7mz3: Difference between revisions

Latest revision as of 19:21, 18 October 2023

Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNAStructure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNA

Structural highlights

7mz3 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 2.418Å
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]

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

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OCA

[1] 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

[2] 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

[3] 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

[4] 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

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7mz3 is ON HOLD  until Paper Publication
+==Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNA==
+<StructureSection load='7mz3' size='340' side='right'caption='[[7mz3]], [[Resolution|resolution]] 2.42&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7mz3]] 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=7MZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MZ3 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]] 2.418&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DZM:3-DEAZA-3-METHYLADENINE'>DZM</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=7mz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mz3 OCA], [https://pdbe.org/7mz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mz3 RCSB], [https://www.ebi.ac.uk/pdbsum/7mz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mz3 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>
-Authors: Koag, M.-C., Lee, S.
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-Description: Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNA
+== References ==
-[[Category: Unreleased Structures]]
+<references/>
-[[Category: Lee, S]]
+__TOC__
-[[Category: Koag, M.-C]]
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Koag M-C]]
+[[Category: Lee S]]

7mz3: Difference between revisions

Latest revision as of 19:21, 18 October 2023

Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNAStructure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNA

Structural highlights

Function

See Also

References

Contents

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7mz3: Difference between revisions

Latest revision as of 19:21, 18 October 2023

Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNAStructure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNA

Structural highlights

Function

See Also

References

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