1s5j

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{{Seed}}
 
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[[Image:1s5j.png|left|200px]]
 
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==Insight in DNA Replication: The crystal structure of DNA Polymerase B1 from the archaeon Sulfolobus solfataricus==
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The line below this paragraph, containing "STRUCTURE_1s5j", creates the "Structure Box" on the page.
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<StructureSection load='1s5j' size='340' side='right'caption='[[1s5j]], [[Resolution|resolution]] 2.40&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'>[[1s5j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S5J 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]] 2.4&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_1s5j| PDB=1s5j | 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=1s5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s5j OCA], [https://pdbe.org/1s5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s5j RCSB], [https://www.ebi.ac.uk/pdbsum/1s5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s5j ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOL1_SACS2 DPOL1_SACS2] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. DNA polymerase I, DNA ligase and the flap endonuclease may be constitutively associated with the PCNA heterotrimer forming a scanning complex able to couple DNA synthesis and Okazaki fragment maturation.<ref>PMID:12535540</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/s5/1s5j_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1s5j 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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To minimize the large number of mispairs during genome duplication owing to the large amount of DNA to be synthesized, many replicative polymerases have accessory domains with complementary functions. We describe the crystal structure of replicative DNA polymerase B1 from the archaeon Sulfolobus solfataricus. Comparison between other known structures indicates that although the protein is folded into the typical N-terminal, editing 3'-5'exonuclease, and C-terminal right-handed polymerase domains, it is characterized by the unusual presence of two extra alpha helices in the N-terminal domain interacting with the fingers helices to form an extended fingers subdomain, a structural feature that can account for some functional features of the protein. We explore the structural basis of specific lesion recognition, the initial step in DNA repair, describing how the N-terminal subdomain pocket of archaeal DNA polymerases could allow specific recognition of deaminated bases such as uracil and hypoxanthine in addition to the typical DNA bases.
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===Insight in DNA Replication: The crystal structure of DNA Polymerase B1 from the archaeon Sulfolobus solfataricus===
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Insights into DNA replication: the crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricus.,Savino C, Federici L, Johnson KA, Vallone B, Nastopoulos V, Rossi M, Pisani FM, Tsernoglou D Structure. 2004 Nov;12(11):2001-8. PMID:15530364<ref>PMID:15530364</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 1s5j" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15530364}}, adds the Publication Abstract to the page
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15530364 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15530364}}
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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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1S5J is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S5J OCA].
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[[Category: Saccharolobus solfataricus]]
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[[Category: Federici L]]
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==Reference==
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[[Category: Johnson KA]]
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<ref group="xtra">PMID:15530364</ref><references group="xtra"/>
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[[Category: Nastopoulos V]]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Pisani FM]]
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[[Category: Sulfolobus solfataricus]]
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[[Category: Rossi M]]
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[[Category: Federici, L.]]
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[[Category: Savino C]]
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[[Category: Johnson, K A.]]
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[[Category: Tsernoglou D]]
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[[Category: Nastopoulos, V.]]
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[[Category: Pisani, F M.]]
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[[Category: Rossi, M.]]
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[[Category: Savino, C.]]
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[[Category: Tsernoglou, D.]]
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[[Category: Disulfide bond]]
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[[Category: Dna polymerase]]
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[[Category: Replication]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:47:47 2009''
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Current revision

Insight in DNA Replication: The crystal structure of DNA Polymerase B1 from the archaeon Sulfolobus solfataricus

PDB ID 1s5j

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