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Finding Homologues and Homology Modeling: Attacking the Problem of a 5'-nucleotidase

This article discusses the process of finding homologues and using homology modeling to tackle the problem of a 5'-nucleotidase. It explores the sequence, structure, and function of the protein, as well as the findings from PSI-BLAST, Pfam, and Meta servers. The discussion includes the construction of a homology model and the comparison of the model to the native protein.

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Finding Homologues and Homology Modeling: Attacking the Problem of a 5'-nucleotidase

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  1. Overview • The problem • Finding a homologue • The findings • Sequence, structure, function • Homology modeling • From native protein to model protein • Discussion • Conclusion

  2. sbc04-02: sbc04-02: The sequence • Similar to RIKEN cDNA • Direct submit • A 5’nucleotidase • Purine and pyrimidine metabolisms

  3. How to attack the problem!!! • PSI-BLAST • Found-homologues with no structure • Pfam • Found-domain • Meta • Found-distant homologues with structure • Logo • Found-conserved residues

  4. PSI-BLAST/Pfam • PSI-BLAST • High similarity to Cytosolic purine 5’-nucliotidase • Identical to ”similar to RIKEN cDNA” • Pfam • Domain 5’-nucleotidase-no structure

  5. EC-number • Describes protein function • EC 3.1.3.5 • 5’-ribonucleotide phosphohydrolase • Pathways • Purine metabolism • Pyrimidine metabolism • Nicotinate and nicotinamide metabolism 5’-ribonucleotide + H2O = ribonucleoside + phosphate

  6. Example of mechanismA cytosolic 5’-nucleotidase in red blood cells • Degradation of adenosine nucleotides • Dephosphorylation of AMP by 5’-nucleotidase • 5’-nucleotidase regulation • AMP • Inorganic phosphate AMP + H2O = adenosine + inorganic phosphate

  7. Meta server • Provided new homologues • HAD-like super familly • Best homology modell used: d1zrn • Modell of whole protein: ProQ-LG 3.877 and ProQ-MX 0.353 • Modell of domain: ProQ-LG 4.223 and ProQ-MX 0.469

  8. d1zrn, homologue to the sequence • Haloacid dehalogenase • Degrades environmentally dangerous halogenated organic compounds • The elephant • The head • The body • The neck • Active site

  9. d1zrn model • Structure quite similar to native protein • α-helices • Loops • β-strands

  10. The model: whole protein and domain only d1zrn model, whole protein d1zrn model, domain only

  11. Logo • Conserved residues, coloured in green • Internal • Loops

  12. Native protein-Haloacid dehalogenase Long, coherent helices Short, snug loops Protein model-5’-nucleotidase Short, incoherent helices Long loops Discussion • Conclusion: • The model is probably not correct at all • logo, loops, helices • Look at analogues

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