5iil

From Proteopedia

(Difference between revisions)

Revision as of 07:19, 3 June 2020

Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dG and incorporated dA

Structural highlights

5iil 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:	5iii, 5iij, 5iik, 5iim, 5iin, 5iio
Gene:	POLL (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.^[1] ^[2]

Publication Abstract from PubMed

8-oxo-7,8-dihydroxy-2'-deoxyguanosine (8-oxo-dG) has high mutagenic potential as it is prone to mispair with deoxyadenine (dA). In order to maintain genomic integrity, post-replicative 8-oxo-dG:dA mispairs are removed through DNA polymerase lambda (Pol lambda)-dependent MUTYH-initiated base excision repair (BER). Here, we describe seven novel crystal structures and kinetic data that fully characterize 8-oxo-dG bypass by Pol lambda. We demonstrate that Pol lambda has a flexible active site that can tolerate 8-oxo-dG in either the anti- or syn-conformation. Importantly, we show that discrimination against the pro-mutagenic syn-conformation occurs at the extension step and identify the residue responsible for this selectivity. This residue acts as a kinetic switch, shunting repair toward long-patch BER upon correct dCMP incorporation, thus enhancing repair efficiency. Moreover, this switch also provides a potential mechanism to increase repair fidelity of MUTYH-initiated BER.

A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG.,Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M EMBO J. 2016 Aug 1. pii: e201694332. PMID:27481934^[3]

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

References

↑ Garcia-Diaz M, Bebenek K, Kunkel TA, Blanco L. Identification of an intrinsic 5'-deoxyribose-5-phosphate lyase activity in human DNA polymerase lambda: a possible role in base excision repair. J Biol Chem. 2001 Sep 14;276(37):34659-63. Epub 2001 Jul 16. PMID:11457865 doi:10.1074/jbc.M106336200
↑ Maga G, Ramadan K, Locatelli GA, Shevelev I, Spadari S, Hubscher U. DNA elongation by the human DNA polymerase lambda polymerase and terminal transferase activities are differentially coordinated by proliferating cell nuclear antigen and replication protein A. J Biol Chem. 2005 Jan 21;280(3):1971-81. Epub 2004 Nov 10. PMID:15537631 doi:10.1074/jbc.M411650200
↑ Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M. A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG. EMBO J. 2016 Aug 1. pii: e201694332. PMID:27481934 doi:http://dx.doi.org/10.15252/embj.201694332

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/5iil"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dG and incorporated dA==
-<StructureSection load='5iil' size='340' side='right' caption='[[5iil]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
+<StructureSection load='5iil' size='340' side='right'caption='[[5iil]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5iil]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IIL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IIL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5iil]] 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=5IIL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IIL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <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=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5iii|5iii]], [[5iij|5iij]], [[5iik|5iik]], [[5iim|5iim]], [[5iin|5iin]], [[5iio|5iio]]</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=5iil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iil OCA], [http://pdbe.org/5iil PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iil RCSB], [http://www.ebi.ac.uk/pdbsum/5iil PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iil ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLL ([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://proteopedia.org/fgij/fg.htm?mol=5iil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iil OCA], [http://pdbe.org/5iil PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iil RCSB], [http://www.ebi.ac.uk/pdbsum/5iil PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iil ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 20: / Line 21: @@
 </div>
 <div class="pdbe-citations 5iil" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Burak, M J]]
 [[Category: Garcia-Diaz, M]]
 [[Category: Guja, K E]]
 [[Category: Transferase-dna complex]]

5iil

From Proteopedia

Revision as of 07:19, 3 June 2020

Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dG and incorporated dA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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