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New page: '''Unreleased structure''' The entry 4ppx is ON HOLD Authors: Eckenroth, B.E., Doublie, S. Description: DNA Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position |
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The | ==DNA Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position== | ||
<StructureSection load='4ppx' size='340' side='right'caption='[[4ppx]], [[Resolution|resolution]] 2.08Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4ppx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PPX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PPX FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.08Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SDH:(5S)-7-AMINO-1-[2-DEOXY-5-O-(TRIHYDROXY-LAMBDA~5~-PHOSPHANYL)-BETA-D-ERYTHRO-PENTOFURANOSYL]-1,3,6,8-TETRAAZASPIRO[4.4]NON-7-ENE-2,4,9-TRIONE'>SDH</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ppx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ppx OCA], [https://pdbe.org/4ppx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ppx RCSB], [https://www.ebi.ac.uk/pdbsum/4ppx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ppx ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The first high-resolution crystal structure of spiroiminodihydantoin (dSp1) was obtained in the context of the DNA polymerase beta active site and reveals two areas of significance. First, the structure verifies the recently determined S configuration at the spirocyclic carbon. Second, the distortion of the DNA duplex is similar to that of the single-oxidation product 8-oxoguanine. For both oxidized lesions, adaptation of the syn conformation results in similar backbone distortions in the DNA duplex. The resulting conformation positions the dSp1 A-ring as the base-pairing face whereas the B-ring of dSp1 protrudes into the major groove. | |||
Crystal Structure of DNA Polymerase beta with DNA Containing the Base Lesion Spiroiminodihydantoin in a Templating Position.,Eckenroth BE, Fleming AM, Sweasy JB, Burrows CJ, Doublie S Biochemistry. 2014 Mar 26. PMID:24649945<ref>PMID:24649945</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4ppx" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: Doublie S]] | |||
[[Category: Eckenroth BE]] | |||
Latest revision as of 20:20, 20 September 2023
DNA Polymerase Beta E295K with Spiroiminodihydantoin in Templating PositionDNA Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position
Structural highlights
FunctionDPOLB_HUMAN Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.[1] [2] [3] [4] Publication Abstract from PubMedThe first high-resolution crystal structure of spiroiminodihydantoin (dSp1) was obtained in the context of the DNA polymerase beta active site and reveals two areas of significance. First, the structure verifies the recently determined S configuration at the spirocyclic carbon. Second, the distortion of the DNA duplex is similar to that of the single-oxidation product 8-oxoguanine. For both oxidized lesions, adaptation of the syn conformation results in similar backbone distortions in the DNA duplex. The resulting conformation positions the dSp1 A-ring as the base-pairing face whereas the B-ring of dSp1 protrudes into the major groove. Crystal Structure of DNA Polymerase beta with DNA Containing the Base Lesion Spiroiminodihydantoin in a Templating Position.,Eckenroth BE, Fleming AM, Sweasy JB, Burrows CJ, Doublie S Biochemistry. 2014 Mar 26. PMID:24649945[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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