Structure of E. coli DnaC helicase loader: Difference between revisions
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===3D Structure: Homology Model=== | ===3D Structure: Homology Model=== | ||
No empirical (X-ray crystallographic) 3D structure for the ''[http://microbewiki.kenyon.edu/index.php/Escherichia_coli E. coli]'' DnaC protein ([http://www.uniprot.org/uniprot/P0AEF0 UniProt P0AEF0]) is available in | No empirical (X-ray crystallographic) 3D structure for the ''[http://microbewiki.kenyon.edu/index.php/Escherichia_coli E. coli]'' DnaC protein ([http://www.uniprot.org/uniprot/P0AEF0 UniProt P0AEF0]) is available in November, 2012, although one or more [[#Crystal Structure of DnaC Is "In The Pipeline"|might become available]]. In view of this, homology models were constructed using the automated Swiss-Model server<ref name="methods">A model was created in 2008 by Swiss-Model using its totally automated ''first approach'' mode with template [[2qgz]]. In 2012, Swiss-Model's automated mode chose a different template, [[3ecc]], and created a similar model. </ref><ref name="swissmodel">Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/2/195 Free full text]. Server: [http://swissmodel.expasy.org swissmodel.expasy.org]</ref>. In 2008, Swiss-Model deemed the only usable template<ref name="3ec2_notemplate">In December, 2008, Swiss-Model deemed the sequence alignment of ''E. coli'' DnaC with ''A. aeolicus'' DnaC to be too unreliable to permit using the [[3ec2]] structure of the latter as a template for homology modeling of <i>E. coli</i> DnaC.</ref> for the homology model to be the crystal structure of a "putative primosome component" from ''[http://microbewiki.kenyon.edu/index.php/Streptococcus_pyogenes Streptococcus pyogenes]'' ([[2qgz]]) determined by the Northeast Structural Genomics Consortium, "to be published". In 2012, after some changes to the Swiss-Model server, it chose a different template, producing a very similar homology model. This second template was a crystal structure (also "to be published") of the DnaC helicase loader of ''[http://microbewiki.kenyon.edu/index.php/Aquifex_aeolicus Aquafex aeolicus]'' ([[3ec2]])<ref name="3ec2_notemplate" />. The agreement between the models built upon two templates having only 27% sequence identity gives confidence that fold and topology of the models are likely to be correct. Furthermore, the two homology models had identical registrations of sequence with structure. Nevertheless, because the sequence identity between the templates and the target <i>E. coli</i> DnaC is only ~20%, there may be significant errors in the registration of the <i>E. coli</i> DnaC sequence with the structure. Further, the positions of sidechains in homology models are generally unreliable. | ||
We thank the authors of [[2qgz]] and [[3ec2]] for releasing their structure data at the [[Protein Data Bank]] prior to full publication. Without these data, the homology model of ''E. coli'' DnaC would not have been posssible in December, 2008. | We thank the authors of [[2qgz]] and [[3ec2]] for releasing their structure data at the [[Protein Data Bank]] prior to full publication. Without these data, the homology model of ''E. coli'' DnaC would not have been posssible in December, 2008. | ||