Daniel J Rigden

Summary

Country: Brazil

Publications

  1. ncbi A structural model for the rolA protein and its interaction with DNA
    D J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia, Brazil
    Proteins 37:697-708. 1999
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. 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
  8. 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
  9. ncbi 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
  10. ncbi Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases
    Daniel J Rigden
    National Center of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia, D F 70770 900, Brazil
    Trends Biochem Sci 28:230-4. 2003

Collaborators

Detail Information

Publications67

  1. ncbi A structural model for the rolA protein and its interaction with DNA
    D J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia, Brazil
    Proteins 37:697-708. 1999
    ..This model predicts Lys 24 and Arg 27 to be involved in sequence-specific interactions and eight other residues to hydrogen-bond phosphate groups of the DNA...
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi 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
    ....
  5. ncbi 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...
  6. ncbi 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...
  7. 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...
  8. 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
    ....
  9. ncbi 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...
  10. ncbi Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases
    Daniel J Rigden
    National Center of Genetic Resources and Biotechnology, Cenargen Embrapa, Brasilia, D F 70770 900, Brazil
    Trends Biochem Sci 28:230-4. 2003
    ..Some members of this superfamily are important surface antigens in pathogenic bacteria and might represent drug and/or vaccine targets...
  11. ncbi Structural modeling of a plant disease resistance gene product domain
    D J Rigden
    National Centre of Genetic Resources and Biotechnology, Brasilia, Brazil
    Proteins 41:133-43. 2000
    ..According to the new hypothesis, regions located N-terminal and C-terminal to the modeled portion, containing highly conserved sequence motifs, could form a separate domain...
  12. ncbi The protease inhibitor chagasin of Trypanosoma cruzi adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer
    D J Rigden
    National Centre of Genetic Resources and Biotechnology, Cenargen Embrapa, S A I N Parque Rural, Final W5 Norte, 70770 900, Brasilia, Brazil
    FEBS Lett 504:41-4. 2001
    ..Limited sequence resemblance suggests that chagasin may represent the result of a rare horizontal gene transfer from host to parasite...
  13. ncbi 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...
  14. ncbi 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...
  15. ncbi A diverse family of serine proteinase genes expressed in cotton boll weevil (Anthonomus grandis): implications for the design of pest-resistant transgenic cotton plants
    Osmundo B Oliveira-Neto
    EMBRAPA Recursos Geneticos e Biotecnologia, S A I N Parque Estação Biológica, Final W3, Asa Norte, Brasilia, DF 70770 900, Brazil
    Insect Biochem Mol Biol 34:903-18. 2004
    ....
  16. ncbi 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...
  17. ncbi Molecular cloning of alpha-amylases from cotton boll weevil, Anthonomus grandis and structural relations to plant inhibitors: an approach to insect resistance
    Osmundo B Oliveira-Neto
    EMBRAPA Recursos Geneticos e Biotecnologia, Brasilia DF, Brazil
    J Protein Chem 22:77-87. 2003
    ..19 and alpha-AI1 inhibitors on A. grandis alpha-amylase activity. This work suggests that genetic engineering of cotton to express alpha-amylase inhibitors may offer a novel route to A. grandis resistance...
  18. ncbi 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
    ....
  19. ncbi 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...
  20. ncbi 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...
  21. ncbi 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...
  22. ncbi 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...
  23. ncbi 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...
  24. ncbi 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...
  25. ncbi 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
  26. 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...
  27. ncbi 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...
  28. ncbi 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...
  29. ncbi Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of Brachiaria brizantha
    Julio C M Rodrigues
    Embrapa Genetic Resources and Biotechnology, CP 02372, CEP 70770 900 Brasilia DF, Brazil
    Plant Mol Biol 53:745-57. 2003
    ..Some of the clones identified as apomictic-specific shared homology with known genes enabling their functional annotation. The relationships of these functions to the generation of the apomictic trait are discussed...
  30. ncbi Prediction of antimicrobial peptides based on the adaptive neuro-fuzzy inference system application
    Fabiano C Fernandes
    Centro de Analises Proteomicas e Bioquimicas, Pos Graduacao em Ciencias Genomicas e Biotecnologia, UCB, Brasilia, DF, Brazil
    Biopolymers 98:280-7. 2012
    ..In summary, due to the fuzzy nature ofAMP physicochemical properties, the ANFIS approach presented here can provide an efficient solution for screening putative AMP sequences and for exploration of properties characteristic of AMPs...
  31. ncbi Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases
    Octavio L Franco
    Centro Nacional de Recursos Genéticos e Biotecnologia, Cenargen Embrapa, Brasilia DF, Brazil
    Eur J Biochem 269:397-412. 2002
    ..In this review, we summarize existing knowledge of insect alpha-amylases, plant alpha-amylase inhibitors and their interaction. Positive results recently obtained for transgenic plants and future prospects in the area are reviewed...
  32. ncbi 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...
  33. ncbi 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...
  34. ncbi 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...
  35. ncbi 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...
  36. 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
    ....
  37. ncbi 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...
  38. ncbi 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...
  39. ncbi 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...
  40. ncbi 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...
  41. ncbi 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...
  42. 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...
  43. ncbi 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
    ....
  44. doi 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
    ....
  45. 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...
  46. ncbi 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...
  47. 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
    ....
  48. ncbi 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...
  49. 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...
  50. ncbi 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...
  51. ncbi 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...
  52. ncbi 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...
  53. ncbi 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...
  54. ncbi Engineering the pH-dependence of kinetic parameters of maize glutathione S-transferase I by site-directed mutagenesis
    Nikolaos E Labrou
    Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, GR 11855 Athens, Greece
    Biomol Eng 21:61-6. 2004
    ..These findings complement the conclusions about the catalytic mechanism deduced from the crystal structure of the enzyme and provide the basis for rationally designing engineered forms of GST I with valuable properties...
  55. ncbi 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...
  56. ncbi 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
  57. ncbi The putative effector-binding site of Leishmania mexicana pyruvate kinase studied by site-directed mutagenesis
    Veronique Hannaert
    Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Universite Catholique de Louvain, ICP TROP 74 39 Avenue Hippocrate, B 1200 Brussels, Belgium
    FEBS Lett 514:255-9. 2002
    ..This hypothesis was tested by site-directed mutagenesis. The allosteric activation by F-2,6-P(2) appeared to be entirely abrogated in the mutated enzymes confirming our predictions...
  58. ncbi 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. ncbi 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...
  60. ncbi 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...
  61. 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...
  62. ncbi 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...
  63. ncbi 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...
  64. pmc Weeds, worms, and more. Papain's long-lost cousin, phytochelatin synthase
    Philip A Rea
    Plant Science Institute, Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Plant Physiol 136:2463-74. 2004
  65. ncbi 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...
  66. 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...
  67. ncbi 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
    ....