This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4ycx

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 15:44, 15 November 2017

Binary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate

Structural highlights

4ycx 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:	, , ,
Related:	4yd1, 4yd2
Gene:	POLM, polmu (HUMAN)
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPOLM_HUMAN] Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). Participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Among the many proteins used to repair DNA double-strand breaks by nonhomologous end joining (NHEJ) are two related family X DNA polymerases, Pol lambda and Pol micro. Which of these two polymerases is preferentially used for filling DNA gaps during NHEJ partly depends on sequence complementarity at the break, with Pol lambda and Pol micro repairing complementary and noncomplementary ends, respectively. To better understand these substrate preferences, we present crystal structures of Pol micro on a 2-nt gapped DNA substrate, representing three steps of the catalytic cycle. In striking contrast to Pol lambda, Pol micro "skips" the first available template nucleotide, instead using the template base at the 5' end of the gap to direct nucleotide binding and incorporation. This remarkable divergence from canonical 3'-end gap filling is consistent with data on end-joining substrate specificity in cells, and provides insights into polymerase substrate choices during NHEJ.

Creative template-dependent synthesis by human polymerase mu.,Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek K Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):E4530-6. doi:, 10.1073/pnas.1505798112. Epub 2015 Aug 3. PMID:26240373^[5]

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

References

↑ Nick McElhinny SA, Ramsden DA. Polymerase mu is a DNA-directed DNA/RNA polymerase. Mol Cell Biol. 2003 Apr;23(7):2309-15. PMID:12640116
↑ Ruiz JF, Juarez R, Garcia-Diaz M, Terrados G, Picher AJ, Gonzalez-Barrera S, Fernandez de Henestrosa AR, Blanco L. Lack of sugar discrimination by human Pol mu requires a single glycine residue. Nucleic Acids Res. 2003 Aug 1;31(15):4441-9. PMID:12888504
↑ Capp JP, Boudsocq F, Besnard AG, Lopez BS, Cazaux C, Hoffmann JS, Canitrot Y. Involvement of DNA polymerase mu in the repair of a specific subset of DNA double-strand breaks in mammalian cells. Nucleic Acids Res. 2007;35(11):3551-60. Epub 2007 May 5. PMID:17483519 doi:http://dx.doi.org/10.1093/nar/gkm243
↑ DeRose EF, Clarkson MW, Gilmore SA, Galban CJ, Tripathy A, Havener JM, Mueller GA, Ramsden DA, London RE, Lee AL. Solution structure of polymerase mu's BRCT Domain reveals an element essential for its role in nonhomologous end joining. Biochemistry. 2007 Oct 30;46(43):12100-10. Epub 2007 Oct 4. PMID:17915942 doi:10.1021/bi7007728
↑ Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek K. Creative template-dependent synthesis by human polymerase mu. Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):E4530-6. doi:, 10.1073/pnas.1505798112. Epub 2015 Aug 3. PMID:26240373 doi:http://dx.doi.org/10.1073/pnas.1505798112

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/4ycx"

@@ Line 1: / Line 1: @@
 ==Binary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate==
 <StructureSection load='4ycx' size='340' side='right' caption='[[4ycx]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ycx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YCX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ycx]] 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=4YCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YCX FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yd1|4yd1]], [[4yd2|4yd2]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLM, polmu ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></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=4ycx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ycx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ycx RCSB], [http://www.ebi.ac.uk/pdbsum/4ycx PDBsum]</span></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=4ycx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ycx OCA], [http://pdbe.org/4ycx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ycx RCSB], [http://www.ebi.ac.uk/pdbsum/4ycx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ycx ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4ycx" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 23: / Line 26: @@
 </StructureSection>
 [[Category: DNA-directed DNA polymerase]]
+[[Category: Human]]
 [[Category: Bebenek, K]]
 [[Category: Gosavi, R A]]

4ycx

From Proteopedia

Revision as of 15:44, 15 November 2017

Binary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox