Daniel John Rigden

Summary

Affiliation: University of Liverpool
Country: UK

Publications

  1. 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
  2. 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
  3. doi 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
  4. ncbi 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
  5. doi 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
  6. doi 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
  7. 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
  8. doi Ab initio modeling led annotation suggests nucleic acid binding function for many DUFs
    Daniel J Rigden
    University of Liverpool, Institute of Integrative Biology, United Kingdom
    OMICS 15:431-8. 2011
  9. ncbi Implications of a genomic search for autophagy-related genes in trypanosomatids
    D J Rigden
    School of Biological Sciences, University of Liverpool, Liverpool, UK
    Biochem Soc Trans 33:972-4. 2005
  10. 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

Collaborators

Detail Information

Publications26

  1. 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...
  2. 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...
  3. doi 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...
  4. ncbi 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...
  5. doi 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...
  6. doi 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...
  7. 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
    ....
  8. doi Ab initio modeling led annotation suggests nucleic acid binding function for many DUFs
    Daniel J Rigden
    University of Liverpool, Institute of Integrative Biology, United Kingdom
    OMICS 15:431-8. 2011
    ..These predictions contribute to the function annotation of thousands of proteins...
  9. ncbi Implications of a genomic search for autophagy-related genes in trypanosomatids
    D J Rigden
    School of Biological Sciences, University of Liverpool, Liverpool, UK
    Biochem Soc Trans 33:972-4. 2005
    ..The results are consistent with taxon-specific addition of components to a core autophagy machinery during evolution...
  10. 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...
  11. pmc An inactivated nuclease-like domain in RecC with novel function: implications for evolution
    Daniel John Rigden
    School of Biological Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
    BMC Struct Biol 5:9. 2005
    ..The crystal structure of the RecBCD prokaryotic DNA repair machinery shows that RecB contains such a nuclease domain at its C-terminus. The RecC C-terminal region was reported as having a novel fold...
  12. pmc New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins
    Daniel J Rigden
    Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
    PLoS ONE 6:e21507. 2011
    ..The analysis presented here will inform ongoing efforts toward prediction of similar calcium-binding motifs from sequence information alone...
  13. 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...
  14. 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
  15. doi 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...
  16. doi Distinct roles for Caf1, Ccr4, Edc3 and CutA in the co-ordination of transcript deadenylation, decapping and P-body formation in Aspergillus nidulans
    Igor Y Morozov
    School of Biological Sciences, The University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
    Mol Microbiol 76:503-16. 2010
    ..As with DeltacutA, Deltaedc3 led to reduced rates of transcript degradation. These data link P-bodies to both the optimization and regulation of transcript degradation...
  17. 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...
  18. 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
    ....
  19. 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...
  20. 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
    ..SUPPLEMENTARY INFORMATION: Supplementary data are available at ftp://ftp.ncbi.nih.gov/pub/galperin/Sporulation.html...
  21. pmc CUCU modification of mRNA promotes decapping and transcript degradation in Aspergillus nidulans
    Igor Y Morozov
    University of Liverpool, School of Biological Sciences, Crown Street, Liverpool L69 7ZB, United Kingdom
    Mol Cell Biol 30:460-9. 2010
    ..We propose that 3' modification of adenylated mRNA, which is likely to represent a common eukaryotic process, primes the transcript for decapping and efficient degradation...
  22. 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...
  23. doi 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...
  24. doi 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...
  25. 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...
  26. ncbi Molecular cloning of a cysteine proteinase cDNA from the cotton boll weevil Anthonomus grandis (Coleoptera: Curculionidae)
    Osmundo Brilhante De Oliveira Neto
    EMBRAPA Recursos Geneticos e Biotecnologia, Parque Estação Biológica, Final W5, Brasilia, Brazil
    Biosci Biotechnol Biochem 68:1235-42. 2004
    ..The isolated gene will facilitate the search for highly active inhibitors towards boll weevil larvae that may provide a new opportunity to control this important insect pest...