View source for 5kfr


==Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 20 mM Mn2+ for 600s==
<StructureSection load='5kfr' size='340' side='right' caption='[[5kfr]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5kfr]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KFR FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=STP:2-DEOXYADENOSINE+5-O-(1-THIOTRIPHOSPHATE)'>STP</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kfa|5kfa]], [[5kfb|5kfb]], [[5kfc|5kfc]], [[5kg0|5kg0]], [[5kg1|5kg1]], [[5kg2|5kg2]], [[5kg3|5kg3]], [[5kg4|5kg4]], [[5kg5|5kg5]], [[5kg6|5kg6]], [[5kg7|5kg7]], [[5kfd|5kfd]], [[5kfe|5kfe]], [[5kfs|5kfs]], [[5kft|5kft]], [[5kfu|5kfu]], [[5kfv|5kfv]], [[5kfw|5kfw]], [[5kfx|5kfx]], [[5kfg|5kfg]], [[5kfy|5kfy]], [[5kfz|5kfz]], [[5kfh|5kfh]], [[5kfk|5kfk]], [[5kfl|5kfl]], [[5kfi|5kfi]], [[5kfj|5kfj]], [[5kfm|5kfm]], [[5kfn|5kfn]], [[5kfo|5kfo]], [[5kfp|5kfp]], [[5kfq|5kfq]], [[5kff|5kff]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=5kfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kfr OCA], [http://pdbe.org/5kfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kfr RCSB], [http://www.ebi.ac.uk/pdbsum/5kfr PDBsum]</span></td></tr>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] Defects in POLH are the cause of xeroderma pigmentosum variant type (XPV) [MIM:[http://omim.org/entry/278750 278750]]; also designated as XP-V. Xeroderma pigmentosum (XP) is an autosomal recessive disease due to deficient nucleotide excision repair. It is characterized by hypersensitivity of the skin to sunlight, followed by high incidence of skin cancer and frequent neurologic abnormalities. XPV shows normal nucleotide excision repair, but an exaggerated delay in recovery of replicative DNA synthesis. Most XPV patients do not develop clinical symptoms and skin neoplasias until a later age. Clinical manifestations are limited to photo-induced deterioration of the skin and eyes.<ref>PMID:10385124</ref> <ref>PMID:10398605</ref> <ref>PMID:11032022</ref> <ref>PMID:11121129</ref> <ref>PMID:11773631</ref>  
== Function ==
[[http://www.uniprot.org/uniprot/POLH_HUMAN POLH_HUMAN]] DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Plays an important role in the repair of UV-induced pyrimidine dimers. Depending on the context, it inserts the correct base, but causes frequent base transitions and transversions. May play a role in hypermutation at immunoglobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity. Targets POLI to replication foci.<ref>PMID:10385124</ref> <ref>PMID:11743006</ref> <ref>PMID:11376341</ref> <ref>PMID:14630940</ref> <ref>PMID:14734526</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
It is generally assumed that an enzyme-substrate (ES) complex contains all components necessary for catalysis and that conversion to products occurs by rearrangement of atoms, protons, and electrons. However, we find that DNA synthesis does not occur in a fully assembled DNA polymerase-DNA-deoxynucleoside triphosphate complex with two canonical metal ions bound. Using time-resolved x-ray crystallography, we show that the phosphoryltransfer reaction takes place only after the ES complex captures a third divalent cation that is not coordinated by the enzyme. Binding of the third cation is incompatible with the basal ES complex and requires thermal activation of the ES for entry. It is likely that the third cation provides the ultimate boost over the energy barrier to catalysis of DNA synthesis.

Capture of a third Mg(2)(+) is essential for catalyzing DNA synthesis.,Gao Y, Yang W Science. 2016 Jun 10;352(6291):1334-7. doi: 10.1126/science.aad9633. PMID:27284197<ref>PMID:27284197</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5kfr" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Gao, Y]]
[[Category: Yang, W]]
[[Category: Dna polymerase]]
[[Category: In crystallo reaction]]
[[Category: Metal ion dependent catalysis]]
[[Category: Replication]]
[[Category: Transferase-dna complex]]