3b39: Difference between revisions

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[[Image:3b39.jpg|left|200px]]
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{{STRUCTURE_3b39|  PDB=3b39  |  SCENE=  }}
'''Structure of the DnaG primase catalytic domain bound to ssDNA'''


==Structure of the DnaG primase catalytic domain bound to ssDNA==
<StructureSection load='3b39' size='340' side='right'caption='[[3b39]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3b39]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B39 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</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=3b39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b39 OCA], [https://pdbe.org/3b39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b39 RCSB], [https://www.ebi.ac.uk/pdbsum/3b39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b39 ProSAT]</span></td></tr>
</table>
== Function ==
[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 ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/3b39_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3b39 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Primases are essential RNA polymerases required for the initiation of DNA replication, lagging strand synthesis and replication restart. Many aspects of primase function remain unclear, including how the enzyme associates with a moving nucleic acid strand emanating from a helicase and orients primers for handoff to replisomal components. Using a new screening method to trap transient macromolecular interactions, we determined the structure of the Escherichia coli DnaG primase catalytic domain bound to single-stranded DNA. The structure reveals an unanticipated binding site that engages nucleic acid in two distinct configurations, indicating that it serves as a nonspecific capture and tracking locus for template DNA. Bioinformatic and biochemical analyses show that this evolutionarily constrained region enforces template polarity near the active site and is required for primase function. Together, our findings reverse previous proposals for primer-template orientation and reconcile disparate studies to re-evaluate replication fork organization.


==Overview==
Identification of a DNA primase template tracking site redefines the geometry of primer synthesis.,Corn JE, Pelton JG, Berger JM Nat Struct Mol Biol. 2008 Feb;15(2):163-9. Epub 2008 Jan 13. PMID:18193061<ref>PMID:18193061</ref>
Primases are essential RNA polymerases required for the initiation of DNA replication, lagging strand synthesis and replication restart. Many aspects of primase function remain unclear, including how the enzyme associates with a moving nucleic acid strand emanating from a helicase and orients primers for handoff to replisomal components. Using a new screening method to trap transient macromolecular interactions, we determined the structure of the Escherichia coli DnaG primase catalytic domain bound to single-stranded DNA. The structure reveals an unanticipated binding site that engages nucleic acid in two distinct configurations, indicating that it serves as a nonspecific capture and tracking locus for template DNA. Bioinformatic and biochemical analyses show that this evolutionarily constrained region enforces template polarity near the active site and is required for primase function. Together, our findings reverse previous proposals for primer-template orientation and reconcile disparate studies to re-evaluate replication fork organization.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
3B39 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B39 OCA].
</div>
<div class="pdbe-citations 3b39" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Identification of a DNA primase template tracking site redefines the geometry of primer synthesis., Corn JE, Pelton JG, Berger JM, Nat Struct Mol Biol. 2008 Feb;15(2):163-9. Epub 2008 Jan 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18193061 18193061]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
[[Category: Escherichia coli]]
== References ==
[[Category: Protein complex]]
<references/>
[[Category: Berger, J M.]]
__TOC__
[[Category: Corn, J E.]]
</StructureSection>
[[Category: Pelton, J G.]]
[[Category: Escherichia coli K-12]]
[[Category: Dna replication]]
[[Category: Large Structures]]
[[Category: Dna-directed rna polymerase]]
[[Category: Berger JM]]
[[Category: Metal-binding]]
[[Category: Corn JE]]
[[Category: Nucleotidyltransferase]]
[[Category: Pelton JG]]
[[Category: Primosome]]
[[Category: Protein-dna complex]]
[[Category: Toprim fold]]
[[Category: Transcription]]
[[Category: Transferase]]
[[Category: Transferase/dna complex]]
[[Category: Zinc]]
[[Category: Zinc-finger]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:21:16 2008''

Latest revision as of 15:01, 30 August 2023

Structure of the DnaG primase catalytic domain bound to ssDNAStructure of the DnaG primase catalytic domain bound to ssDNA

Structural highlights

3b39 is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.35Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Primases are essential RNA polymerases required for the initiation of DNA replication, lagging strand synthesis and replication restart. Many aspects of primase function remain unclear, including how the enzyme associates with a moving nucleic acid strand emanating from a helicase and orients primers for handoff to replisomal components. Using a new screening method to trap transient macromolecular interactions, we determined the structure of the Escherichia coli DnaG primase catalytic domain bound to single-stranded DNA. The structure reveals an unanticipated binding site that engages nucleic acid in two distinct configurations, indicating that it serves as a nonspecific capture and tracking locus for template DNA. Bioinformatic and biochemical analyses show that this evolutionarily constrained region enforces template polarity near the active site and is required for primase function. Together, our findings reverse previous proposals for primer-template orientation and reconcile disparate studies to re-evaluate replication fork organization.

Identification of a DNA primase template tracking site redefines the geometry of primer synthesis.,Corn JE, Pelton JG, Berger JM Nat Struct Mol Biol. 2008 Feb;15(2):163-9. Epub 2008 Jan 13. PMID:18193061[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ Corn JE, Pelton JG, Berger JM. Identification of a DNA primase template tracking site redefines the geometry of primer synthesis. Nat Struct Mol Biol. 2008 Feb;15(2):163-9. Epub 2008 Jan 13. PMID:18193061 doi:10.1038/nsmb.1373

3b39, resolution 2.35Å

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