1jxl

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[[Image:1jxl.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide==
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|PDB= 1jxl |SIZE=350|CAPTION= <scene name='initialview01'>1jxl</scene>, resolution 2.10&Aring;
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<StructureSection load='1jxl' size='340' side='right'caption='[[1jxl]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> and <scene name='pdbligand=DG3:2&#39;-3&#39;-DIDEOXYGUANOSINE-5&#39;-TRIPHOSPHATE'>DG3</scene>
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<table><tr><td colspan='2'>[[1jxl]] is a 3 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=1JXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JXL 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]] 2.1&#8491;</td></tr>
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|GENE= dpo4 ([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=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1jxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxl OCA], [https://pdbe.org/1jxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jxl RCSB], [https://www.ebi.ac.uk/pdbsum/1jxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jxl ProSAT]</span></td></tr>
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</table>
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'''Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide'''
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== Function ==
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[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
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== Evolutionary Conservation ==
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==Overview==
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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/jx/1jxl_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=1jxl 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 ==
Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) is a DinB homolog that belongs to the recently described Y-family of DNA polymerases, which are best characterized by their low-fidelity synthesis on undamaged DNA templates and propensity to traverse normally replication-blocking lesions. Crystal structures of Dpo4 in ternary complexes with DNA and an incoming nucleotide, either correct or incorrect, have been solved at 1.7 A and 2.1 A resolution, respectively. Despite a conserved active site and a hand-like configuration similar to all known polymerases, Dpo4 makes limited and nonspecific contacts with the replicating base pair, thus relaxing base selection. Dpo4 is also captured in the crystal translocating two template bases to the active site at once, suggesting a possible mechanism for bypassing thymine dimers.
Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) is a DinB homolog that belongs to the recently described Y-family of DNA polymerases, which are best characterized by their low-fidelity synthesis on undamaged DNA templates and propensity to traverse normally replication-blocking lesions. Crystal structures of Dpo4 in ternary complexes with DNA and an incoming nucleotide, either correct or incorrect, have been solved at 1.7 A and 2.1 A resolution, respectively. Despite a conserved active site and a hand-like configuration similar to all known polymerases, Dpo4 makes limited and nonspecific contacts with the replicating base pair, thus relaxing base selection. Dpo4 is also captured in the crystal translocating two template bases to the active site at once, suggesting a possible mechanism for bypassing thymine dimers.
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==About this Structure==
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Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.,Ling H, Boudsocq F, Woodgate R, Yang W Cell. 2001 Oct 5;107(1):91-102. PMID:11595188<ref>PMID:11595188</ref>
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1JXL 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=1JXL OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication., Ling H, Boudsocq F, Woodgate R, Yang W, Cell. 2001 Oct 5;107(1):91-102. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11595188 11595188]
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</div>
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[[Category: DNA-directed DNA polymerase]]
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<div class="pdbe-citations 1jxl" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Sulfolobus solfataricus]]
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[[Category: Boudsocq, F.]]
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[[Category: Ling, H.]]
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[[Category: Woodgate, R.]]
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[[Category: Yang, W.]]
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[[Category: CA]]
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[[Category: DG3]]
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[[Category: EDO]]
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[[Category: MG]]
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[[Category: dna polymerase]]
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[[Category: protein-dna complex]]
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[[Category: y-family]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 12:24:41 2008''
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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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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Saccharolobus solfataricus]]
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[[Category: Boudsocq F]]
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[[Category: Ling H]]
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[[Category: Woodgate R]]
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[[Category: Yang W]]

Current revision

Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

PDB ID 1jxl

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