3kde: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3kde]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KDE FirstGlance]. <br> | <table><tr><td colspan='2'>[[3kde]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KDE FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kde OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kde RCSB], [http://www.ebi.ac.uk/pdbsum/3kde 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=3kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kde OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kde RCSB], [http://www.ebi.ac.uk/pdbsum/3kde PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/PELET_DROME PELET_DROME]] P-element transposase that specifically mediates transposition of P-elements. Mediates both; precise and imprecise excision.<ref>PMID:2416475</ref> <ref>PMID:20010837</ref> | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.,Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC Nat Struct Mol Biol. 2010 Jan;17(1):117-23. Epub 2009 Dec 13. PMID:20010837<ref>PMID:20010837</ref> | THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.,Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC Nat Struct Mol Biol. 2010 Jan;17(1):117-23. Epub 2009 Dec 13. PMID:20010837<ref>PMID:20010837</ref> | ||
From | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
== References == | == References == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Drosophila melanogaster]] | [[Category: Drosophila melanogaster]] | ||
[[Category: Berger, J M | [[Category: Berger, J M]] | ||
[[Category: Lyubimov, A Y | [[Category: Lyubimov, A Y]] | ||
[[Category: Rio, D C | [[Category: Rio, D C]] | ||
[[Category: Sabogal, A | [[Category: Sabogal, A]] | ||
[[Category: Beta-alpha-beta]] | [[Category: Beta-alpha-beta]] | ||
[[Category: Dna binding protein-dna complex]] | [[Category: Dna binding protein-dna complex]] | ||
Revision as of 09:31, 25 December 2014
Crystal structure of the THAP domain from D. melanogaster P-element transposase in complex with its natural DNA binding siteCrystal structure of the THAP domain from D. melanogaster P-element transposase in complex with its natural DNA binding site
Structural highlights
Function[PELET_DROME] P-element transposase that specifically mediates transposition of P-elements. Mediates both; precise and imprecise excision.[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedTHAP-family C(2)CH zinc-coordinating DNA-binding proteins function in diverse eukaryotic cellular processes, such as transposition, transcriptional repression, stem-cell pluripotency, angiogenesis and neurological function. To determine the molecular basis for sequence-specific DNA recognition by THAP proteins, we solved the crystal structure of the Drosophila melanogaster P element transposase THAP domain (DmTHAP) in complex with a natural 10-base-pair site. In contrast to C(2)H(2) zinc fingers, DmTHAP docks a conserved beta-sheet into the major groove and a basic C-terminal loop into the adjacent minor groove. We confirmed specific protein-DNA interactions by mutagenesis and DNA-binding assays. Sequence analysis of natural and in vitro-selected binding sites suggests that several THAPs (DmTHAP and human THAP1 and THAP9) recognize a bipartite TXXGGGX(A/T) consensus motif; homology suggests THAP proteins bind DNA through a bipartite interaction. These findings reveal the conserved mechanisms by which THAP-family proteins engage specific chromosomal target elements. THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.,Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC Nat Struct Mol Biol. 2010 Jan;17(1):117-23. Epub 2009 Dec 13. PMID:20010837[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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