1v33

From Proteopedia

(Difference between revisions)

Revision as of 13:52, 11 September 2015

Crystal structure of DNA primase from Pyrococcus horikoshii

Structural highlights

1v33 is a 1 chain structure with sequence from 'pyrococcus shinkaii'. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1v34
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, TOPSAN

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.

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

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/1v33"

@@ Line 2: / Line 2: @@
 <StructureSection load='1v33' size='340' side='right' caption='[[1v33]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1v33]] is a 1 chain structure with 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=1V33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V33 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1v33]] 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=1V33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V33 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1v34|1v34]]</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=1v33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v33 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v33 RCSB], [http://www.ebi.ac.uk/pdbsum/1v33 PDBsum], [http://www.topsan.org/Proteins/RSGI/1v33 TOPSAN]</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=1v33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v33 OCA], [http://pdbe.org/1v33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v33 RCSB], [http://www.ebi.ac.uk/pdbsum/1v33 PDBsum], [http://www.topsan.org/Proteins/RSGI/1v33 TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ 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 1v33" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus horikoshii]]
+[[Category: Pyrococcus shinkaii]]
 [[Category: Hanaoka, F]]
 [[Category: Ito, N]]

1v33

From Proteopedia

Revision as of 13:52, 11 September 2015

Crystal structure of DNA primase from Pyrococcus horikoshii

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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