6btf

From Proteopedia

(Difference between revisions)

Current revision

DNA Polymerase Beta I260Q Ternary Complex

Structural highlights

6btf is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:	, ,
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

DNA polymerase beta (pol beta) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol beta must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair. Here, we use a combination of X-ray crystallography, fluorescence resonance energy transfer and nuclear magnetic resonance to show that pol beta's ability to access the appropriate conformations both before and upon binding to nucleotide substrates is integral to its fidelity. Importantly, we also demonstrate that the inability of the I260Q mutator variant of pol beta to properly navigate this conformational landscape results in error-prone DNA synthesis. Our work reveals that precatalytic conformational rearrangements themselves are an important underlying mechanism of substrate selection by DNA pol beta.

I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity.,Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublie S, Loria JP, Sweasy JB Nucleic Acids Res. 2018 Sep 17. pii: 5098607. doi: 10.1093/nar/gky825. PMID:30239932^[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
↑ Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublie S, Loria JP, Sweasy JB. I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity. Nucleic Acids Res. 2018 Sep 17. pii: 5098607. doi: 10.1093/nar/gky825. PMID:30239932 doi:http://dx.doi.org/10.1093/nar/gky825

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6btf"

Categories: Homo sapiens | Large Structures | Doublie S | Eckenroth BE

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6btf is ON HOLD  until Paper Publication
+==DNA Polymerase Beta I260Q Ternary Complex==
+<StructureSection load='6btf' size='340' side='right'caption='[[6btf]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6btf]] 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=6BTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BTF 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]] 1.75&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6btf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6btf OCA], [https://pdbe.org/6btf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6btf RCSB], [https://www.ebi.ac.uk/pdbsum/6btf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6btf 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 ==
+DNA polymerase beta (pol beta) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol beta must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair. Here, we use a combination of X-ray crystallography, fluorescence resonance energy transfer and nuclear magnetic resonance to show that pol beta's ability to access the appropriate conformations both before and upon binding to nucleotide substrates is integral to its fidelity. Importantly, we also demonstrate that the inability of the I260Q mutator variant of pol beta to properly navigate this conformational landscape results in error-prone DNA synthesis. Our work reveals that precatalytic conformational rearrangements themselves are an important underlying mechanism of substrate selection by DNA pol beta.
-Authors: Eckenroth, B.E., Doublie, S.
+I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity.,Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublie S, Loria JP, Sweasy JB Nucleic Acids Res. 2018 Sep 17. pii: 5098607. doi: 10.1093/nar/gky825. PMID:30239932<ref>PMID:30239932</ref>
-Description: DNA Polymerase Beta I260Q Ternary Complex
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Eckenroth, B.E]]
+<div class="pdbe-citations 6btf" style="background-color:#fffaf0;"></div>
-[[Category: Doublie, S]]
+==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]]

6btf

From Proteopedia

Current revision

DNA Polymerase Beta I260Q Ternary Complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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