Daniel J Rigden

Summary

Affiliation: University of Liverpool
Country: UK

Publications

  1. pmc Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
    Jimmy H Saw
    Department of Microbiology, University of Hawai i, 2538 The Mall, Honolulu, HI 96822, USA
    Genome Biol 9:R161. 2008
  2. pmc Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)
    Gustavo R Oliveira
    EMBRAPA Recursos Geneticos e Biotecnologia, PqEB Final W5 Norte Brasília, DF, Brasil
    BMC Biotechnol 11:85. 2011
  3. pmc Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
    Bioinformatics 24:1793-7. 2008
  4. ncbi request reprint The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
    Trends Biochem Sci 29:335-9. 2004
  5. ncbi request reprint The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
    J Mol Biol 343:971-84. 2004
  6. ncbi request reprint Understanding the cell in terms of structure and function: insights from structural genomics
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
    Curr Opin Biotechnol 17:457-64. 2006
  7. ncbi request reprint An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: surprising relationship to insect ecdysteroid phosphate phosphatase
    Lyndsay Davies
    School of Biological Sciences, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, United Kingdom
    Proteins 67:720-31. 2007
  8. pmc Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure
    Luciane V Mello
    University of Liverpool, UK
    BMC Genomics 10:611. 2009
  9. pmc Regulation of ecdysteroid signalling during Drosophila development: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration
    Hajime Takeuchi
    Cellular Regulation and Signalling Division, School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
    Biochem J 389:637-45. 2005
  10. doi request reprint Ab initio protein modelling reveals novel human MIT domains
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Liverpool, UK
    FEBS Lett 583:872-8. 2009

Collaborators

Detail Information

Publications72

  1. pmc Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
    Jimmy H Saw
    Department of Microbiology, University of Hawai i, 2538 The Mall, Honolulu, HI 96822, USA
    Genome Biol 9:R161. 2008
    ..The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life...
  2. pmc Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)
    Gustavo R Oliveira
    EMBRAPA Recursos Geneticos e Biotecnologia, PqEB Final W5 Norte Brasília, DF, Brasil
    BMC Biotechnol 11:85. 2011
    ..In vitro directed molecular evolution through DNA shuffling and phage display screening was applied to enhance the insecticidal activity of variants of the Cry8Ka1 protein of Bacillus thuringiensis...
  3. pmc Sequence analysis of GerM and SpoVS, uncharacterized bacterial 'sporulation' proteins with widespread phylogenetic distribution
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
    Bioinformatics 24:1793-7. 2008
    ..SpoVS is predicted to adopt the AlbA archaeal chromatin protein fold, which suggests that it is a DNA-binding protein, most likely a novel transcriptional regulator...
  4. ncbi request reprint The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
    Trends Biochem Sci 29:335-9. 2004
  5. ncbi request reprint The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
    J Mol Biol 343:971-84. 2004
    ..The analysis presented here has consequences for the prediction of calcium binding from sequence alone...
  6. ncbi request reprint Understanding the cell in terms of structure and function: insights from structural genomics
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
    Curr Opin Biotechnol 17:457-64. 2006
    ..Attention is now turning to means of combining these predictions with information from various other sources...
  7. ncbi request reprint An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: surprising relationship to insect ecdysteroid phosphate phosphatase
    Lyndsay Davies
    School of Biological Sciences, University of Liverpool, Biosciences Building, Liverpool L69 7ZB, United Kingdom
    Proteins 67:720-31. 2007
    ..The surprising relationship described and explored here between EPP and Sts-1 has implications for our understanding of the function(s) of both...
  8. pmc Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure
    Luciane V Mello
    University of Liverpool, UK
    BMC Genomics 10:611. 2009
    ..In the present work, we investigate the evolution and expression of aspartic proteases in Strongyloides ratti, which permits a unique comparison between parasitic and free-living adult forms within its life-cycle...
  9. pmc Regulation of ecdysteroid signalling during Drosophila development: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration
    Hajime Takeuchi
    Cellular Regulation and Signalling Division, School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
    Biochem J 389:637-45. 2005
    ....
  10. doi request reprint Ab initio protein modelling reveals novel human MIT domains
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Liverpool, UK
    FEBS Lett 583:872-8. 2009
    ..As a proof of principle, we have confirmed the novel MIT annotation for USP54 by in vitro profiling of binding to CHMP proteins...
  11. doi request reprint Does distant homology with Evf reveal a lipid binding site in Bacillus thuringiensis cytolytic toxins?
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown Street, Liverpool, UK
    FEBS Lett 583:1555-60. 2009
    ..Here, distant homology between the structure of Cyt toxins and Erwinia virulence factor (Evf) is demonstrated which, along with sequence conservation analysis, allows a putative lipid binding site to be localised in the toxins...
  12. ncbi request reprint The histidine phosphatase superfamily: structure and function
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
    Biochem J 409:333-48. 2008
    ....
  13. doi request reprint A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods
    Luciane V Mello
    Structural and Chemical Biology, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
    FEBS Lett 586:3908-13. 2012
    ..The newly assigned activity is sporadically present in phyla not containing near relatives of the similarly active repair protein AlkB...
  14. pmc Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions
    Sylvie Urbé
    Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, United Kingdom
    Mol Biol Cell 23:1095-103. 2012
    ....
  15. ncbi request reprint Analysis of glycoside hydrolase family 98: catalytic machinery, mechanism and a novel putative carbohydrate binding module
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, UK
    FEBS Lett 579:5466-72. 2005
    ..Distant homologies and domain contexts suggest that the N-terminal domain is a novel carbohydrate binding module...
  16. pmc Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, United Kingdom
    RNA 10:1845-51. 2004
    ..A group of present-day archaebacteria contain a ThrRS obtained from a bacterium by horizontal gene transfer. In some of these cases a vestigial version of the original archaeal ThrRS, of potentially novel function, is maintained...
  17. ncbi request reprint A distant evolutionary relationship between GPI-specific phospholipase D and bacterial phosphatidylcholine-preferring phospholipase C
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
    FEBS Lett 569:229-34. 2004
    ..The databases contain hitherto unnoticed close homologues of GPI-PLD from yeast and Dictyostelium discoideum...
  18. doi request reprint Cathepsin L digestion of nanobioconjugates upon endocytosis
    Violaine See
    Centre for Cell Imaging, University of Liverpool, UK
    ACS Nano 3:2461-8. 2009
    ..Preservation of the bioconjugates can be achieved by a combination of cathepsin inhibition and endosome disruption...
  19. doi request reprint Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module
    Luciane V Mello
    School of Biological Sciences, University of Liverpool, Liverpool, UK
    FEBS Lett 584:2421-6. 2010
    ..Conserved residues in the BACON domain are also characteristic of carbohydrate binding while its biased phyletic distribution and other data suggest mucin as a potential specific target...
  20. doi request reprint Structural variability of the ubiquitin specific protease DUSP-UBL double domains
    Paul R Elliott
    The University of Liverpool, Institute of Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom
    FEBS Lett 585:3385-90. 2011
    ..We identified structural features that dictate different dispositions between constituent domains, which in turn may influence respective binding properties...
  21. pmc Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement
    Jaclyn Bibby
    Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
    Acta Crystallogr D Biol Crystallogr 69:2194-201. 2013
    ..Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided. ..
  22. doi request reprint AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models
    Jaclyn Bibby
    Institute of Integrative Biology, University of Liverpool, Liverpool, England
    Acta Crystallogr D Biol Crystallogr 68:1622-31. 2012
    ..It carries out the modelling using locally installed Rosetta, creates search ensembles and automatically performs molecular replacement and model rebuilding...
  23. doi request reprint Molecular replacement using ab initio polyalanine models generated with ROSETTA
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
    Acta Crystallogr D Biol Crystallogr 64:1288-91. 2008
    ..Unsuccessful cases are also reported for comparison and the factors influencing the success of this route to structure solution are discussed...
  24. ncbi request reprint Autophagy in protists: Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion
    Daniel J Rigden
    School of Biological Sciences, University of Liverpool, Liverpool, UK
    Autophagy 5:784-94. 2009
    ..Yet, in these organisms mitochondrial function can often be rapidly remodeled; we contend that in these species turnover of mitochondrial proteins is the product of intraorganellar protease activity...
  25. pmc Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors
    Shin ichiro Yoshimura
    Cancer Research Centre and 2 Institute of Integrative Biology, University of Liverpool, Liverpool L3 9TA, England, UK
    J Cell Biol 191:367-81. 2010
    ..DENND1C, DENND3, DENND5A/5B, MTMR5/13, and MADD activate Rab13, Rab12, Rab39, Rab28, and Rab27A/27B, respectively. Together, these findings provide a basis for future studies on Rab regulation and function...
  26. doi request reprint The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection
    Xose M Fernandez-Suarez
    Life Technologies, Inchinnan Business Park, Paisley PA4 9RF, UK, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK and National Center for Biotechnology Information NCBI, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 42:D1-6. 2014
    ..oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). ..
  27. pmc Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 14:2870-90. 2012
    ..These profiles should help further experimental studies of uncharacterized widespread sporulation genes, which would ultimately allow delineation of the minimal set(s) of sporulation-specific genes in Bacilli and Clostridia...
  28. ncbi request reprint A new type of antimicrobial protein with multiple histidines from the hard tick, Amblyomma hebraeum
    Ren Lai
    Cellular Regulation and Signaling Division, School of Biological Sciences, University of Liverpool, Liverpool, UK
    FASEB J 18:1447-9. 2004
    ..Our findings describe a new type of antimicrobial protein with multiple cysteine and histidine residues, and with unique secondary structure...
  29. doi request reprint Identification and modelling of a PPM protein phosphatase fold in the Legionella pneumophila deAMPylase SidD
    Daniel J Rigden
    University of Liverpool, Institute of Integrative Biology, Liverpool, UK
    FEBS Lett 585:2749-54. 2011
    ..Assignment of a PPM fold to SidD offers an important pointer towards identification of further deAMPylases...
  30. pmc Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors
    Daniel J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, S A I N Parque Rural, Final W5 Norte, 70770 900 Brasília, Brazil
    Protein Sci 11:1971-7. 2002
    ....
  31. ncbi request reprint Design of new benzoxazole-2-thione-derived inhibitors of Streptococcus pneumoniae hyaluronan lyase: structure of a complex with a 2-phenylindole
    Daniel J Rigden
    Institute of Pharmacy, University of Regensburg, 93040 Regensburg, Germany
    Glycobiology 16:757-65. 2006
    ..These benzoxazole-2-thiones constitute a new class of inhibitors of bacterial Hyals and are well suited for further optimization of their selectivity, potency, and pharmacokinetic properties...
  32. ncbi request reprint Genome-based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase
    Daniel J Rigden
    Embrapa Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia DF, Brazil
    Proteins 52:203-11. 2003
    ..This observation may help the identification and classification of other carbohydrate binding modules...
  33. ncbi request reprint Structures of phosphate and trivanadate complexes of Bacillus stearothermophilus phosphatase PhoE: structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily
    Daniel J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, SAIN Parque Rural, Final W5, Asa Norte, 70770 900 Brasília, Brazil
    J Mol Biol 325:411-20. 2003
    ..Even within this group substrate specificity is clearly variable highlighting the difficulties of computational functional annotation in the cofactor-dependent phosphoglycerate mutase superfamily...
  34. ncbi request reprint Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae
    Daniela Bumbaca
    Center for Immunobiology and Vaccine Development, Children s Hospital Oakland Research Institute, Oakland, California 94609, USA
    Proteins 66:547-58. 2007
    ..It appears to be one of the very few unambiguous pneumococcal adhesin molecules known to date. A hypothetical model constructed by ab initio techniques predicts a novel beta-sandwich protein structure...
  35. ncbi request reprint The structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai reveals unprecedented structural displacement of the calcium-binding loop: possiblerelationship to cooperative substrate binding
    Daniel J Rigden
    EMBRAPA Recursos Geneticos e Biotecnologia, Cenargen Embrapa, Brasilia, DF, Brazil
    Acta Crystallogr D Biol Crystallogr 59:255-62. 2003
    ....
  36. doi request reprint Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?
    James W A Allen
    Department of Biochemistry, University of Oxford, UK
    FEBS J 275:2385-402. 2008
    ....
  37. ncbi request reprint Unexpected catalytic site variation in phosphoprotein phosphatase homologues of cofactor-dependent phosphoglycerate mutase
    Daniel J Rigden
    Embrapa Genetic Resources and Biotechnology, Cenargen Embrapa, Parque Estação Biológica, Final W3 Norte, 70770 900 Brasília, Brazil
    FEBS Lett 536:77-84. 2003
    ..Unexpected variation in catalytic and substrate-binding residues is observed in the models...
  38. ncbi request reprint Nucleotide sequence and phylogenetic analyses of the DNA polymerase gene of Anticarsia gemmatalis nucleopolyhedrovirus
    Caren Cristina Dalmolin
    EMBRAPA Recursos Geneticos e Biotecnologia, Parque Estação Biológica PqEB, W5 Norte Final, CEP 70770 900 Brasilia DF, Brazil
    Virus Res 110:99-109. 2005
    ....
  39. ncbi request reprint 6-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in Trypanosomatidae. Molecular characterization, database searches, modelling studies and evolutionary analysis
    Nathalie Chevalier
    Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Universite Catholique de Louvain, Brussels, Belgium
    FEBS J 272:3542-60. 2005
    ..A possible explanation for the evolution of multiple monofunctional enzymes and for the presence of the ankyrin-motif repeats in the PFK-2 isoenzymes is presented...
  40. ncbi request reprint The structure-function relationship in the clostripain family of peptidases
    Nikolaos E Labrou
    Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, Greece
    Eur J Biochem 271:983-92. 2004
    ..Two possible binding sites for the calcium required for auto-activation could be located. Database searches show that clostripain homologues are not confined to bacterial lineages and reveal an intriguing variety of domain architectures...
  41. ncbi request reprint Structures of Streptococcus pneumoniae hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides. Insights into specificity and mechanism of action
    Daniel J Rigden
    Children s Hospital Oakland Research Institute, Oakland, California 94609, USA
    J Biol Chem 278:50596-606. 2003
    ..The more efficient processive degradation mechanism has come to be preferred for the unsulfated substrate hyaluronan...
  42. pmc PrfA protein of Bacillus species: prediction and demonstration of endonuclease activity on DNA
    Daniel J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia, Brazil, D F 70770 900
    Protein Sci 11:2370-81. 2002
    ..This activity, much lower on linear or relaxed circular double-stranded DNA or on single-stranded DNA, is consistent with a role for this protein in chromosome segregation, DNA recombination, or DNA repair...
  43. ncbi request reprint Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity
    Daniel J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, S A I N Parque Rural, Final W5, Asa Norte, Brasilia, 70770 900, Brazil
    J Mol Biol 315:1129-43. 2002
    ..This PhoE structure will therefore serve as a valuable basis for inference of structural and functional characteristics of these proteins...
  44. ncbi request reprint Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of Streptococcus pneumoniae
    Daniela Bumbaca
    Children s Hospital Oakland Research Institute, Oakland, California 94609, USA
    OMICS 8:341-56. 2004
    ..pneumoniae SP0082 protein and its homologs in other streptococci as fibronectin-binding surface adhesins. The SSURE domain is likely to contain a novel protein fold, which was tentatively modeled using ab initio modeling methods...
  45. ncbi request reprint Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments
    Daniel J Rigden
    Embrapa Genetic Resources and Biotechnology, Cenargen Embrapa, S A I N Parque Rural, Final W5, Asa Norte, 70770 900, Brasilia, Brazil
    Protein Eng 15:65-77. 2002
    ..Finally, a prediction is made for geminivirus AL1 protein which is in full agreement with biochemical data, yielding a plausible, novel threading result...
  46. ncbi request reprint Fold recognition analysis of glycosyltransferase families: further members of structural superfamilies
    Octavio L Franco
    Embrapa Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia DF, Brazil
    Glycobiology 13:707-12. 2003
    ..Furthermore, bioinformatics studies indicate the apparent ease with which mechanism-inverting or retaining-may change during evolution...
  47. ncbi request reprint Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands?
    Daniel J Rigden
    National Center of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia, D F 70770 900, Brazil
    Trends Microbiol 11:295-7. 2003
  48. ncbi request reprint An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands
    Daniel J Rigden
    National Center of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia D F 70770 900, Brazil
    FEMS Microbiol Lett 221:103-10. 2003
    ..This loop is thus more widespread than hitherto recognized and the evolution of EF-hand-like domains is probably more complex than previously appreciated...
  49. ncbi request reprint Inhibition of trypsin by cowpea thionin: characterization, molecular modeling, and docking
    Francislete R Melo
    Departamento de Biologia Celular, Universidade de Brasilia, Brasilia DF, Brasil
    Proteins 48:311-9. 2002
    ..In the final model, Lys11 occupies the S1 specificity pocket of trypsin as part of a canonical style interaction...
  50. ncbi request reprint Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from Prosopis juliflora
    Octavio L Franco
    EMBRAPA Recursos Geneticos e Biotecnologia, Cenargen, Brasilia, Brazil
    Proteins 49:335-41. 2002
    ..The predicted coincidence of trypsin and papain binding sites, once confirmed, would facilitate the search, by phage display for example, for mutants highly active against both proteinases...
  51. ncbi request reprint Beta-helical catalytic domains in glycoside hydrolase families 49, 55 and 87: domain architecture, modelling and assignment of catalytic residues
    Daniel J Rigden
    Embrapa Genetic Resources and Biotechnology, Cenargen Embrapa, S A I N Parque Rural, Final W5, Asa Norte, 70770 900 Brasília DF, Brazil
    FEBS Lett 530:225-32. 2002
    ..Further analysis of domain architecture reveals the association of carbohydrate binding modules with catalytic GH beta-helices, as well as an unexpected pair of beta-helix domains in GH family 55...
  52. ncbi request reprint Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13
    Daniel J Rigden
    Embrapa Genetic Resources and Biotechnology, Cenargen Embrapa, S A I N Parque Rural, Final W5, Asa Norte, 70770 900, Brasilia, Brazil
    FEBS Lett 523:17-22. 2002
    ..The catalytic, nucleophilic residue common to all these families is thereby determined and candidate catalytic proton donors identified within each family...
  53. ncbi request reprint Leishmania donovani phosphofructokinase. Gene characterization, biochemical properties and structure-modeling studies
    Claudia Lopez
    Instituto de Biologia Experimental, Universidad Central de Venezuela, Caracas, Venezuela
    Eur J Biochem 269:3978-89. 2002
    ..Modelling studies and site-directed mutagenesis were employed to shed light on the structural basis for the AMP effector specificity and on ATP/PPi specificity among PFKs...
  54. ncbi request reprint Use of phage display to select novel cystatins specific for Acanthoscelides obtectus cysteine proteinases
    Francislete R Melo
    Embrapa Cenargen, S A I N Parque Estação Biológica, Final W3, Asa Norte, 70770 900 Brasília, DF, Brazil
    Biochim Biophys Acta 1651:146-52. 2003
    ..obtectus cysteine proteinases than the original sequence and could represent good candidate genes for the production of transgenic plants resistant to this insect pest...
  55. pmc Plant-like traits associated with metabolism of Trypanosoma parasites
    Veronique Hannaert
    Research Unit for Tropical Diseases and Laboratory of Biochemistry, Christian de Duve Institute of Cellular Pathology and Universite catholique de Louvain, B 1200 Brussels, Belgium
    Proc Natl Acad Sci U S A 100:1067-71. 2003
    ..Several of the proteins encoded by these genes are now, in the parasites, found inside highly specialized peroxisomes, called glycosomes, absent from all other eukaryotes, including euglenoids...
  56. ncbi request reprint Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling
    Daniel J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, S A I N Parque Rural, Final W5, Asa Norte, 70770 900 Brasília, Brazil
    J Mol Biol 328:909-20. 2003
    ..These studies will facilitate the development of iPGM inhibitors which, due to the demonstrated importance of this enzyme in many bacteria, would be of great potential clinical significance...
  57. ncbi request reprint The crystal structure of Trypanosoma brucei enolase: visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition
    Maria Teresa da Silva Giotto
    Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, Sao Carlos SP, Brazil
    J Mol Biol 331:653-65. 2003
    ..Evidence suggests that this is the first direct visualization of the elusive inhibitory metal site, whose existence has hitherto only been inferred from kinetic data...
  58. ncbi request reprint Characterization and functional investigation of an Arabidopsis cDNA encoding a homologue to the d-PGMase superfamily
    Fabienne Bourgis
    Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, Universite Libre de Bruxelles, CP 242, Bd du Triomphe, B 1050 Bruxelles, Belgium
    J Exp Bot 56:1129-42. 2005
    ..Two overexpressing At-74 lines showed a clear increase in glucose uptake. This paper introduces the At-74 homologue of the d-PGMase superfamily members and supports a possible role of At-74 in carbohydrate metabolism...
  59. pmc Characterization of the ligandin site of maize glutathione S-transferase I
    Irine A Axarli
    Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
    Biochem J 382:885-93. 2004
    ..The inactivation of other GST isoenzymes by VBAR was also investigated, and it was concluded that VBAR may have wide applicability as an affinity label for probing structure-function relationships of GST isoenzymes...
  60. ncbi request reprint Kinetic characterization, structure modelling studies and crystallization of Trypanosoma brucei enolase
    Veronique Hannaert
    Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Universite Catholique de Louvain, Brussels, Belgium
    Eur J Biochem 270:3205-13. 2003
    ..T. brucei enolase crystals diffracting at 2.3 A resolution were obtained and will permit us to pursue the determination of structure...
  61. ncbi request reprint Molecular modeling and inhibitory activity of cowpea cystatin against bean bruchid pests
    Juliana M Aguiar
    Laboratório de Química e Função de Proteínas e Peptídeos, UENF, Campos dos Goytacazes, RJ, Brazil
    Proteins 63:662-70. 2006
    ..The application of this knowledge in plant protein mutation programs aiming at enhancement of plant defenses to pests is discussed...
  62. ncbi request reprint Alternate structural conformations of Streptococcus pneumoniae hyaluronan lyase: insights into enzyme flexibility and underlying molecular mechanism of action
    Daniel J Rigden
    Children s Hospital Oakland Research Institute, Oakland, CA 94609, USA
    J Mol Biol 358:1165-78. 2006
    ..One of these new structures resembles the S.agalactiae enzyme conformation, and provides evidence of a uniform mechanistic/dynamic behavior of this protein across different bacteria...
  63. pmc Mutagenic definition of a papain-like catalytic triad, sufficiency of the N-terminal domain for single-site core catalytic enzyme acylation, and C-terminal domain for augmentative metal activation of a eukaryotic phytochelatin synthase
    Nataliya D Romanyuk
    Plant Science Institute, Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Plant Physiol 141:858-69. 2006
    ....
  64. ncbi request reprint Autophagy and related processes in trypanosomatids: insights from genomic and bioinformatic analyses
    Murielle Herman
    Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Universite Catholique de Louvain, Brussels, Belgium
    Autophagy 2:107-18. 2006
    ..A bioinformatics analysis of the trypanosomatidal proteins was carried out, highlighting the paucity of information available regarding their structures and enabling prioritization of targets for future structural biology work...
  65. ncbi request reprint Monomorphic subtelomeric DNA in the filamentous fungus, Metarhizium anisopliae,contains a RecQ helicase-like gene
    Peter W Inglis
    EMBRAPA Recursos Geneticos e Biotecnologia, Parque Estação Biológica, Final Av W 5 Norte, Brasilia DF, CEP 70770900, C P 02372, Brazil
    Mol Genet Genomics 274:79-90. 2005
    ..Hybridization analyses showed that TAH1 homologues are present in all other anomalous M. anisopliae strains studied, as well as in some other polymorphic strains, where the recQ-like gene also appears to be telomere-associated...
  66. ncbi request reprint Acyl carrier protein phosphodiesterase (AcpH) of Escherichia coli is a non-canonical member of the HD phosphatase/phosphodiesterase family
    Jacob Thomas
    Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Biochemistry 46:129-36. 2007
    ..We conclude that AcpH is a member of the HD protein family despite the lack of the signature histidine residue...
  67. ncbi request reprint Evolutionary analysis of fructose 2,6-bisphosphate metabolism
    Paul A M Michels
    Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Universite Catholique de Louvain, Brussels, Belgium
    IUBMB Life 58:133-41. 2006
    ....
  68. pmc The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase
    Zhong Yu
    Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
    Nucleic Acids Res 35:2107-15. 2007
    ..We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase...
  69. ncbi request reprint Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics
    Marcos V de A S Navarro
    Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, Sao Carlos SP, Brazil
    FEBS J 274:5077-89. 2007
    ..One of the new sulfate structures contains a novel metal-binding site IV within the catalytic site cleft...
  70. ncbi request reprint Identification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families
    Daniel J Rigden
    Embrapa Genetic Resources and Biotechnology, Cenargen Embrapa, Estação Parque Biológico, Final W5, Asa Norte, 70770 900, Brasilia DF, Brazil
    FEBS Lett 544:103-11. 2003
    ..Only 327 GH sequences still have no structurally identified catalytic domain...
  71. ncbi request reprint Analysis of structure and function of putative surface-exposed proteins encoded in the Streptococcus pneumoniae genome: a bioinformatics-based approach to vaccine and drug design
    Daniel J Rigden
    National Center of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia, Brazil, D F 70770 900
    Crit Rev Biochem Mol Biol 38:143-68. 2003
    ..The information obtained from the genome analysis will be instrumental in the development of a more effective prophylactic and/or therapeutic agents to prevent and to treat infections due to S. pneumoniae...
  72. ncbi request reprint L-Ascorbic acid 6-hexadecanoate, a potent hyaluronidase inhibitor. X-ray structure and molecular modeling of enzyme-inhibitor complexes
    Alexander Botzki
    Institute of Pharmacy, University of Regensburg, Universitatsstrasse 31, 93040 Regensburg, Germany
    J Biol Chem 279:45990-7. 2004
    ..The long alkyl chain seemed to interact with an extended, hydrophobic channel formed by mostly conserved amino acids Ala-84, Leu-91, Tyr-93, Tyr-220, and Leu-344 in BTH...