Molecular symmetry of glyceraldehyde-3-phosphate dehydrogenase from Bacillus coagulans

Griffith, Jeffrey K.; Lee, B.; Murdock, Archie L.; Amelunxen, Remi E.

doi:10.1016/s0022-2836(83)80145-4

Cited by 21 publications

(11 citation statements)

References 27 publications

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“…There are slight deviations of less than 0.5°from ideal 222 molecular symmetry in the final refined tetramer. There is no single perfect molecular 2-fold axis as has been reported for human skeletal muscle holo-GAPDH (Mercer et al, 1976) and Bacillus coagulans apo-GAPDH (no NAD+ bound) (Griffith et al, 1983). GAPDHs from some sources have shown cooperativity in the binding of NAD+ (Conway & Koshland, 1968;De Vijlder et al, 1969;Seydoux et al, 1973).…”

Section: Resultsmentioning

confidence: 97%

Crystal Structure of Glycosomal Glyceraldehyde-3-phosphate Dehydrogenase from Leishmania mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site

et al. 1995

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The structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the trypanosomatid parasite Leishmania mexicana has been determined by X-ray crystallography. The protein crystallizes in space group P2(1)2(1)2(1) with unit cell parameters a = 99.0 A, b = 126.5 A, and c = 138.9 A. There is one 156,000 Da protein tetramer per asymmetric unit. The model of the protein with bound NAD+s and phosphates has been refined against 86% complete data from 10.0 to 2.8 A to a crystallographic Rfactor of 0.198. Density modification by noncrystallographic symmetry averaging was used during model building. The final model of the L. mexicana GAPDH tetramer shows small deviations of less than 0.5 degrees from ideal 222 molecular symmetry. The structure of L. mexicana GAPDH is very similar to that of glycosomal GAPDH from the related trypanosomatid Trypanosoma brucei. A significant structural difference between L. mexicana GAPDH and most previously determined GAPDH structures occurs in a loop region located at the active site. This unusual loop conformation in L. mexicana GAPDH occludes the inorganic phosphate binding site which has been seen in previous GAPDH structures. A new inorganic phosphate position is observed in the L. mexicana GAPDH structure. Model building studies indicate that this new anion binding site is well situated for nucleophilic attack of the inorganic phosphate on the thioester intermediate in the GAPDH-catalyzed reaction. Since crystals of L. mexicana GAPDH can be grown reproducibly and diffract much better than those of T. brucei GAPDH, L. mexicana GAPDH will be used as a basis for structure-based drug design targeted against trypanosomatid GAPDHs.

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Section: Resultsmentioning

confidence: 97%

Crystal Structure of Glycosomal Glyceraldehyde-3-phosphate Dehydrogenase from Leishmania mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site

et al. 1995

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“…Many structures of GAPDH from eukaryotes [ 5 , 6 , 7 ], bacteria [ 8 , 9 ], and archaea [ 10 , 11 ] have been reported. Eukaryotic and bacterial structures may have the same catalytic process, which is different from that of archaea.…”

Section: Introductionmentioning

confidence: 99%

Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid

et al. 2021

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Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a highly conserved enzyme involved in the ubiquitous process of glycolysis and presents a loop (residues 208–215 of Escherichia coli GAPDH) in two alternative conformations (I and II). It is uncertain what triggers this loop rearrangement, as well as which is the precise site from which phosphate attacks the thioacyl intermediate precursor of 1,3-bisphosphoglycerate (BPG). To clarify these uncertainties, we determined the crystal structures of complexes of wild-type GAPDH (WT) with NAD and phosphate or G3P, and of essentially inactive GAPDH mutants (C150S, H177A), trapping crystal structures for the thioacyl intermediate or for ternary complexes with NAD and either phosphate, BPG, or G3P. Analysis of these structures reported here lead us to propose that phosphate is located in the “new Pi site” attacks the thioester bond of the thioacyl intermediate to generate 1,3-bisphosphoglyceric acid (BPG). In the structure of the thioacyl intermediate, the mobile loop is in conformation II in subunits O, P, and R, while both conformations coexist in subunit Q. Moreover, only the Q subunit hosts bound NADH. In the R subunit, only the pyrophosphate part of NADH is well defined, and NADH is totally absent from the O and P subunits. Thus, the change in loop conformation appears to occur after NADH is produced, before NADH is released. In addition, two new D-glyceraldehyde-3-phosphate (G3P) binding forms are observed in WT.NAD.G3P and C150A+H177A.NAD.G3P. In summary, this paper improves our understanding of the GAPDH catalytic mechanism, particularly regarding BPG formation.

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“…Two major interests have driven these studies: ®rstly to establish the structural basis for the extreme thermostability of GAPDH from the archaea and thermophiles and secondly to gain insight to the basis of the cooperativity of cofactor binding. The range of structural studies is wide and in microbial sources includes the mesophiles Escherichia coli (Due Â e et al, 1996) and Bacillus coagulans (Grif®th et al, 1983), the moderately thermophilic Bacillus stearothermophilus (Skarzynski & Wonacott, 1988;Didierjean et al, 1997), the thermophilic Thermus aquaticus (Tanner et al, 1996) and the hyperthermophilic Thermotoga maritima (Korndo È rfer et al, 1995). The glycosomal GAPDHs of Trypanosoma brucei (Vellieux et al, 1993), Leishmania mexicana (Kim et al, 1995) and Tryponasoma cruzi (Souza et al, 1998) have been studied.…”

Section: Introductionmentioning

confidence: 99%

The structure of glyceraldehyde 3-phosphate dehydrogenase fromAlcaligenes xylosoxidansat 1.7 Å resolution

Antonyuk

Eady

Strange

et al. 2003

Acta Crystallogr D Biol Cryst

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The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the Gram-negative denitrifying bacterial species Alcaligenes xylosoxidans was purified and crystallized as a contaminant protein during purification of nitrous oxide reductase. This is the first structure of a GAPDH from a denitrifying species. The crystal structure was solved at 1.7 A resolution by molecular replacement using the structure of GAPDH from Bacillus stearothermophilus as a starting model. The quality of the structure enabled the amino-acid sequence of the A. xylosoxidans GAPDH to be assigned. The structure is that of the apo-enzyme, lacking the NAD+ cofactor and with the active-site residue Cys154 oxidized. The global structure of the enzyme has a homotetrameric quaternary structure similar to that observed for its bacterial and eukaryotic counterparts. The essential role of Cys154 in the enzyme activity has been confirmed. In monomer O two half-occupancy sulfate ions were found at the active site, which are analogous to the substrate and the "attacking" phosphate seen in B. stearothermophilus. One half-occupancy sulfate ion is also located in the substrate-binding site of monomer P.

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Molecular symmetry of glyceraldehyde-3-phosphate dehydrogenase from Bacillus coagulans

Cited by 21 publications

References 27 publications

Crystal Structure of Glycosomal Glyceraldehyde-3-phosphate Dehydrogenase from Leishmania mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site

Crystal Structure of Glycosomal Glyceraldehyde-3-phosphate Dehydrogenase from Leishmania mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site

Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid

The structure of glyceraldehyde 3-phosphate dehydrogenase fromAlcaligenes xylosoxidansat 1.7 Å resolution

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