1v34

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{{Seed}}
 
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[[Image:1v34.png|left|200px]]
 
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==Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex==
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The line below this paragraph, containing "STRUCTURE_1v34", creates the "Structure Box" on the page.
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<StructureSection load='1v34' size='340' side='right'caption='[[1v34]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
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<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>
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{{STRUCTURE_1v34| PDB=1v34 | SCENE= }}
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v3/1v34_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1v34 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex===
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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<ref>PMID:14750947</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1v34" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_14750947}}, adds the Publication Abstract to the page
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 14750947 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_14750947}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1V34 is a [[Single protein]] structure of sequence from [http://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].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/14750947 14750947]
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[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
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[[Category: Single protein]]
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[[Category: Hanaoka F]]
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[[Category: Hanaoka, F.]]
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[[Category: Ito N]]
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[[Category: Ito, N.]]
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[[Category: Nureki O]]
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[[Category: Nureki, O.]]
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[[Category: Shirouzu M]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Yokoyama S]]
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[[Category: Shirouzu, M.]]
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[[Category: Yokoyama, S.]]
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[[Category: Nucleotidyl transferase]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 15:26:30 2008''
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Current revision

Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex

PDB ID 1v34

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