Structure of E. coli DnaC helicase loader: Difference between revisions

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{{Theoretical_model}}
{{Theoretical_model}}
<StructureSection load='Dnac_from_2ggz_a.pdb' size='300' side='right' scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/8' caption=''>
<StructureSection load='Dnac_from_2ggz_a.pdb' size='400' side='right' scene='User:Eric_Martz/Sandbox_4/Dnac_model_from_2ggz_a/8' caption=''>


==Overview==
==Overview==
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As indicated [[#3D Structure: Homology Model|above]], in 2008, Swiss-Model found only one usable template for homology modeling, despite the existence of an empirical 3D crystal structure for DnaC with a slightly higher sequence identity.
As indicated [[#3D Structure: Homology Model|above]], in 2008, Swiss-Model found only one usable template for homology modeling, despite the existence of an empirical 3D crystal structure for DnaC with a slightly higher sequence identity.
{{Clear}}
{{Clear}}
===Gaps in the Template Model===
The template was 2QGZ (<scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>initial scene</scene>). The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms).
The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). These gaps, which occur between the residues marked /\ below, were apparently ignored in making the model, which has a continuous main chain.
{{Clear}}
==Confirmation of Homology Model By Related Structures==
When the [[PDB]] is searched with the DnaC sequence, the best match (December, 2008) is 23% sequence identity with 183 amino acids in the DnaC helicase loader of ''Aquifex aeolicus'', [[3ec2]] and [[3ecc]]. In order to find whether these structures have the same fold as the template ([[2qgz]] with 19% sequence identity to ''E. coli'' DnaC) used for the homology model, <font color="#3030ff">'''2qgz'''</font> <scene name='User:Eric_Martz/Sandbox_6/2qgz_3ec2_aligned_pdb/1'>was structurally aligned</scene> with <font color="#ff0000">'''3ec2'''</font><ref>The structural alignment of 2qgz with 3ec2 was performed with the ''Magic Fit'' function of DeepView version 3.6beta2. 2qgz 115-259 aligned with 3ec2 42-185 (3 gaps in 3ec2's alignment: 128-9, 134-5, 155-9). 135 alpha carbons were aligned with RMS 2.76 Å. The sequence identity between 2qgz and 3ec2 is 28% over the 185 amino acid length of the shorter, 3ec2. ''Magic Fit'' is a sequence-alignment-guided structural alignment (see [[Structural_alignment_tools#DeepView_.3D_Swiss-PDBViewer|Structural alignment tools]]).</ref>. The similarity of folds lends considerable confidence to the homology model of ''E. coli'' DnaC. This was further confirmed by the 2012 Swiss Model run, when 3ecc was selected as the best template (see discussion above).
The second best sequence-identity hit in the PDB is 39% identity with 54 amino acids (positions 9-63 of chain A) of replication factor C ([[2chg]]), which align with 72-124 of DnaC. When the above homology model of DnaC (made with template 2QGZ) is <scene name='User:Eric_Martz/Sandbox_4/2chg9-63_aligned_with_dnac_mod/1'>structurally aligned</scene> with residues 9-63 of 2CHG<ref>Structural alignment done with DeepView 3.6b3 using Magic Fit of carbon alphas.</ref>, 43 alpha carbons (out of 54) aligned with RMS deviation 2.3 &Aring;. <font color="#ff0000">'''Residues 21-63 of 2CHG'''</font> aligned with <font color="#3030ff">'''residues 80-124 of the DnaC homology model'''</font>. (Non-aligned portions are pastel.) This result adds firther confidence to this region of the homology model, since the structural alignment of 2CHG:A21-63 occurred in the same range as the sequence alignment (which was 72-124 in DnaC).
''Download'' the above structural alignments:
*[[:Image:2qgz_3ec2_aligned.pdb|2qgz_3ec2_aligned.pdb]]
*[[:Image:2chg9-63_aligned_with_dnac_model.pdb|2chg9-63_aligned_with_dnac_model.pdb]]
{{Clear}}
==Crystal Structure of DnaC Is "In The Pipeline"==
A sequence-based search at the international [http://targetdb.pdb.org/ Structural Genomics TargetDB] reveals that the closest completed structure is [[2qgz]], the one chosen by SwissModel as a template. ([[3ec2]] and [[3ecc]] were not determined by a structural genomics project.) A number of crystal and NMR structures have sequence identities up to 37% but over shorter stretches, and with higher E values.
Diffraction data have been obtained (but the solved structure not yet deposited) for a ''Listeria monocytogenes'' sequence of 307 residues, pI 5.2, with an E value of 1.6e-05, though only 21% sequence identity. Diffraction-quality crystals (but not yet diffraction data) have not been obtained for any sequence with such a low E value.
''E. coli'' DnaC (245 residues, pI 9.4) has been crystallized by RIKEN Structural Genomics Initiative (Japan), but the crystals may not be of diffraction quality. It has been cloned, expressed as a soluble protein, and purified (but not yet crystallized) by 3 Structural Genomics Groups (RIKEN Structural Genomics Initiative (Japan), Montreal-Kingston Bacterial Structural Genomics Initiative, Midwest Center for Structural Genomics), as have several proteins with >40% sequence identity.
Thus, there is reason for optimism that either a crystal structure, or a more suitable template for homology modeling, might be forthcoming.
==3D structures of DnaC helicase loader==
[[DnaC helicase loader]]
==Additional Resources==
For additional information, see: [[DNA Replication, Repair, and Recombination]]
For additional information, see: [[Nucleic Acids]]
<br />
</StructureSection>
{| class="wikitable" style="text-align:center"
{| class="wikitable" style="text-align:center"
  |+ Templates for 2008 Homology Modeling of E. coli DnaC (245 amino acids)
  |+ Templates for 2008 Homology Modeling of E. coli DnaC (245 amino acids)
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(a) Lengths not in parentheses are for crystallographic results, and are counts of amino acids with coordinates; they exclude disordered residues ("gaps" in the model). Lengths in parentheses are for the target sequence of DnaC, or sequences of the crystallized protein (from SEQRES in the PDB file).
(a) Lengths not in parentheses are for crystallographic results, and are counts of amino acids with coordinates; they exclude disordered residues ("gaps" in the model). Lengths in parentheses are for the target sequence of DnaC, or sequences of the crystallized protein (from SEQRES in the PDB file).


===Gaps in the Template Model===
The template was 2QGZ (<scene name='User:Eric_Martz/Sandbox_4/2qgz/3'>initial scene</scene>). The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are <scene name='User:Eric_Martz/Sandbox_4/2qgz/5'>three loops</scene> in this segment of the template that lack coordinates due to [[disorder]] in the crystal (marked with spacefilled alpha-carbon atoms).
The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). These gaps, which occur between the residues marked /\ below, were apparently ignored in making the model, which has a continuous main chain.
{{Clear}}
Below is the alignment produced by Swiss Model, used in making the 3D model. Vertical bars for identity were inserted by hand (I may have missed some).
Below is the alignment produced by Swiss Model, used in making the 3D model. Vertical bars for identity were inserted by hand (I may have missed some).
<pre>
<pre>
Line 171: Line 203:
       270      280      290      300         
       270      280      290      300         
</pre>
</pre>
==Confirmation of Homology Model By Related Structures==
When the [[PDB]] is searched with the DnaC sequence, the best match (December, 2008) is 23% sequence identity with 183 amino acids in the DnaC helicase loader of ''Aquifex aeolicus'', [[3ec2]] and [[3ecc]]. In order to find whether these structures have the same fold as the template ([[2qgz]] with 19% sequence identity to ''E. coli'' DnaC) used for the homology model, <font color="#3030ff">'''2qgz'''</font> <scene name='User:Eric_Martz/Sandbox_6/2qgz_3ec2_aligned_pdb/1'>was structurally aligned</scene> with <font color="#ff0000">'''3ec2'''</font><ref>The structural alignment of 2qgz with 3ec2 was performed with the ''Magic Fit'' function of DeepView version 3.6beta2. 2qgz 115-259 aligned with 3ec2 42-185 (3 gaps in 3ec2's alignment: 128-9, 134-5, 155-9). 135 alpha carbons were aligned with RMS 2.76 Å. The sequence identity between 2qgz and 3ec2 is 28% over the 185 amino acid length of the shorter, 3ec2. ''Magic Fit'' is a sequence-alignment-guided structural alignment (see [[Structural_alignment_tools#DeepView_.3D_Swiss-PDBViewer|Structural alignment tools]]).</ref>. The similarity of folds lends considerable confidence to the homology model of ''E. coli'' DnaC. This was further confirmed by the 2012 Swiss Model run, when 3ecc was selected as the best template (see discussion above).
The second best sequence-identity hit in the PDB is 39% identity with 54 amino acids (positions 9-63 of chain A) of replication factor C ([[2chg]]), which align with 72-124 of DnaC. When the above homology model of DnaC (made with template 2QGZ) is <scene name='User:Eric_Martz/Sandbox_4/2chg9-63_aligned_with_dnac_mod/1'>structurally aligned</scene> with residues 9-63 of 2CHG<ref>Structural alignment done with DeepView 3.6b3 using Magic Fit of carbon alphas.</ref>, 43 alpha carbons (out of 54) aligned with RMS deviation 2.3 &Aring;. <font color="#ff0000">'''Residues 21-63 of 2CHG'''</font> aligned with <font color="#3030ff">'''residues 80-124 of the DnaC homology model'''</font>. (Non-aligned portions are pastel.) This result adds firther confidence to this region of the homology model, since the structural alignment of 2CHG:A21-63 occurred in the same range as the sequence alignment (which was 72-124 in DnaC).
''Download'' the above structural alignments:
*[[:Image:2qgz_3ec2_aligned.pdb|2qgz_3ec2_aligned.pdb]]
*[[:Image:2chg9-63_aligned_with_dnac_model.pdb|2chg9-63_aligned_with_dnac_model.pdb]]
{{Clear}}
==Crystal Structure of DnaC Is "In The Pipeline"==
A sequence-based search at the international [http://targetdb.pdb.org/ Structural Genomics TargetDB] reveals that the closest completed structure is [[2qgz]], the one chosen by SwissModel as a template. ([[3ec2]] and [[3ecc]] were not determined by a structural genomics project.) A number of crystal and NMR structures have sequence identities up to 37% but over shorter stretches, and with higher E values.
Diffraction data have been obtained (but the solved structure not yet deposited) for a ''Listeria monocytogenes'' sequence of 307 residues, pI 5.2, with an E value of 1.6e-05, though only 21% sequence identity. Diffraction-quality crystals (but not yet diffraction data) have not been obtained for any sequence with such a low E value.
''E. coli'' DnaC (245 residues, pI 9.4) has been crystallized by RIKEN Structural Genomics Initiative (Japan), but the crystals may not be of diffraction quality. It has been cloned, expressed as a soluble protein, and purified (but not yet crystallized) by 3 Structural Genomics Groups (RIKEN Structural Genomics Initiative (Japan), Montreal-Kingston Bacterial Structural Genomics Initiative, Midwest Center for Structural Genomics), as have several proteins with >40% sequence identity.
Thus, there is reason for optimism that either a crystal structure, or a more suitable template for homology modeling, might be forthcoming.


==ConSurf Coloring Script==
==ConSurf Coloring Script==
Line 268: Line 280:
</pre>
</pre>


==3D structures of DnaC helicase loader==
[[DnaC helicase loader]]
==Additional Resources==
For additional information, see: [[DNA Replication, Repair, and Recombination]]
For additional information, see: [[Nucleic Acids]]
<br />
</StructureSection>
==Notes & References ==
==Notes & References ==
<references />
<references />

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, David Canner, Michal Harel, Alexander Berchansky, Joel L. Sussman
DOI: https://dx.doi.org/10.14576/333957.1802412 (?)
Citation: Martz E, Canner D, Harel M, Berchansky A, 2013, "Structure of E. coli DnaC helicase loader", Proteopedia, DOI: https://dx.doi.org/10.14576/333957.1802412
Retrieved from "https://proteopedia.openfox.io/w/Structure_of_E._coli_DnaC_helicase_loader"