Constructing an enzyme-centric view of metabolism.

MOTIVATION: The current paradigm for viewing metabolism, such as the Boehringer Chart or KEGG, takes a metabolite-centric view that is not ideal for genomics analysis because the same enzyme can appear in multiple places. Therefore an enzyme-centric view is also required. RESULTS: We have eliminated synonymous compound names taken from the ENZYME database ensuring that it is computationally parseable at all levels. Based on these results, we have written a software to create enzyme-centric graphs from reaction data, and we have created a second dataset with hub molecules removed, allowing a greater depth of information to be extracted from these graphs. We also present a detailed analysis of the various stages of the reconditioning process and the characteristics of the subgraphs resulting from the application of our software to the revised datasets. AVAILABILITY: Complete datasets and supplementary material may be downloaded from http://helix.ex.ac.uk/metabolism. The software for the creation of enzyme-centric graphs from reaction data is available on request from the authors.

The structure of human liver fructose-1,6-bisphosphate aldolase.

The X-ray crystallographic structure of the human liver isozyme of fructose-1,6-bisphosphate aldolase has been determined by molecular replacement using a tetramer of the human muscle isozyme as a search model. The liver aldolase (B isozyme) crystallized in space group C2, with unit-cell parameters a = 291.1, b = 489.8, c = 103.4 A, alpha = 90, beta = 103.6, gamma = 90 degrees. These large unit-cell parameters result from the presence of 18 subunits in the asymmetric unit: four catalytic tetramers and a dimer from a fifth tetramer positioned on the twofold crystallographic axis. This structure provides further insight into the factors affecting isozyme specificity. It reveals small differences in secondary structure that occur in regions previously determined to be isozyme specific. Two of these regions are at the solvent-exposed enzyme surface away from the active site of the enzyme. The most significant changes are in the flexible C-terminal region of the enzyme, where there is an insertion of an extra alpha-helix. Point mutations of the human liver aldolase are responsible for the disease hereditary fructose intolerance. Sequence information is projected onto the new crystal structure in order to indicate how these mutations bring about reduced enzyme activity and affect structural stability.

Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis.

The three-dimensional structure of the vanadium bromoperoxidase protein from the marine red macroalgae Corallina officinalis has been determined by single isomorphous replacement at 2.3 A resolution. The enzyme subunit is made up of 595 amino acid residues folded into a single alpha+beta domain. There are 12 bromoperoxidase subunits, arranged with 23-point group symmetry. A cavity is formed by the N terminus of each subunit in the centre of the dodecamer. The subunit fold and dimer organisation of the Cor. officinalis vanadium bromoperoxidase are similar to those of the dimeric enzyme from the brown algae Ascophyllum nodosum, with which it shares 33 % sequence identity. The different oligomeric state of the two algal enzymes seems to reflect separate mechanisms of adaptation to harsh environmental conditions and/or to chemically active substrates and products. The residues involved in the vanadate binding are conserved between the two algal bromoperoxidases and the vanadium chloroperoxidase from the fungus Curvularia inaequalis. However, most of the other residues forming the active-site cavity are different in the three enzymes, which reflects differences in the substrate specificity and stereoselectivity of the reaction. A dimer of the Cor. officinalis enzyme partially superimposes with the two-domain monomer of the fungal enzyme.

Structure of a phosphoglycerate mutase:3-phosphoglyceric acid complex at 1.7 A.

The crystal structure of the tetrameric glycolytic enzyme phosphoglycerate mutase from the yeast Saccharomyces cerevisiae has been determined to 1.7 A resolution in complex with the sugar substrate. The difference map indicates that 3-phosphoglycerate is bound at the base of a 12 A cleft, positioning C2 of the substrate within 3.5 A of the primary catalytic residue, histidine 8.

Crystal structure of the glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus.

The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the archaea shows low sequence identity (16-20%) with its eubacterial and eukaryotic counterparts. The crystal structure of the apo GAPDH from Sulfolobus solfataricus has been determined by multiple isomorphous replacement at 2.05 A resolution. The enzyme has several differences in secondary structure when compared with eubacterial GAPDHs, with an overall increase in the number of alpha-helices. There is a relocation of the active-site residues within the catalytic domain of the enzyme. The thermostability of the S. solfataricus enzyme can be attributed to a combination of an ion pair cluster and an intrasubunit disulphide bond.

Preliminary X-ray analysis of a new crystal form of the vanadium-dependent bromoperoxidase from Corallina officinalis.

A new crystal form of the vanadium-dependent bromoperoxidase from Corallina officinalis has been obtained. The crystals exhibit a 'teardrop' morphology and are grown from 2 M ammonium dihydrogen phosphate pH and diffract to beyond 1.7 A resolution. They are in tetragonal space group P4222 with unit-cell dimensions of a = b = 201.9, c = 178.19 A, alpha = beta = gamma = 90 degrees. A 2.3 A resolution native data set has been collected at the Hamburg Synchrotron. A mercury derivative data set has also been collected, and the heavy-atom positions have been determined. The self-rotation function and the positions of the heavy atoms are consistent with the molecule being a dodecamer with local 23 symmetry.