4ymo: Difference between revisions

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New page: '''Unreleased structure''' The entry 4ymo is ON HOLD Authors: Lee, s, Koag, M-C Description: Structure of human DNA polymerase beta complexed with N7BG in the template opposite to inco...
 
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'''Unreleased structure'''


The entry 4ymo is ON HOLD
==Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE==
<StructureSection load='4ymo' size='340' side='right'caption='[[4ymo]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4ymo]] 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=4YMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YMO 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]] 2.148&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0KX:2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE'>0KX</scene>, <scene name='pdbligand=7BG:2-AMINO-7-BENZYL-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-6-OXO-6,9-DIHYDRO-1H-PURIN-7-IUM'>7BG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=4ymo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ymo OCA], [https://pdbe.org/4ymo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ymo RCSB], [https://www.ebi.ac.uk/pdbsum/4ymo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ymo 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: Lee, s, Koag, M-C
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
Description: Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE
== References ==
[[Category: Unreleased Structures]]
<references/>
[[Category: Lee, S, Koag, M-C]]
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Koag M-C]]
[[Category: Lee S]]

Latest revision as of 16:04, 1 March 2024

Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITEStructure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE

Structural highlights

4ymo 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 2.148Å
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]

See Also

References

  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

4ymo, resolution 2.15Å

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