3b39

From Proteopedia

(Difference between revisions)

Current revision

Structure 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.

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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3b39"

Categories: Escherichia coli K-12 | Large Structures | Berger JM | Corn JE | Pelton JG

@@ Line 1: / Line 1: @@
 ==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=''>
+<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 [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B39 FirstGlance]. <br>
+<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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dde|1dde]], [[1dd9|1dd9]], [[1eqn|1eqn]]</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]] 2.35&#8491;</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=83333 Escherichia coli K-12])</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>
-<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=3b39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b39 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b39 RCSB], [http://www.ebi.ac.uk/pdbsum/3b39 PDBsum]</span></td></tr>
 </table>
 == 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 ==
 [[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>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3b39" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli k-12]]
+[[Category: Escherichia coli K-12]]
-[[Category: Berger, J M]]
+[[Category: Large Structures]]
-[[Category: Corn, J E]]
+[[Category: Berger JM]]
-[[Category: Pelton, J G]]
+[[Category: Corn JE]]
-[[Category: Dna replication]]
+[[Category: Pelton JG]]
-[[Category: Dna-directed rna polymerase]]
-[[Category: Metal-binding]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Primosome]]
-[[Category: Protein-dna complex]]
-[[Category: Toprim fold]]
-[[Category: Transcription]]
-[[Category: Transferase]]
-[[Category: Transferase-dna complex]]
-[[Category: Zinc-finger]]

3b39

From Proteopedia

Current revision

Structure of the DnaG primase catalytic domain bound to ssDNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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