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==The structure of the S. aureus DnaG RNA Polymerase Domain bound to GTP and Manganese==
==The structure of the S. aureus DnaG RNA Polymerase Domain bound to GTP and Manganese==
<StructureSection load='4edk' size='340' side='right' caption='[[4edk]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='4edk' size='340' side='right'caption='[[4edk]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4edk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EDK FirstGlance]. <br>
<table><tr><td colspan='2'>[[4edk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EDK FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4e2k|4e2k]], [[4ee1|4ee1]], [[4edg|4edg]], [[4edr|4edr]], [[4edt|4edt]], [[4edv|4edv]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</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=4edk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4edk OCA], [https://pdbe.org/4edk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4edk RCSB], [https://www.ebi.ac.uk/pdbsum/4edk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4edk 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=4edk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4edk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4edk RCSB], [http://www.ebi.ac.uk/pdbsum/4edk PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/PRIM_STAAU PRIM_STAAU]] 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_STAAU DNAG_STAAU] RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication.[HAMAP-Rule:MF_00974]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Primases are DNA-dependent RNA polymerases found in all cellular organisms. In bacteria, primer synthesis is carried out by DnaG, an essential enzyme that serves as a key component of DNA replication initiation, progression, and restart. How DnaG associates with nucleotide substrates and how certain naturally prevalent nucleotide analogs impair DnaG function are unknown. We have examined one of the earliest stages in primer synthesis and its control by solving crystal structures of the S. aureus DnaG catalytic core bound to metal ion cofactors and either individual nucleoside triphosphates or the nucleotidyl alarmones, pppGpp and ppGpp. These structures, together with both biochemical analyses and comparative studies of enzymes that use the same catalytic fold as DnaG, pinpoint the predominant nucleotide-binding site of DnaG and explain how the induction of the stringent response in bacteria interferes with primer synthesis.
 
Binding Mechanism of MetalNTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases.,Rymer RU, Solorio FA, Tehranchi AK, Chu C, Corn JE, Keck JL, Wang JD, Berger JM Structure. 2012 Jul 10. PMID:22795082<ref>PMID:22795082</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[RNA polymerase|RNA polymerase]]
*[[Nerve growth factor|Nerve growth factor]]
== References ==
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
[[Category: Berger, J M]]
[[Category: Berger JM]]
[[Category: Chu, C]]
[[Category: Chu C]]
[[Category: Corn, J E]]
[[Category: Corn JE]]
[[Category: Rymer, R U]]
[[Category: Rymer RU]]
[[Category: Solorio, F A]]
[[Category: Solorio FA]]
[[Category: Wang, J D]]
[[Category: Wang JD]]
[[Category: Catalytic domain]]
[[Category: Nucleoside polyphosphate]]
[[Category: Nucleoside triphosphate]]
[[Category: Protein-ligand complex]]
[[Category: Transferase]]

Latest revision as of 14:03, 1 March 2024

The structure of the S. aureus DnaG RNA Polymerase Domain bound to GTP and ManganeseThe structure of the S. aureus DnaG RNA Polymerase Domain bound to GTP and Manganese

Structural highlights

4edk is a 1 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DNAG_STAAU RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication.[HAMAP-Rule:MF_00974]

See Also

4edk, resolution 2.00Å

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