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 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 August, 2012, although one or more [[#Crystal Structure of DnaC Is "In The Pipeline"|may become available shortly]]. 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 build upon two templates having only XX% sequence identity gives confidence that fold and topology of the models are likely to be correct. However, 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. | ||