binding site and binding structure, detailed overview. The NAD+ binding domain consist of six parallel and one anti-parallel beta-strands, surrounded by four alpha-helices, the typical structure of a Rossmann fold
might be an inhibitor, trehalose induces a conformational change in ecGAPDH in the current structure. The rotation of GAPDH also induced a conformational change in its active site. This suggests that the binding of trehalose to GAPDH induced a conformational change in its active site to prevent the binding of NAD+, although the NAD+- and trehalose-binding sites differ from one another
about 85% of maximal activity at pH 7.5 and pH 8.5, 50 mM Tris-chloride buffer. About 75% of maximal activity at pH 7.5 and pH 8.5, 50 mM triethanolamine-chloride buffer
secreted GAPDH is located on the bacterial surface and released to the culture medium of enterohemorrhagic and enteropathogenic strains, secreted GAPDH remains associated with colonic Caco-2 epithelial cells after adhesion and binds human plasminogen and fribinogen, non-pathogenic Escherichia coli strains do not secrete GAPDH
when the cell is exposed to high levels of H2O2, GAPDH is irreversibly inhibited presumably by the formation of sulphenic acid in the active site cysteine, becoming a switch that balances the equilibrium between the glycolytic cycle and the pentose phosphate metabolic pathway and promoting the formation of NADPH to combat ROS-produced cell stress
GAPDH-deficient cells are more sensitive to bleomycin or methyl methanesulfonate. In cells challenged with these genotoxic agents, GAPDH deficiency results in reduced cell viability and filamentous growth
GAPDH is required for the efficient repair of DNA lesions in Escherichia coli. Interaction occur between GAPDH and enzymes of the base excision repair pathway, namely the AP-endonuclease Endo IV and uracil DNA glycosylase. GAPDH is a component of a protein complex dedicated to the maintenance of genomic DNA integrity. Interaction of GAPDH with the single-stranded DNA binding protein may recruit GAPDH to the repair sites and implicates GAPDH in DNA repair pathways activated by profuse DNA damage, such as homologous recombination or the SOS response.
the EMP pathway can be controlled through the glyceraldehyde 3-phosphate node by NAD+-GAPDH activity, recombinant NADP+-GAPDH heterologous activity can also exert a similar response, which modulates the glucose uptake and also the acetic acid production rate
glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme in the glycolytic pathway that catalyzes the conversion of D-glyceraldehyde 3-phosphate to 1,3-diphosphoglycerate
apart from its glycolytic function, GAPDH displays a battery of moonlighting activities. Primary location of the tetrameric GAPDH is in the cytoplasm, where it conducts its canonical role in glycolysis
glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyses the conversion of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate using NAD+ as a cofactor. It is a moonlighting enzyme playing multiple roles in the regulation of mRNA stability, intracellular membrane trafficking, iron uptake and transport, DNA replication and repair, and nuclear RNA transport
glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme in the glycolytic pathway that catalyzes the conversion of D-glyceraldehyde 3-phosphate to 1,3-diphosphoglycerate
each GAPDH monomer contains a molecule of glyceraldehyde-3 phosphate in a non-previously identified site. The catalytic Cys149 is covalently attached to an about 300 Da molecule, possibly glutathione. This modification alters the conformation of an adjacent alpha-helix in the catalytic domain, right opposite to the NAD+ binding site. The conformation of the alpha-helix is stabilized after soaking the crystals with NAD+. Enzyme structure analysis, structure modeling, detailed overview
the S-loop of GAPDH is required for interaction of the enzyme with its cofactor and with other proteins. NAD+-bound GAPDH S-loop fixation occurs by the formation of a complex with the coenzyme NAD+. The structure of trehalose-bound ecGAPDH is compared with the structures of both NAD+-free and NAD+-bound ecGAPDH. At the S-loop, the bound trehalose in the GAPDH structure induces a 2.4° rotation compared with the NAD+-free ecGAPDH structure and a 3.1° rotation compared with the NAD+-bound ecGAPDH structure
the S-loop of GAPDH is required for interaction of the enzyme with its cofactor and with other proteins. NAD+-bound GAPDH S-loop fixation occurs by the formation of a complex with the coenzyme NAD+. The structure of trehalose-bound ecGAPDH is compared with the structures of both NAD+-free and NAD+-bound ecGAPDH. At the S-loop, the bound trehalose in the GAPDH structure induces a 2.4° rotation compared with the NAD+-free ecGAPDH structure and a 3.1° rotation compared with the NAD+-bound ecGAPDH structure
three-dimensional structure analysis of EcGAPDH1 compared with the structures of HuGAPDH and MrsaGAPDH shows that the main difference is the loop conformation, especially the S-loop
three-dimensional structure analysis of EcGAPDH1 compared with the structures of HuGAPDH and MrsaGAPDH shows that the main difference is the loop conformation, especially the S-loop
each of the subunits can be divided into two domains: the N-terminal NAD+-binding domain and the C-terminal catalytic domain. The NAD+-binding domain is typically a Rossman fold containing eight beta-strands, namely beta1 (Lys3-Asn7), beta2 (Asp28-Asn33), beta3 (Val58-Phe60), beta4 (Ser64-Val67), beta5 (Lys70-Tyr75), beta6 (Ile92-Glu95), beta7 (Lys116-Ile119) and beta8 (Ile144-Ser146). The strands are connected by either helices or short loops. beta3 and beta5 are antiparallel to the other six parallel beta-strands. There are four alpha-helices in this domain: alpha1 (Gly10-Val23), alpha2 (Ser37-His47), alpha3 (Ser102-Ser106) and alpha4 (Gln107-Ala112). The catalytic domain contains eight mixed beta-sheets, beta9 (Ile168-Ala178), beta10 (Ile205-His207), beta11 (Leu226-Val231), beta12 (Ser239-Leu247), beta13 (Phe270-Thr273), beta14 (Ser289-Asp292), beta15 (Glu297-Val301) and beta16 (Leu304-Tyr313), and three long alpha-helices, alpha5 (Ser149-Gly167), alpha6 (Thr252-Thr264) and alpha7 (Gln317-Lys332). The catalytically active residues Cys150 and His177 are situated in alpha5 and beta9, respectively
GAPDH of enterohemorrhagic and enteropathogenic Escherichia coli-strains is ADP-ribosylated either in the cytoplasm or in the extracellular medium. GAPDH catalyzes its own modification involving residue C149 at the active site, reaction requires NAD+
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native, non-modified and selenium-modified enzymes, 5.5 mg/ml protein in 10 mM HEPES, pH 7.5, and 1.43 M sodium citrate, 18°C, 3 days, method optimization, crystals from the selenium modified enzyme are soaked for 10 min in 5 mM NAD+ dissolved in mother liquor with or without 25% trehalose, X-ray diffraction structure determination and analysis at 1.64-2.14 A resolution using single-wavelength anomalous dispersion (SAD) phasing with a selenium-modified enzyme, molecular replacement
purified recombinant enzyme GAPDH complexed with trehalose, hanging drop vapour diffusion method, mixing of 20 mg/ml protein in 20 mM Tris, 130 mM NaCl pH 7.5, with reservoir solution containing 2.8 M ammonium sulfate, 0.1 M MES, pH 5.5-6.5, 4°C, two to three weeks, GAPDH crystals are treated with a cryoprotectant consisting of 15% v/v trehalose at -173°C, X-ray diffraction structure determination and analysis at 2.1 A resolution, molecular replacement using the Escherichia coli GAPDH structure (PDB ID 1s7c) as a starting model
purified recombinant isozyme EcGAPDH1, sitting drop vapour diffusion method, mixing of 240 nl of 30 mg/ml protein in 4 mM NaCl, and 5 mM Tris-HCl pH 8.0, with 240 nl of reservoir solution containing reservoir solution consisting of 100 mM sodium acetate, pH 4.6, 30% w/v PEG 400,and 200 mM calcium acetate, and equilibration against 0.1 ml of reservoir solution, 1 week, method optimization, X-ray diffraction structure determination and analysis at 1.88 A resolution, molecular replacement using the structure of GAPDH from methicillin-resistant Staphylococcus aureus MRSA252 (PDB ID 3lvf) as search model, model building
structure determination by formation of soluble recombinant rat sperm glyceraldehyde-3-phosphate dehydrogenase as a heterotetramer with the Escherichia coli glyceraldehyde-3-phosphate dehydrogenase in a ratio of 1:3. Glyceraldehyde 3-phosphate binds in the Ps pocket in the active site of the sperm enzyme subunit in the presence of NAD
dissociation constant for NAD+ is 300times higher than that of the wild-type enzyme. Conformational equilibrium between the syn and the anti forms with a preference for the anti conformer
the gapA gene from Escherichia coli strain MG1655 is replaced by the gene gapN from Streptococcus mutans, EC 1.2.1.9, UniProt ID Q59931. The specific NADP+-GAPDH activity of the strain MG1655DgapA::gapN is 4.6times lower relative to strain MG1655DELTAgapA::gapN/pTrcgapN and no NAD+-GAPDH activity is detected. The specific NADP+-GAPDH activity levels in the derivative strain reveal that growth rate and glucose uptake differences are attributable to gapN expression level. The NADH/NAD+ ratio in the strain MG1655DELTAgapA::gapN/pTrcgapN decreases by 25% as compared to wild-type strain. In contrast, the NADPH/NADP+ ratio increases 2times indicating that the alteration in the turnover of NAD(P)H via glyceraldehyde 3-phosphate oxidation affects the redox levels of the strain MG1655DELTAgapA::gapN/pTrcgapN, which increases 2.8times the NADPH/NADH ratio
generation of an engineered synthetic Escherichia coli codon optimized sequence of a human gene that codifies for a 32.4 kDa protein for recombinant expression
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene gapA, complementation of the mutant Escherichia coli strain MG1655DELTAgapA by the Streptococcus mutans gapN gene, EC 1.2.1.9, UniProt ID Q59931, expressed from plasmid pTrcgapN
GAPDH is a multi-functional protein that is used as a control marker for basal function, it is known to undergo cysteine oxidation under different types of cellular stress
Eyschen, J.; Vitoux, B.; Marraud, M.; Cung, M.T.; Branlant, G.
Engineered glycolytic glyceraldehyde-3-phosphate dehydrogenase binds the anti conformation of NAD+ nicotinamide but does not experience A-specific hydride transfer
Role of secreted glyceraldehyde-3-phosphate dehydrogenase in the infection mechanism of enterohemorrhagic and enteropathogenic Escherichia coli: interaction of the extracellular enzyme with human plasminogen and fibrinogen
Structure of insoluble rat sperm glyceraldehyde-3-phosphate dehydrogenase (GAPDH) via heterotetramer formation with Escherichia coli GAPDH reveals target for contraceptive design
Rodriguez-Hernandez, A.; Romo-Arevalo, E.; Rodriguez-Romero, A.
A novel substrate-binding site in the X-ray structure of an oxidized E. coli glyceraldehyde 3-phosphate dehydrogenase elucidated by single-wavelength anomalous dispersion