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.
3u7h
From Proteopedia
(Difference between revisions)
| (4 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:3u7h.jpg|left|200px]] | ||
| - | < | + | ==Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTTp)== |
| - | + | <StructureSection load='3u7h' size='340' side='right'caption='[[3u7h]], [[Resolution|resolution]] 2.00Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[3u7h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U7H FirstGlance]. <br> | |
| - | or | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | - | + | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yj5|1yj5]], [[3u7e|3u7e]], [[3u7f|3u7f]], [[3u7g|3u7g]]</div></td></tr> | |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pnkp ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=3u7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u7h OCA], [https://pdbe.org/3u7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u7h RCSB], [https://www.ebi.ac.uk/pdbsum/3u7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u7h ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/PNKP_MOUSE PNKP_MOUSE]] Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Polynucleotide kinase/phosphatase (PNKP) is a critical mammalian DNA repair enzyme that generates 5'-phosphate and 3'-hydroxyl groups at damaged DNA termini that are required for subsequent processing by DNA ligases and polymerases. The PNKP phosphatase domain recognizes 3'-phosphate termini within DNA nicks, gaps, or at double- or single-strand breaks. Here we present a mechanistic rationale for the recognition of damaged DNA termini by the PNKP phosphatase domain. The crystal structures of PNKP bound to single-stranded DNA substrates reveals a narrow active site cleft that accommodates a single-stranded substrate in a sequence-independent manner. Biochemical studies suggest that the terminal base pairs of double-stranded substrates near the 3'-phosphate are destabilized by PNKP to allow substrate access to the active site. A positively charged surface distinct from the active site specifically facilitates interactions with double-stranded substrates, providing a complex DNA binding surface that enables the recognition of diverse substrates. | ||
| - | + | Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates.,Coquelle N, Havali-Shahriari Z, Bernstein N, Green R, Glover JN Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21022-7. Epub 2011 Dec 14. PMID:22171004<ref>PMID:22171004</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | == | + | </div> |
| - | + | <div class="pdbe-citations 3u7h" style="background-color:#fffaf0;"></div> | |
| - | [[Category: | + | == References == |
| - | [[Category: Bernstein, N | + | <references/> |
| - | [[Category: Coquelle, N | + | __TOC__ |
| - | [[Category: Glover, J N.M | + | </StructureSection> |
| - | [[Category: Green, R | + | [[Category: Large Structures]] |
| - | [[Category: Havali, Z | + | [[Category: Lk3 transgenic mice]] |
| + | [[Category: Bernstein, N]] | ||
| + | [[Category: Coquelle, N]] | ||
| + | [[Category: Glover, J N.M]] | ||
| + | [[Category: Green, R]] | ||
| + | [[Category: Havali, Z]] | ||
[[Category: Dna repair]] | [[Category: Dna repair]] | ||
[[Category: Had family]] | [[Category: Had family]] | ||
Current revision
Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTTp)
| |||||||||||
