4nln: Difference between revisions

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 ==Structure of human DNA polymerase beta complexed with nicked DNA containing a template 8BrG and incoming CTP==
-<StructureSection load='4nln' size='340' side='right' caption='[[4nln]], [[Resolution|resolution]] 2.26&Aring;' scene=''>
+<StructureSection load='4nln' size='340' side='right'caption='[[4nln]], [[Resolution|resolution]] 2.26&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nln]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NLN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nln]] 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=4NLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NLN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.261&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1bpx|1bpx]], [[3isb|3isb]], [[4nlk|4nlk]], [[4nlz|4nlz]], [[4nm1|4nm1]], [[4nm2|4nm2]]</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=4nln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nln OCA], [https://pdbe.org/4nln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nln RCSB], [https://www.ebi.ac.uk/pdbsum/4nln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nln ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4nln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nln OCA], [http://pdbe.org/4nln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nln RCSB], [http://www.ebi.ac.uk/pdbsum/4nln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nln ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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 ==
--Halogenated guanine (haloG), a major DNA adduct formed by reactive halogen species during inflammation, is a promutagenic lesion that promotes misincorporation of G opposite the lesion by various DNA polymerases. Currently, the structural basis for such misincorporation is unknown. To gain insights into the mechanism of misincorporation across haloG by polymerase, we determined seven X-ray structures of human DNA polymerase beta (polbeta) bound to DNA bearing 8-bromoguanine (BrG). We determined two pre-catalytic ternary-complex structures of polbeta with an incoming nonhydrolyzable dGTP or dCTP analog paired with templating BrG. We also determined five binary-complex structures of polbeta in complex with DNA containing BrG:C/T at post-insertion and post-extension sites. In the BrG:dGTP ternary structure, BrG adopts syn conformation and forms Hoogsteen base pairing with the incoming dGTP analog. In the BrG:dCTP ternary structure, BrG adopts anti conformation and forms Watson-Crick base pairing with the incoming dCTP analog. In addition, our polbeta binary post-extension structures show Hoogsteen BrG:G base pair and Watson-Crick BrG:C base pair. Taken together, the first structures of haloG-containing DNA bound to a protein indicate that both BrG:G and BrG:C base pairs are accommodated in the active site of polbeta. Our structures suggest that Hoogsteen-type base pairing between G and C8-modified G could be accommodated in the active site of a DNA polymerase, promoting G to C mutation.
-Structural basis for promutagenicity of 8-halogenated guanine.,Koag MC, Min K, Lee S J Biol Chem. 2014 Jan 14. PMID:24425881<ref>PMID:24425881</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4nln" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Koag, M C]]
+[[Category: Large Structures]]
-[[Category: Lee, S]]
+[[Category: Koag M-C]]
-[[Category: Min, K]]
+[[Category: Lee S]]
-[[Category: Monzingo, A F]]
+[[Category: Min K]]
-[[Category: Dna binding]]
+[[Category: Monzingo AF]]
-[[Category: Helix-turn-helix motif]]
-[[Category: Lyase-dna complex]]
-[[Category: Nucleotidyl transferase]]
-[[Category: Nucleus]]
-[[Category: Polymerase fold]]
-[[Category: Transferase]]