Structure determination of crystalline lobster d-glyceraldehyde-3-phosphate dehydrogenase

Buehner, Manfred; Ford, Geoffrey C.; Moras, Dino; Olsen, Kenneth W.; Rossmann, Michael G.

doi:10.1016/0022-2836(74)90249-6

Cited by 139 publications

(62 citation statements)

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“…This appears not to be the case with glyceraldehyde-phosphate dehydrogenase. This enzyme has been shown by X-ray crystallography to be composed of two pairs of polypeptide chains [14,15]. The pairwise arrangement is barely visible with the cross-linking method.…”

Section: Discussionmentioning

confidence: 99%

“…These compounds react exclusively with the protein's amino groups [12]. We varied over a wide range the reaction conditions, such as reagent concentration and carbonchain length of the bifunctional reagent, and applied the method to enzymes the X-ray analysis of which has been published (lactate dehydrogenase [13,14] and glyceraldehyde-phosphate dehydrogenase [14,15]) as well as to enzymes with known chain numbers but unknown symmetry (alcohol dehydrogenase, aldolase', catalase, fumarase, P-galactosidase, and pyruvate kinase ').…”

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confidence: 99%

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Investigation of the Symmetry of Oligomeric Enzymes with Bifunctional Reagents

Hucho¹,

Müllner²,

Sund³

1975

Eur J Biochem

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1. The symmetry of proteins composed of identical polypeptide chains has been investigated by means of cross-linking with bifunctional reagents and subsequent sodium dodecylsulfate -polyacrylamide gel electrophoresis. The majority of the investigations were performed with diimidates of different chain lengths (C, -C,z), which react exclusively with amino groups. Aldolase, catalase, fumarase, pyruvate kinase, tetrameric proteins with identical polypeptide chains, reveal a D2 symmetry, i.e. they appear to be composed of two pairs of polypeptide chains. The validity of this conclusion is demonstrated with lactate dehydrogenase. This enzyme, shown by X-ray analysis to have a D, symmetry, yields after cross-linking and subsequent polyacrylamide electrophoresis the band pattern expected for a protein with this quaternary structure and similar to the pattern obtained with the above enzymes.2. The influence of the experimental conditions on the cross-linking reaction has been investigated. The selectivity of the bifunctional reagent for the different contact domains within the quaternary structure of a protein depends on the reaction time, the chain length and on the concentration of the reagent. In general the D2 symmetry becomes more obvious with increasing chain length and with increasing concentration of the diimidate. Diethylpyrocarbonate showed very little selectivity.3. Problems and limitations of the method have been investigated. The four polypeptide chains of B-galactosidase could not be cross-linked with the investigated reagents. Glyceraldehyde-phosphate dehydrogenase barely showed the predicted cross-linking pattern, although its D, symmetry has been demonstrated by X-ray analysis. Yeast alcohol dehydrogenase shows a pattern which did not indicate any substructure with respect to the quaternary structure. Catalase yielded a complicated band pattern indicating that the cross-linking prevented complete unfolding of the polypeptide chains in sodium dodecylsulfate. These pattern did not occur after cross-linking with diethyl pyrocarbonate.4. The applicability of molecular-weight determinations with sodium dodecylsulfate -polyacrylamide gel electrophoresis to cross-linked proteins has been investigated. Calibrations obtained with cross-linked proteins are very similar to that obtained with non-cross-linked polypeptide chains.Even with catalase the R, values of the predominant bands fit into this calibration.The allosteric properties of a protein are closely related to its subunit assembly. In recent years the interest focussed on the interaction between polypeptide chains because knowledge of the structure of subunit contacts and the symmetry of the oligomer This work has been dcscribed in a preliminary report [l]. Enzymes. Alcohol dehydrogcnase or alcohol : NAD+ oxidorcductase (EC 1.1.1.1); aldolase or D-fructose-1,6-bisphosphate Dglyceraldehyde-3-phosphate-lyase (EC 4.1.2.1 3) : catalase or hydrogen-peroxide : hydrogen-peroxide oxidoreductase (EC 1.1 1.1 .h) appears to be of great importance for the understand...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Investigation of the Symmetry of Oligomeric Enzymes with Bifunctional Reagents

Hucho¹,

Müllner²,

Sund³

1975

Eur J Biochem

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“…Therefore, it appears that in its presence, Zn 2 + , Cys17, and the chromophoric species are somehow interrelated. As an example, the Racker band observed in the NAD + -bound form of E. coli glyceraldehyde-3-phosphate dehydrogenase results from a charge-transfer interaction between Cys159 and the nicotinamide ring (17,18). Many other possible structures could result in an absorption band at 315 nm, including various thioether/thioester cross-links like those found in photoactive yellow protein (19), apo-galactose oxidase (20), and model complexes of apo-galactose oxidase (21).…”

Section: Discussionmentioning

confidence: 99%

Mechanistic Insights Revealed Through Characterization of a Novel Chromophore in Selenophosphate Synthetase from Escherichia coli

Wolfe

2003

IUBMB Life

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SummaryThe incorporation of selenium into specific proteins and tRNAs requires selenophosphate (SePO 3 ), whose formation is catalyzed by selenophosphate synthetase. In a Mg/ATP-dependent reaction, selenophosphate synthetase catalyzes the phosphorylation of selenide to yield AMP, inorganic phosphate, and SePO 3 . In this report, a previously unrecognized chromophore covalently attached to selenophosphate synthetase is characterized. The UV/Vis spectrum of selenophosphate synthetase has a feature centered at 315 nm that is irreversibly destroyed by alkylation. Moreover, addition of Zn 2 + , which is known to inhibit selenophosphate synthetase, reversibly quenches the 315 nm absorption. Since Zn 2 + is known to bind to Cys17, these data strongly suggest that this residue participates in the 315 nm absorption. Upon incubation with both Mg 2 + and ATP, the l max of the chromophore shifts to 340 nm, and it is shown that the shift requires binding of nucleotide having a hydrolyzable g-phosphoryl group. These data indicate that either the chromophore is directly involved in phosphoryl transfer or indirectly reflects a phosphorylation-dependent conformational change in selenophosphate synthetase. This work provides the first spectroscopic handle on catalytic steps associated with SePO 3 synthesis, which will be used to study the molecular structure of the chromophore and its role in the catalytic mechanism of selenophosphate synthetase. IUBMB Life, 55: 689-693, 2003

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“…Crowther (1969) and also Main & Rossmann (1966) were able to formulate the problem of phasing in the presence of non-crystallographic symmetry in terms of a simple set of simultaneous complex equations. However, real advances came with applying the conditions of noncrystallographic symmetry in real space, which was the key to the solution of glyceraldehyde-3-phosphate dehydrogenase (Buehner et al, 1974), tobacco mosaic virus disk protein (Bloomer et al, 1978) and other structures, aided by Gerard Bricogne's program for electron density averaging (Bricogne, 1976), which became a standard of excellence. Electron density averaging was the ®rst of numerous methods that employed density modi®cation justi®ed by physical expectations of the structure.…”

Section: Technological Developments (1958±1980s)mentioning

confidence: 99%

From the Structures of Simple Salts to Those of Sophisticated Viruses

Rossmann¹

1998

Acta Cryst Sect A

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An account is given of the development of X-ray crystallography from its beginnings in 1912 to its present successes in the determination of virus structures. Brief mention is made of early inorganic and subsequent organic molecule structure determinations, which eventually laid the foundations for the ®rst protein structures in 1957±1959. Various experimental and computational advances were required for these successes. However, additional technical advances were necessary before the ®rst near atomic resolution structures of spherical viruses became possible in 1978±1979. Current emphasis is in probing the multifunctional biological properties of viral capsids when they infect cells.

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Structure determination of crystalline lobster d-glyceraldehyde-3-phosphate dehydrogenase

Cited by 139 publications

References 31 publications

Investigation of the Symmetry of Oligomeric Enzymes with Bifunctional Reagents

Investigation of the Symmetry of Oligomeric Enzymes with Bifunctional Reagents

Mechanistic Insights Revealed Through Characterization of a Novel Chromophore in Selenophosphate Synthetase from Escherichia coli

From the Structures of Simple Salts to Those of Sophisticated Viruses

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