Overview

1
Overview

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

2
The sequence
sbc04-02
sbc04-02

• Similar to RIKEN cDNA
• Direct submit
• A 5nucleotidase
• 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
• a-helices
• Loops
• ß-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
Discussion

• Native protein-Haloacid dehalogenase
• Long, coherent helices
• Short, snug loops

• Protein model-5-nucleotidase
• Short, incoherent helices
• Long loops

• Conclusion
• The model is probably not correct at all
• logo, loops, helices
• Look at analogues