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1s5j

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[[Image:1s5j.jpg|left|200px]]
 
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{{Structure
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==Insight in DNA Replication: The crystal structure of DNA Polymerase B1 from the archaeon Sulfolobus solfataricus==
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|PDB= 1s5j |SIZE=350|CAPTION= <scene name='initialview01'>1s5j</scene>, resolution 2.40&Aring;
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<StructureSection load='1s5j' size='340' side='right'caption='[[1s5j]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
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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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|ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]
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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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|GENE= DPO1, POLS, SSO0552 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])
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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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}}
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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/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=1s5j ConSurf].
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<div style="clear:both"></div>
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'''Insight in DNA Replication: The crystal structure of DNA Polymerase B1 from the archaeon Sulfolobus solfataricus'''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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==Overview==
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<references/>
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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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__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 [[Single protein]] 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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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:[http://www.ncbi.nlm.nih.gov/pubmed/15530364 15530364]
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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: Single protein]]
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[[Category: Rossi M]]
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[[Category: Sulfolobus solfataricus]]
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[[Category: Savino C]]
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[[Category: Federici, L.]]
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[[Category: Tsernoglou D]]
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[[Category: Johnson, K A.]]
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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: MG]]
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[[Category: SO4]]
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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 Thu Mar 20 14:00:46 2008''
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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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