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| | ==Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex== | | ==Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex== |
| - | <StructureSection load='1v34' size='340' side='right' caption='[[1v34]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='1v34' size='340' side='right'caption='[[1v34]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1v34]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V34 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V34 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1v34]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V34 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1v33|1v33]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1v34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v34 OCA], [http://pdbe.org/1v34 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v34 RCSB], [http://www.ebi.ac.uk/pdbsum/1v34 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v34 ProSAT], [http://www.topsan.org/Proteins/RSGI/1v34 TOPSAN]</span></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=1v34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v34 OCA], [https://pdbe.org/1v34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v34 RCSB], [https://www.ebi.ac.uk/pdbsum/1v34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v34 ProSAT], [https://www.topsan.org/Proteins/RSGI/1v34 TOPSAN]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PRIS_PYRHO PRIS_PYRHO]] Catalytic subunit of DNA primase, an RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. The small subunit contains the primase catalytic core and has DNA synthesis activity on its own. Binding to the large subunit stabilizes and modulates the activity, increasing the rate of DNA synthesis while decreasing the length of the DNA fragments, and conferring RNA synthesis capability. The DNA polymerase activity may enable DNA primase to also catalyze primer extension after primer synthesis. May also play a role in DNA repair.<ref>PMID:14750947</ref> | + | [https://www.uniprot.org/uniprot/PRIS_PYRHO PRIS_PYRHO] Catalytic subunit of DNA primase, an RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. The small subunit contains the primase catalytic core and has DNA synthesis activity on its own. Binding to the large subunit stabilizes and modulates the activity, increasing the rate of DNA synthesis while decreasing the length of the DNA fragments, and conferring RNA synthesis capability. The DNA polymerase activity may enable DNA primase to also catalyze primer extension after primer synthesis. May also play a role in DNA repair.<ref>PMID:14750947</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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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: Pyrococcus shinkaii]] | + | [[Category: Large Structures]] |
| - | [[Category: Hanaoka, F]] | + | [[Category: Pyrococcus horikoshii]] |
| - | [[Category: Ito, N]] | + | [[Category: Hanaoka F]] |
| - | [[Category: Nureki, O]] | + | [[Category: Ito N]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Nureki O]] |
| - | [[Category: Shirouzu, M]] | + | [[Category: Shirouzu M]] |
| - | [[Category: Yokoyama, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Nucleotidyl transferase]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PRIS_PYRHO Catalytic subunit of DNA primase, an RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. The small subunit contains the primase catalytic core and has DNA synthesis activity on its own. Binding to the large subunit stabilizes and modulates the activity, increasing the rate of DNA synthesis while decreasing the length of the DNA fragments, and conferring RNA synthesis capability. The DNA polymerase activity may enable DNA primase to also catalyze primer extension after primer synthesis. May also play a role in DNA repair.[1]
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
BACKGROUND: In chromosomal DNA replication, DNA primase initiates the synthesis of a dinucleotide on a single-stranded template DNA, and elongates it to form a primer RNA for the replicative DNA polymerase. Although the apo-structure of an archaeal primase has been reported, the mechanism of primer synthesis by the eukaryotic-type primase still remains to be elucidated. RESULTS: In this study, we present the crystal structure of the eukaryotic-type DNA primase from the hyperthermophilic archaeon (Pyrococcus horikoshii) with the uridine 5'-triphosphate (UTP). In the present primase-UTP complex, the primase binds the triphosphate moiety of the UTP at the active site, which includes Asp95, Asp97, and Asp280, the essential residues for the nucleotidyl transfer reaction. CONCLUSION: The nucleotide binding geometry in this complex explains the previous biochemical analyses of the eukaryotic primase. Based on the complex structure, we constructed a model between the DNA primase and a primer/template DNA for the primer synthesis. This model facilitates the comprehension of the reported features of DNA primase.
Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.,Ito N, Nureki O, Shirouzu M, Yokoyama S, Hanaoka F Genes Cells. 2003 Dec;8(12):913-23. PMID:14750947[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ito N, Nureki O, Shirouzu M, Yokoyama S, Hanaoka F. Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes Cells. 2003 Dec;8(12):913-23. PMID:14750947
- ↑ Ito N, Nureki O, Shirouzu M, Yokoyama S, Hanaoka F. Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes Cells. 2003 Dec;8(12):913-23. PMID:14750947
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