Overview
• The problem
– Finding a homologue
• The findings
– Sequence, structure, function
• Homology modeling
– From native protein to model protein
• Discussion
• Conclusion
sbc04-02:
sbc04-02:
The sequence
• Similar to RIKEN cDNA
– Direct submit
• A 5’nucleotidase
– Purine and pyrimidine
metabolisms
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
PSI-BLAST/Pfam
• PSI-BLAST
– High similarity to Cytosolic purine 5’nucliotidase
– Identical to ”similar to RIKEN cDNA”
• Pfam
– Domain 5’-nucleotidase-no structure
EC-number
• Describes protein function
• EC 3.1.3.5
– 5’-ribonucleotide phosphohydrolase
5’-ribonucleotide + H2O = ribonucleoside + phosphate
– Pathways
• Purine metabolism
• Pyrimidine metabolism
• Nicotinate and nicotinamide metabolism
Example of mechanism
A cytosolic 5’-nucleotidase in red blood cells
• Degradation of adenosine nucleotides
– Dephosphorylation of AMP by 5’-nucleotidase
AMP + H2O = adenosine + inorganic phosphate
• 5’-nucleotidase regulation
– AMP
– Inorganic phosphate
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 ProQMX 0.469
d1zrn, homologue to the
sequence
• Haloacid dehalogenase
– Degrades environmentally
dangerous halogenated
organic compounds
• The elephant
– The head
– The body
– The neck
• Active site
d1zrn model
• Structure quite similar
to native protein
– α-helices
– Loops
– β-strands
The model: whole protein and
domain only
d1zrn model, whole protein
d1zrn model, domain only
Logo
• Conserved residues,
coloured in green
– Internal
– Loops
Discussion
• Native protein• Protein model-5’Haloacid dehalogenase
nucleotidase
– Long, coherent helices
– Short, snug loops
– Short, incoherent helices
– Long loops
Conclusion:
• The model is probably not correct at all
 logo, loops, helices
• Look at analogues