4 - Central Institute of Brackishwater Aquaculture
4 - Central Institute of Brackishwater Aquaculture
4 - Central Institute of Brackishwater Aquaculture
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National Workshop-cum-Train~ng on Biolnforrnatics and Information Management in <strong>Aquaculture</strong><br />
30s ribosomal protein S2<br />
GTP-binding protein EngA<br />
Acetyl glucosaminyl<br />
transferase<br />
Rib<strong>of</strong>lavin-specific<br />
deaminase<br />
Translation ,post modification<br />
GTP-dependent binding, GTPase <strong>of</strong><br />
unknown physiological role.<br />
Acetylglucosaminyl transferase activity<br />
Putative enzymes<br />
Holliday junction is the central intermediate in homologous recombination which<br />
is formed as a result <strong>of</strong> a reciprocal exchange <strong>of</strong> DNA strands between two nearly<br />
identical DNA molecules. Homologous genetic recombination is essential in<br />
maintaining genomic stability such as to protect genomes from double-strand<br />
breakage or inter strand cross linkage. RuvA, RuvB and RuvC proteins form two<br />
complexes: a RuvAB complex with helicase which conducts branch migration<br />
activities and a RuvABC ,complex that resolves Holliday junction [West, 19971.<br />
The RuvB hexamer is the chemo mechanical motor <strong>of</strong> the RuvAB complex. RuvB<br />
converts chemical energy from ATP into the dynamic force behind branch<br />
migration <strong>of</strong> Holliday junctions formed during DNA recombination and DNA<br />
replication. RuvA and RuvB bind to the four strand DNA structure formed in the<br />
Holliday junction intermediate, and migrate the strands through each other,<br />
using an assumed coiling mechanism. The binding <strong>of</strong> the RuvC protein to the<br />
RuvAB complex is thought to cleave the DNA strands, thereby resolving the<br />
Holliday junction. Inhibition <strong>of</strong> this protein stops genomic stability such as to<br />
protect genomes from double-strand breaks or interstrand cross links<br />
[Kowalczykowski, 20001.<br />
3.2 Homology Modeling: The 3D structure <strong>of</strong> DNA helicase RuvB protein <strong>of</strong> C.<br />
pneumoniae was modelled based on the crystal structure <strong>of</strong> Therrnotoga<br />
maritima RuvB holliday junction branch migration motor protein[Putnam et al.,<br />
20011 (PDB ID: 1IN4) using Modeller9vZ. The target protein sequence shows<br />
the following results when clustered based on a distance matrix with Modeller.<br />
(Figure 4)<br />
weighted pair-group average clustering based on a distance matrix:<br />
Figure 4: Template proteins clustering based on a distance matrix.
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