris in close interaction with the host plant Brassica oleracea. The bacterium was infiltrated into leaves of the susceptible cultivar and later recovered for proteome analysis. Recovered cells were used for protein extraction and separated by two-dimensional electrophoresis. Proteins were analysed by peptide mass fingerprinting or de novo sequencing and identified by searches in public databases. The approach used in this study may be extremely useful in further analyses in order to develop novel strategies to control this important plant pathogen.

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Section: Resultsmentioning

confidence: 99%

In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea

Andrade

Silva

Pereira³

et al. 2008

FEMS Microbiology Letters

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“…In this study, we have demonstrated that esculetin acts as a ligand for PGK2, GPD2, and GPI. The PGK2 is "open": the N-terminal domain that can bind 3PG and the C-terminal domain that binds ATP are far apart to interact with the substrates (Blake and Evans , 1974;Watson et al, 1982;Bernstein et al, 1998;Flachner et al, 2004;Lee et al, 2006). Binding 3PG results in a 13-degree rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize (Harlos et al, 1992;Davies et al, 1994;Auerbach et al, 1997;Bernstein et al, 1997;Szilágyi et al, 2001;Kovári et al, 2002).…”

Section: Discussionmentioning

confidence: 99%

Esculetin Inhibits Cancer Cell Glycolysis by Binding Tumor PGK2, GPD2, and GPI

Liu

et al. 2020

Front. Pharmacol.

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Glycolysis can improve the tolerance of tissue cells to hypoxia, and its intermediates provide raw materials for the synthesis and metabolism of the tumor cells. If it can inhibit the activity of glycolysis-related enzymes and control the energy metabolism of tumor, it can be targeted for the treatment of malignant tumor. The target proteins phosphoglycerate kinase 2 (PGK2), glycerol-3-phosphate dehydrogenase (GPD2), and glucose-6-phosphate isomerase (GPI) were screened by combining transcriptome, proteomics, and reverse docking. We detected the binding constant of the active compound using microscale thermophoresis (MST). It was found that esculetin bound well with three potential target proteins. Esculetin significantly inhibited the rate of glycolysis, manifested by differences of cellular lactate production and glucose consumption in HepG2 cells with or without esculetin. It was found that GPD2 bound strongly to GPI, revealing the direct interaction between the two glycolysis-related proteins. Animal tests have further demonstrated that esculetin may have anticancer effects by affecting the activity of PGK2, GPD2, and GPI. The results of this study demonstrated that esculetin can affect the glucose metabolism by binding to glycolytic proteins, thus playing an anti-tumor role, and these proteins which have direct interactions are potential novel targets for tumor treatment by esculetin.

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“…In comparative modeling by MODELLER 9v9 [10], a total of 250 initial models were generated from multiple templates (PDB id: 2G3Y, 2IE8 [72], 3QOE [73], 1V32, 2E87, 2R3V [74] and 3I4Q), followed by secondary structure restraints and loop refinement using MODELLER 9v9 [10]. DOPE score and molpdf were used to evaluate the models.…”

Section: Methodsmentioning

confidence: 99%

The Structure and Dynamics of BmR1 Protein from Brugia malayi: In Silico Approaches

Khor

Tye

Lim

et al. 2014

IJMS

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Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO) as one of the second leading causes of permanent and long-term disability and thus it is targeted for elimination by year 2020. Therefore, accurate filariasis diagnosis is important for management and elimination programs. A recombinant antigen (BmR1) from the Bm17DIII gene product was used for antibody-based filariasis diagnosis in “Brugia Rapid”. However, the structure and dynamics of BmR1 protein is yet to be elucidated. Here we study the three dimensional structure and dynamics of BmR1 protein using comparative modeling, threading and ab initio protein structure prediction. The best predicted structure obtained via an ab initio method (Rosetta) was further refined and minimized. A total of 5 ns molecular dynamics simulation were performed to investigate the packing of the protein. Here we also identified three epitopes as potential antibody binding sites from the molecular dynamics average structure. The structure and epitopes obtained from this study can be used to design a binder specific against BmR1, thus aiding future development of antigen-based filariasis diagnostics to complement the current diagnostics.

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Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation

Cited by 11 publications

References 18 publications

In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea

In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea

Esculetin Inhibits Cancer Cell Glycolysis by Binding Tumor PGK2, GPD2, and GPI

The Structure and Dynamics of BmR1 Protein from Brugia malayi: In Silico Approaches

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