4o9m

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==Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA==
==Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA==
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<StructureSection load='4o9m' size='340' side='right' caption='[[4o9m]], [[Resolution|resolution]] 2.29&Aring;' scene=''>
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<StructureSection load='4o9m' size='340' side='right'caption='[[4o9m]], [[Resolution|resolution]] 2.29&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4o9m]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O9M OCA]. <br>
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<table><tr><td colspan='2'>[[4o9m]] 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=4O9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O9M FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2RW:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3S)-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>2RW</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
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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]] 2.295&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></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=2RW:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3S)-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>2RW</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4o9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o9m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o9m RCSB], [http://www.ebi.ac.uk/pdbsum/4o9m PDBsum]</span></td></tr>
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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=4o9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o9m OCA], [https://pdbe.org/4o9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o9m RCSB], [https://www.ebi.ac.uk/pdbsum/4o9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o9m ProSAT]</span></td></tr>
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<table>
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</table>
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== Function ==
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA polymerase beta (pol beta) lyase removal of 5'-deoxyribose phosphate (5'-dRP) from base excision repair (BER) intermediates is critical in mammalian BER involving the abasic site. We found that pol beta also removes 5'-adenylated dRP from BER intermediates after abortive ligation. The crystal structure of a human pol beta-DNA complex showed the 5'-AMP-dRP group positioned in the lyase active site. Pol beta expression rescued methyl methanesulfonate sensitivity in aprataxin (hnt3)- and FEN1 (rad27)-deficient yeast.
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Role of polymerase beta in complementing aprataxin deficiency during abasic-site base excision repair.,Caglayan M, Batra VK, Sassa A, Prasad R, Wilson SH Nat Struct Mol Biol. 2014 May;21(5):497-9. doi: 10.1038/nsmb.2818. Epub 2014 Apr , 28. PMID:24777061<ref>PMID:24777061</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 4o9m" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Batra, V K.]]
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[[Category: Homo sapiens]]
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[[Category: Caglayan, M.]]
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[[Category: Large Structures]]
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[[Category: Prasad, R.]]
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[[Category: Batra VK]]
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[[Category: Sassa, A.]]
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[[Category: Caglayan M]]
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[[Category: Wilson, S H.]]
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[[Category: Prasad R]]
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[[Category: Adenylated tetrahydrofuran]]
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[[Category: Sassa A]]
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[[Category: Aprataxin]]
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[[Category: Wilson SH]]
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[[Category: Lyase]]
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[[Category: Transferase-dna complex]]
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Current revision

Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA

PDB ID 4o9m

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