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| | ==Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)== | | ==Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581)== |
| - | <StructureSection load='1t3w' size='340' side='right' caption='[[1t3w]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='1t3w' size='340' side='right'caption='[[1t3w]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T3W FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1t3w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T3W FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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]] 2.8Å</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=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dd9|1dd9]]</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [https://pdbe.org/1t3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [https://www.ebi.ac.uk/pdbsum/1t3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3w ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaG, dnaP, parB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1t3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t3w OCA], [http://pdbe.org/1t3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t3w RCSB], [http://www.ebi.ac.uk/pdbsum/1t3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t3w ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PRIM_ECOLI PRIM_ECOLI]] DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments on both template strands at replication forks during chromosomal DNA synthesis. | + | [https://www.uniprot.org/uniprot/DNAG_ECOLI DNAG_ECOLI] RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication.[HAMAP-Rule:MF_00974]<ref>PMID:1511009</ref> <ref>PMID:340457</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t3/1t3w_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t3/1t3w_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | ==See Also== | | ==See Also== |
| - | *[[RNA polymerase|RNA polymerase]] | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Dixon, N E]] | + | [[Category: Large Structures]] |
| - | [[Category: Liepinsh, E]] | + | [[Category: Dixon NE]] |
| - | [[Category: Loscha, K V]] | + | [[Category: Liepinsh E]] |
| - | [[Category: Oakley, A J]] | + | [[Category: Loscha KV]] |
| - | [[Category: Otting, G]] | + | [[Category: Oakley AJ]] |
| - | [[Category: Schaeffer, P M]] | + | [[Category: Otting G]] |
| - | [[Category: Wilce, M C.J]] | + | [[Category: Schaeffer PM]] |
| - | [[Category: Dna replication]]
| + | [[Category: Wilce MCJ]] |
| - | [[Category: Dna-directed rna polymerase]]
| + | |
| - | [[Category: Dnag]]
| + | |
| - | [[Category: E. coli]]
| + | |
| - | [[Category: Replication]]
| + | |
| Structural highlights
Function
DNAG_ECOLI RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication.[HAMAP-Rule:MF_00974][1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
During bacterial DNA replication, the DnaG primase interacts with the hexameric DnaB helicase to synthesize RNA primers for extension by DNA polymerase. In Escherichia coli, this occurs by transient interaction of primase with the helicase. Here we demonstrate directly by surface plasmon resonance that the C-terminal domain of primase is responsible for interaction with DnaB6. Determination of the 2.8-angstroms crystal structure of the C-terminal domain of primase revealed an asymmetric dimer. The monomers have an N-terminal helix bundle similar to the N-terminal domain of DnaB, followed by a long helix that connects to a C-terminal helix hairpin. The connecting helix is interrupted differently in the two monomers. Solution studies using NMR showed that an equilibrium exists between a monomeric species with an intact, extended but naked, connecting helix and a dimer in which this helix is interrupted in the same way as in one of the crystal conformers. The other conformer is not significantly populated in solution, and its presence in the crystal is due largely to crystal packing forces. It is proposed that the connecting helix contributes necessary structural flexibility in the primase-helicase complex at replication forks.
Crystal and solution structures of the helicase-binding domain of Escherichia coli primase.,Oakley AJ, Loscha KV, Schaeffer PM, Liepinsh E, Pintacuda G, Wilce MC, Otting G, Dixon NE J Biol Chem. 2005 Mar 25;280(12):11495-504. Epub 2005 Jan 12. PMID:15649896[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Stamford NP, Lilley PE, Dixon NE. Enriched sources of Escherichia coli replication proteins. The dnaG primase is a zinc metalloprotein. Biochim Biophys Acta. 1992 Aug 17;1132(1):17-25. PMID:1511009
- ↑ Rowen L, Kornberg A. Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains. J Biol Chem. 1978 Feb 10;253(3):758-64. PMID:340457
- ↑ Oakley AJ, Loscha KV, Schaeffer PM, Liepinsh E, Pintacuda G, Wilce MC, Otting G, Dixon NE. Crystal and solution structures of the helicase-binding domain of Escherichia coli primase. J Biol Chem. 2005 Mar 25;280(12):11495-504. Epub 2005 Jan 12. PMID:15649896 doi:10.1074/jbc.M412645200
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