PDBe: Protein Data Bank in Europe

The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.

SPINE bioinformatics and data-management aspects of high-throughput structural biology

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high‐throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high‐throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high‐throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

E-MSD: improving data deposition and structure quality

The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458-462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data.

SOAP-based services provided by the European Bioinformatics Institute

SOAP (Simple Object Access Protocol) () based Web Services technology () has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. The European Bioinformatics Institute (EBI) is using this technology to provide robust data retrieval and data analysis mechanisms to the scientific community and to enhance utilization of the biological resources it already provides [N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen and R. Lopez (2004) Nucleic Acids Res., 32, 3–9]. These services are available free to all users from .

E-MSD: an integrated data resource for bioinformatics

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the ‘Structure Integration with Function, Taxonomy and Sequences (SIFTS)’ initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

Crystallographic analysis of Phe-->Leu substitution in the hydrophobic core of barnase

The crystal structure of a barnase mutant, Phe-->Leu7 has been determined to 2.2 A resolution. No structural rearrangement is observed near the mutated residue. The F7L mutation is highly destabilizing and this is caused by the loss of extensive van der Waals contacts that wild-type Phe7 made with its neighbouring residues, and the exposure of a large hydrophobic pocket on the surface of the protein. The side-chain conformations of the mutated Leu7 residue have torsion angles chi(1) ranging from -138 degrees to -168 degrees and chi(2) ranging from +16 degrees to +70 degrees, for the three molecules in the asymmetric unit. These angles do not agree with the most frequently observed conformations in the protein side-chain rotamer library [Ponder & Richards (1987). J. Mol. Biol. 193, 775-791]. However, when compared to a more recent 'backbone-dependent' rotamer library [Dunbrack & Karplus (1993). J. Mol. Biol. 230, 543-574], the side-chain conformation of Leu7 agrees well with that of the most frequently observed rotamers. The side-chain conformation of Leu7 was found to be dictated by two factors: it has the lowest conformational energy and it buries the most hydrophobic surface area.

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms. The SSM results are compared with those obtained from other protein comparison servers, and the advantages and disadvantages of different scores that are used for structure recognition are discussed. A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign.

EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information

This paper describes the design and implementation of a Web-based deposition system, EMDep, for macro-molecular volumes determined by electron microscopy and deposited at the European Bioinformatics Institute (EBI) for inclusion in the Electron Microscopy Data Base (EMDB). EMDep is a flexible and portable system (http://www.ebi.ac.uk/msd-srv/emdep/) that allows for the acceptance and validation of data, by an interactive depositor-driven operation. The system takes full advantage of the knowledge and expertise of the experimenters, rather than relying on the database curators, for the complete and accurate description of the structural experiment and its results.

E-MSD: an integrated data resource for bioinformatics

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

Molecular modeling and mutagenesis studies of the N-terminal domains of galectin-3: evidence for participation with the C-terminal carbohydrate recognition domain in oligosaccharide binding

A model structure (Henrick,K., Bawumia,S., Barboni,E.A.M., Mehul,B. and Hughes, R.C. (1998) Glycobiology:, 8, 45-57) of the carbohydrate recognition domain (CRD, amino acid residues 114-245) of hamster galectin-3 has been extended to include N-terminal domain amino acid residues 91-113 containing one of the nine proline-rich motifs present in full-length hamster galectin-3. The modeling predicts two configurations of the N-terminal tail: in one the tail turns toward the first (SI) and last (S12) beta-strands of the CRD and lies at the apolar dimer interface observed for galectins -1 and -2. In the second folding arrangement the N-terminal tail lies across the carbohydrate-binding pocket of the CRD where it could participate in sugar-binding: in particular tyrosine 102 and adjacent residues may interact with the partly solvent exposed nonreducing N-acetylgalactosamine and fucose substituents of the A-blood group structure GalNAcalpha1,3 [Fucalpha1,2]Galbeta1,4GlcNAc-R. Binding studies using surface plasmon resonance of a recombinant fragment Delta1-93 protein containing residues 94-245 of hamster galectin-3 and a collagenase-derived fragment Delta1-103 containing residues 104-245, as well as alanine mutagenesis of residues 101-105 in Delta1-93 protein, support the prediction that Tyr102 and adjacent residues make significant contributions to oligosaccharide binding.

Discriminating between homodimeric and monomeric proteins in the crystalline state

Scores calculated from intermolecular contacts of proteins in the crystalline state are used to differentiate monomeric and homodimeric proteins, by classification into two categories separated by a cut-off score value. The generalized classification error is estimated by using bootstrap re-sampling on a nonredundant set of 172 water-soluble proteins whose prevalent quaternary state in solution is known to be either monomeric or homodimeric. A statistical potential, based on atom-pair frequencies across interfaces observed with homodimers, is found to yield an error rate of 12.5%. This indicates a small but significant improvement over the measure of solvent accessible surface area buried in the contact interface, which achieves an error rate of 15.4%. A further modification of the latter parameter relating the two most extensive contacts of the crystal results in an even lower error rate of 11.1%.

Deposition of macromolecular structures

Macromolecular structures are being determined at an increasing rate, and are of interest to a wide diversity of researchers. Depositing a macromolecular structure with the Protein Data Bank makes it readily available to the community. Accuracy, consistency and machine-readability of the data are essential, as are clear indications of quality, and sufficient information to allow non-experimentalists to interpret the data. Good-quality depositions are necessary to allow this to be achieved. The PDB's AutoDep system allows deposition and some preliminary automatic checking to take place at multiple sites, prior to full processing and release of the structure by the PDB. However, depositing a structure currently requires the manual entry of a large amount of information at the time of deposition. The data-harvesting approach will allow much more information to be deposited, without placing an additional burden on the depositor. Deposition-ready files will be generated automatically during the course of a structure-determination experiment. The additional information will allow improved validation procedures to be applied to the structures, and the data to be made more useful to the wider scientific community.

Crystal structure of phosphate binding protein labeled with a coumarin fluorophore, a probe for inorganic phosphate

Crystal structures are presented for the A197C mutant of Escherichia coli phosphate binding protein (PBP) and the same mutant labeled at Cys197 with N-[2-(1-maleimidyl)ethyl]-7-(diethylamino)coumarin-3-carboxamide (MDCC). Both proteins are complexed with inorganic phosphate. The latter molecule, MDCC-PBP, exhibits a large increase in fluorescence on binding inorganic phosphate. The resulting high-fluorescence state of the coumarin and the ability of this coumarin to monitor the conformational changes associated with inorganic phosphate binding are interpreted in terms of the specific interactions of MDCC with the protein. The structure helps to explain why this particular label gives a high-fluorescence state on binding inorganic phosphate, while several other related labels do not, and hence aids our general understanding of environmentally sensitive fluorescence probes on proteins.

Evidence for subsites in the galectins involved in sugar binding at the nonreducing end of the central galactose of oligosaccharide ligands: sequence analysis, homology modeling and mutagenesis studies of hamster galectin-3

A model of the carbohydrate recognition domain CRD, residues 111-245, of hamster galectin-3 has been made using homology modeling and dynamics minimization methods. The model is based on the known x-ray structures of bovine galectin-1 and human galectin-2. The oligosaccharides NeuNAc-alpha2,3-Gal-beta1,4-Glc and GalNAc-alpha1, 3-[Fuc-alpha1,2]-Gal-beta1,4-Glc, known to be specific high-affinity ligands for galectin-3, as well as lactose recognized by all galectins were docked in the galectin-3 CRD model structure and a minimized binding conformation found in each case. These studies indicate a putative extended carbohydrate-binding subsite in the hamster galectin-3 involving Arg139, Glu230, and Ser232 for NeuNAc-alpha2,3-; Arg139 and Glu160 for fucose-alpha1,2-; and Arg139 and Ile141 for GalNAc-alpha1,3- substituents on the primary galactose. Each of these positions is variable within the whole galectin family. Two of these residues, Arg139 and Ser232, were selected for mutagenesis to probe their importance in this newly identified putative subsite. Residue 139 adopts main-chain dihedral angles characteristic of an isolated bridge structural feature, while residue 232 is the C-terminal residue of beta-strand-11, and is followed immediately by an inverse gamma-turn. A systematic series of mutant proteins have been prepared to represent the residue variation present in the aligned sequences of galectins-1, -2, and -3. Minimized docked models were generated for each mutant in complex with NeuNAc-alpha2,3-Gal-beta1,4-Glc, GalNAc-alpha1, 3-[Fuc-alpha1,2]-Gal-beta1,4- Glc, and Gal-beta1,4-Glc. Correlation of the computed protein-carbohydrate interaction energies for each lectin-oligosaccharide pair with the experimentally determined binding affinities for fetuin and asialofetuin or the relative potencies of lactose and sialyllactose in inhibiting binding to asiolofetuin is consistent with the postulated key importance of Arg139 in recognition of the extended sialylated ligand.

Disulfide mutants of barnase. I: Changes in stability and structure assessed by biophysical methods and X-ray crystallography

In this series of papers, we examine the effects of introducing disulfide bonds on the properties, structure and thermodynamics of a small globular protein, barnase. Three mutants have been made, in each of which a single crosslink confers different properties. Two of the disulfide bonds, between residues 43 and 80 (43-80) and between residues 85 and 102 (85-102), stabilise the protein, relative to both wild-type and the corresponding (reduced) dithiol forms: 85-102 is more stable than predicted from the entropic destabilisation of the unfolded state; 43-80 is less stable than predicted. The third disulfide bond, between residues 70 and 92 (70-92) destabilises the protein relative to both wild-type and the corresponding dithiol form, implying significant disruption of the folded protein on formation of the disulfide bond. Crystal structures of the three mutant proteins have been solved. All three proteins have essentially the same fold as wild-type, but with left-handed disulfide bonds, which have dihedral geometries that have not been observed in naturally occurring disulfides. In the very stable mutant 85-102, there is no significant difference between the mutant and wild-type structures: these data do not explain the large stability of this protein. The disulfide bond at 43-80 induces small structural rearrangements close to the site of the disulfide bond, associated with some local disorder: the crosslink appears to decrease the stability of the native form of the protein. The destabilising disulfide bond at 70-92 induces considerable structural change, with displacement of a loop and consequent disruption of a stabilising salt-bridge. Our studies do not support the view that the conformation of the disulfide bond is crucial in determining the stability of the mutant proteins.

Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue

The structural basis for the stability of N termini of helices has been analyzed by thermodynamic and crystallographic studies of three suitably engineered mutants of the barley chymotrypsin inhibitor 2 with Ser, Gly, or Ala at the N-cap position (residue 31). Each mutant has a well-organized shell of hydration of the terminal NH groups of the helix. The three structures are virtually superimposable (rms separations for all atoms, including the common water molecules, are 0.15-0.17 A) and show neither changes in conformation at the site of substitution nor changes in the crystal packing. The only changes on going from Ser-31 to Ala-31 to Gly-31 are in the position of a water molecule (Wat-116). This is bound to the Ser-O gamma atom in the Ser-31 structure but is in a weak hydrogen bonding position with the NH of residue 34 (O ... N = 3.28 A) in the Ala-31 mutant, partly replacing the strong Ser-31-O gamma ... N34 hydrogen bond (O ... N = 2.65 A). The corresponding water molecule completely replaces the Ser hydroxyl hydrogen bond to N34 on mutation to Gly (2.74 A). The only other change between the three structures is an additional water molecule in the Ala-31 structure (Wat-150) that partly compensates for the weak Wat-116 ... N34 hydrogen bond. Perturbation of solvation by the side chain of Ala is consistent with earlier hypotheses on the importance of exposure of the termini of helices to the aqueous solvent.

Contribution of buried hydrogen bonds to protein stability. The crystal structures of two barnase mutants

The crystal structures of two barnase mutants, Tyr78-->Phe and Ser91-->Ala, have been determined to 2.2 A resolution. In both cases, a buried hydroxyl group that makes two hydrogen bonds within the protein was replaced by a hydrogen atom. It is found that neither mutation causes any structural changes, within the limits of error, compared with wild-type and so are confirmed to be non-disruptive. Solvent molecules are not observed in the cavities created by removal of the respective hydroxyl groups and no new interactions are introduced. The local water structure surrounding both sites of mutation is well conserved and resembles that of the wild-type. All four water molecules making contacts with the side-chain of residue 78 and two water molecules nearest to residue 91 in the wild-type are found within a sphere of 0.5 A radius, at the equivalent positions of the respective mutant. No new water molecules are found bound to any of the hydrogen bond donor or acceptor residues involved in these two mutation sites. Previous protein engineering experiments established that the solvent-inaccessible phenolic OH of Tyr78 that makes hydrogen bonds with two uncharged groups (main-chain NH and CO) contributes 1.4 kcal mol-1 to protein stability, while the solvent-inaccessible OH of Ser91 that makes hydrogen bonds with an uncharged main-chain NH and a charged group (O gamma 1) contributes 1.9 kcal mol-1. These stability measurements can now be attributed primarily to the loss of the hydrogen bonding interactions because both mutations neither disrupt the respective protein and local solvent structures, upset the overall hydrogen bonding pattern nor introduce new interactions. The mutations Tyr78-->Phe and Ser91-->Ala are thus good examples of "non-disruptive deletions" and the results of mutagenesis can be analysed at the simplest level.

Crystal structural analysis of mutations in the hydrophobic cores of barnase

We have solved and analysed the crystal structures of five mutants in the hydrophobic core of barnase to investigate the structural basis for the contribution of hydrophobic residues and side-chain packing to the stability of globular proteins. In case ease, an amino acid side-chain has been replaced with one of smaller volume. The overall structures of four Ile-->Val mutants (residues 51, 76, 88 and 96) and one Leu-->Val mutant (residue 89) are all isomorphous with the wild-type structure. The magnitude and nature of structural shifts in the three hydrophobic core regions of barnase depend on the local environment of the substitution site, but have some features in common. (1) Side-chain atoms move to a greater extent than do main-chain atoms. (2) Repacking at the substitution site is achieved by either a rigid body shift of side-chain atoms (for Ile-->Val76 and Ile-->Val96 mutants), or by a combination of a side-chain shift and rotation (for Ile-->Val51 and Ile-->Val88 mutants). The mutated residue moves to the greatest extent, and generally in the direction of the created cavity (the largest atomic shift is 0.9 A, for Ile-->Val51). The space left behind from such shifts is not seen to be filled by neighbouring side-chains. (3) Where a cavity remains after mutation, it does not contain any solvent molecules. (4) There is no correlation between the extent of structural movements and the atomic temperature factors of atoms that have moved. (5) Structural movements are not large enough to disrupt hydrogen bonding. Valine 88, in the Ile-->Val88 mutant, is disordered and the electron density suggests several side-chain conformations. The reduction in the volumes of the cavities introduced upon mutation, due to collapse of the surrounding structure, ranges from 11% (Ile-->Val96) to 90% (Ile-->Val51).

Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening followed by a 1,2-hydride shift

The active site and mechanism of D-xylose isomerase have been probed by determination of the crystal structures of the enzyme bound to various substrates, inhibitors and cations. Ring-opening is an obligatory first step of the reaction and is believed to be the rate-determining step for the aldose to ketose conversion. The structure of a complex with a cyclic thio-glucose has been determined and it is concluded that this is an analogue of the Michaelis complex. At -10 degrees C substrates in crystals are observed in the extended chain form. The absence of an appropriately situated base for either the cyclic or extended chain forms from the substrate binding site indicates that the isomerisation does not take place by an enediol or enediolate mechanism. Binding of a trivalent cation places an additional charge at the active site, producing a substrate complex that is analogous to a possible transition state. Of the two binding sites for divalent cations, [1] is permanently occupied under catalytic conditions and is co-ordinated to four carboxylate groups. In the absence of substrate it is exposed to solvent, and in the Michaelis complex analogue, site [1] is octahedrally coordinated, with ligands to O-3 and O-4 of the thiopyranose. In the complex with an open-chain substrate it remains octahedrally co-ordinated, with ligands to O-2 and O-4. Binding at a second cation site [2] is also necessary for catalysis and this site is believed to bind Co2+ more strongly than site [1]. This site is octahedrally co-ordinated to three carboxylate groups (bidentate co-ordination to one of them), an imidazole and a solvent molecule. It is proposed that during the hydride shift the C-O-1 and C-O-2 bonds of the substrate are polarized by the close approach of the site [2] cation. In the transition-state analogue this cation is observed at a site [2'], 1.0 A from site [2] and about 2.7 A from O-1 and O-2 of the substrate. It is likely that co-ordination of the cation to O-1 and O-2 would be concomitant with ionisation of the sugar hydroxyl group. The polarisation of C-O-1 and C-O-2 is assisted by the co-ordination of O-2 to cation [1] and O-1 to a lysine side-chain.(ABSTRACT TRUNCATED AT 400 WORDS)

Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively

The structures of D-xylose isomerase from Arthrobacter strain B3728 containing the polyol inhibitors xylitol and D-sorbitol have been solved at 2.5 A and 2.3 A, respectively. The structures have been refined using restrained least-squares refinement methods. The final crystallographic R-factors for the D-sorbitol (xylitol) bound molecules, for 43,615 (32,989) reflections are 15.6 (14.7). The molecule is a tetramer and the asymmetric unit of the crystal contains a dimer, the final model of which, incorporates a total of 6086 unique protein, inhibitor and magnesium atoms together with 535 bound solvent molecules. Each subunit of the enzyme contains two domains: the main domain is a parallel-stranded alpha-beta barrel, which has been reported in 14 other enzymes. The C-terminal domain is a loop structure consisting of five helical segments and is involved in intermolecular contacts between subunits that make up the tetramer. The structures have been analysed with respect to molecular symmetry, intersubunit contacts, inhibitor binding and active site geometry. The refined model shows the two independent subunits to be similar apart from local deviations due to solvent contacts in the solvent-exposed helices. The enzyme is dependent on a divalent cation for catalytic activity. Two metal ions are required per monomer, and the high-affinity magnesium(II) site has been identified from the structural results presented here. The metal ion is complexed, at the high-affinity site, by four carboxylate side-chains of the conserved residues, Glu180, Glu216, Asp244 and Asp292. The inhibitor polyols are bound in the active site in an extended open chain conformation and complete an octahedral co-ordination shell for the magnesium cation via their oxygen atoms O-2 and O-4. The active site lies in a deep pocket near the C-terminal ends of the beta-strands of the barrel domain and includes residues from a second subunit. The tetrameric molecule can be considered to be a dimer of "active" dimers, the active sites being composed of residues from both subunits. The analysis has revealed the presence of several internal salt-bridges stabilizing the tertiary and quaternary structure. One of these, between Asp23 and Arg139, appears to play a key role in stabilizing the active dimer and is conserved in the known sequences of this enzyme.(ABSTRACT TRUNCATED AT 400 WORDS)

Comparison of backbone structures of glucose isomerase from Streptomyces and Arthrobacter

The C alpha backbones of the glucose isomerase molecules of Streptomyces rubiginosus and Arthrobacter have been determined by X-ray crystallography and compared. Each molecule is a tetramer of eight-stranded alpha/beta barrels, and the mode of association of the tetramers is identical in each case. The Arthrobacter electron density shows four additional amino acids at the carboxyl terminus. There is also an insertion of six amino acids at position 277, and two individual insertions at about positions 348 and 357 (numbering according to the Streptomyces structure). There is a close structural homology throughout the whole molecule, which is most accurate up to position 325. The r.m.s. displacement for 315 homologous C alpha positions up to this position is 0.92 A.

A novel metabolite of tinidazole involving nitro-group migration

After oral doses to dogs of 14C-tinidazole, a 5-nitroimidazolyl antiprotozoal compound, a major and previously unidentified radioactive metabolite was isolated from urine and shown by FAB mass spectrometry and n.m.r. spectroscopy to be ring-hydroxylated. The exact identity of this metabolite was established by X-ray diffraction analysis as ethyl 2-(5-hydroxy-2-methyl-4-nitro-1-imidazolyl)ethyl sulphone. The apparent migration of the nitro group from the 5 position in the parent drug to the 4 position in the metabolite is a novel metabolic route.

X-ray structural studies and molecular orbital calculations (CNDO/2) in a series of cyclopenta[a]phenanthrenes: attempts at correlation with carcinogenicity

Comparative X-ray crystallographic structure analyses have been carried out on seven cyclopenta[a]phenanthrenes, namely 15,16-dihydocyclopenta[a]phenanthren-17-one and its 2-, 6- and 12-methyl homologues (non-carcinogens) and the 7-and 11-methyl and 1,11-methano derivatives (carcinogens). All-valence-electron molecular-orbital calculations by the CNDO/2 method, using the crystallographic parameters, have also been executed. Charge distribution and the energies of the highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) have been calculated. With one exception all the molecules show only small deviations from planarity, the exception being the strongly carcinogenic 11-methyl-17-ketone in which the bay-region methyl group causes out-of-plane deformation of the benzo rings of 12.5 degrees. Among the other six compounds the two carcinogens are readily differentiated by high angle strain induced by a 7-methyl group or a 1,11-methano bridge. As expected, the HOMO's of these molecules to some extent reflect their ease of chemical oxidation at the 6,7-double bond; biological oxidation is less easy to correlate probably due to spatial restrictions at the active site within the mono-oxygenase.