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| | ==Crystal structure of Helicobacter pylori DnaG Primase C terminal domain== | | ==Crystal structure of Helicobacter pylori DnaG Primase C terminal domain== |
| - | <StructureSection load='4ehs' size='340' side='right' caption='[[4ehs]], [[Resolution|resolution]] 1.78Å' scene=''> | + | <StructureSection load='4ehs' size='340' side='right'caption='[[4ehs]], [[Resolution|resolution]] 1.78Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ehs]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EHS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EHS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ehs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EHS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EHS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaG, DnaG Primase, HP_0012 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ehs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ehs OCA], [https://pdbe.org/4ehs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ehs RCSB], [https://www.ebi.ac.uk/pdbsum/4ehs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ehs ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ehs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ehs OCA], [http://pdbe.org/4ehs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ehs RCSB], [http://www.ebi.ac.uk/pdbsum/4ehs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ehs ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DNAG_HELPY DNAG_HELPY] RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. Stimulates the 5'-3' DNA helicase activity of DnaB (PubMed:23585534, PubMed:26264665).[HAMAP-Rule:MF_00974]<ref>PMID:23585534</ref> <ref>PMID:26264665</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4ehs" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4ehs" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Campylobacter pylori]] | + | [[Category: Helicobacter pylori 26695]] |
| - | [[Category: Gourinath, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Rehman, S A.Abdul]] | + | [[Category: Abdul Rehman SA]] |
| - | [[Category: Helicase binding domain]] | + | [[Category: Gourinath S]] |
| - | [[Category: Primase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
DNAG_HELPY RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. Stimulates the 5'-3' DNA helicase activity of DnaB (PubMed:23585534, PubMed:26264665).[HAMAP-Rule:MF_00974][1] [2]
Publication Abstract from PubMed
To better understand the poor conservation of helicase binding domain of primases/DnaG's among the eubacteria, we have determined the crystal structure of the Helicobacter pylori DnaG-CTD at 1.78 A. The structure has a globular subdomain connected to a helical hairpin. Structural comparison has revealed that globular subdomains despite the variation in number of helices have broadly similar arrangements across the species, whereas helical hairpins show different orientations. Further, to study the helicase-primase interaction in H. pylori (Hp), a complex was modeled using the HpDnaG-CTD and HpDnaB-NTD (helicase) crystal structures with the Bacillus stearothermophilus BstDnaB-BstDnaG-CTD (helicase-primase) complex structure as a template. Through the model a non-conserved critical residue Phe534 on helicase binding interface of DnaG-CTD was identified. Mutation guided by molecular dynamics, biophysical and biochemical studies validated our model. We have further concluded that species specific helicase-primase interactions are influenced by electrostatic surface potentials apart from the critical hydrophobic surface residues.
Crystal structure and mode of helicase binding of the C-terminal domain of primase from Helicobacter pylori.,Abdul Rehman SA, Verma V, Mazumder M, Dhar SK, Gourinath S J Bacteriol. 2013 Apr 12. PMID:23585534[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Abdul Rehman SA, Verma V, Mazumder M, Dhar SK, Gourinath S. Crystal structure and mode of helicase binding of the C-terminal domain of primase from Helicobacter pylori. J Bacteriol. 2013 Apr 12. PMID:23585534 doi:10.1128/JB.00091-13
- ↑ Bazin A, Cherrier MV, Gutsche I, Timmins J, Terradot L. Structure and primase-mediated activation of a bacterial dodecameric replicative helicase. Nucleic Acids Res. 2015 Sep 30;43(17):8564-76. doi: 10.1093/nar/gkv792. Epub 2015, Aug 11. PMID:26264665 doi:http://dx.doi.org/10.1093/nar/gkv792
- ↑ Abdul Rehman SA, Verma V, Mazumder M, Dhar SK, Gourinath S. Crystal structure and mode of helicase binding of the C-terminal domain of primase from Helicobacter pylori. J Bacteriol. 2013 Apr 12. PMID:23585534 doi:10.1128/JB.00091-13
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