5db8

From Proteopedia

(Difference between revisions)

Revision as of 14:06, 16 November 2017

Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dA

Structural highlights

5db8 is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	5db6, 5db7, 5db9, 5dba, 5dbb, 5dbc
Gene:	POLB (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

N7-Alkyl-2'-deoxyguanosines are major adducts in DNA that are generated by various alkylating mutagens and drugs. However, the effect of the N7 alkylation on the hydrogen-bonding patterns of the guanine remains poorly understood. We prepared N7-methyl-2'-deoxyguanosine (N7mdG)-containing DNA using a transition-state destabilization strategy, developed a novel polbeta-host-guest complex system, and determined eight crystal structures of N7mdG or dG paired with dC, dT, dG, and dA. The structures of N7mdG:dC and N7mdG:dG are very similar to those of dG:dC and dG:dG, respectively, indicating the involvement of the keto tautomeric form of N7mdG in the base pairings with dC and dG. On the other hand, the structure of N7mdG:dT shows that the mispair forms three hydrogen bonds and adopts a Watson-Crick-like geometry rather than a wobble geometry, suggesting that the enol tautomeric form of N7mdG involves in its base pairing with dT. In addition, N7mdG:dA adopts a novel shifted anti:syn base pair presumably via the enol tautomeric form of N7mdG. The polbeta-host-guest complex structures reveal that guanine-N7 methylation changes the hydrogen-bonding patterns of the guanine when paired with dT or dA and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the formation of the rare enol tautomeric form of guanine.

N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA.,Kou Y, Koag MC, Lee S J Am Chem Soc. 2015 Nov 11;137(44):14067-70. doi: 10.1021/jacs.5b10172. Epub 2015, Nov 2. PMID:26517568^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bennett RA, Wilson DM 3rd, Wong D, Demple B. Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7166-9. PMID:9207062
↑ Matsumoto Y, Kim K, Katz DS, Feng JA. Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups. Biochemistry. 1998 May 5;37(18):6456-64. PMID:9572863 doi:10.1021/bi9727545
↑ DeMott MS, Beyret E, Wong D, Bales BC, Hwang JT, Greenberg MM, Demple B. Covalent trapping of human DNA polymerase beta by the oxidative DNA lesion 2-deoxyribonolactone. J Biol Chem. 2002 Mar 8;277(10):7637-40. Epub 2002 Jan 22. PMID:11805079 doi:10.1074/jbc.C100577200
↑ Parsons JL, Dianova II, Khoronenkova SV, Edelmann MJ, Kessler BM, Dianov GL. USP47 is a deubiquitylating enzyme that regulates base excision repair by controlling steady-state levels of DNA polymerase beta. Mol Cell. 2011 Mar 4;41(5):609-15. doi: 10.1016/j.molcel.2011.02.016. PMID:21362556 doi:10.1016/j.molcel.2011.02.016
↑ Kou Y, Koag MC, Lee S. N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J Am Chem Soc. 2015 Nov 11;137(44):14067-70. doi: 10.1021/jacs.5b10172. Epub 2015, Nov 2. PMID:26517568 doi:http://dx.doi.org/10.1021/jacs.5b10172

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5db8"

Categories: Human | Koag, M C | Lee, S | Human dna polymerase | Transferase-dna complex

@@ Line 1: / Line 1: @@
 ==Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dA==
 <StructureSection load='5db8' size='340' side='right' caption='[[5db8]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5db8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DB8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5db8]] 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=5DB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DB8 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMG:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-7-METHYL-6-OXO-6,9-DIHYDRO-1H-PURIN-7-IUM'>FMG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5db6|5db6]], [[5db7|5db7]], [[5db9|5db9]], [[5dba|5dba]], [[5dbb|5dbb]], [[5dbc|5dbc]]</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=5db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5db8 OCA], [http://pdbe.org/5db8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5db8 RCSB], [http://www.ebi.ac.uk/pdbsum/5db8 PDBsum]</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=5db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5db8 OCA], [http://pdbe.org/5db8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5db8 RCSB], [http://www.ebi.ac.uk/pdbsum/5db8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5db8 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 25: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Koag, M C]]
 [[Category: Lee, S]]
 [[Category: Human dna polymerase]]
 [[Category: Transferase-dna complex]]

5db8

From Proteopedia

Revision as of 14:06, 16 November 2017

Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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