3kde: Difference between revisions

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<StructureSection load='3kde' size='340' side='right'caption='[[3kde]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
<StructureSection load='3kde' size='340' side='right'caption='[[3kde]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3kde]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. 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 [https://proteopedia.org/fgij/fg.htm?mol=3KDE FirstGlance]. <br>
<table><tr><td colspan='2'>[[3kde]] is a 3 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3KDE FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.74&#8491;</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 id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=3kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kde OCA], [https://pdbe.org/3kde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kde RCSB], [https://www.ebi.ac.uk/pdbsum/3kde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kde ProSAT]</span></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=3kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kde OCA], [https://pdbe.org/3kde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kde RCSB], [https://www.ebi.ac.uk/pdbsum/3kde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kde ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://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>
[https://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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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kde ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kde ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
THAP-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<ref>PMID:20010837</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3kde" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Drome]]
[[Category: Drosophila melanogaster]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Berger, J M]]
[[Category: Berger JM]]
[[Category: Lyubimov, A Y]]
[[Category: Lyubimov AY]]
[[Category: Rio, D C]]
[[Category: Rio DC]]
[[Category: Sabogal, A]]
[[Category: Sabogal A]]
[[Category: Beta-alpha-beta]]
[[Category: Dna binding protein-dna complex]]
[[Category: Dna integration]]
[[Category: Dna recombination]]
[[Category: Dna-binding]]
[[Category: Dna-binding domain]]
[[Category: Metal-binding]]
[[Category: P-element transposase]]
[[Category: Thap domain]]
[[Category: Zinc-finger]]

Latest revision as of 13:16, 21 February 2024

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

3kde is a 3 chain structure with sequence from Drosophila melanogaster. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.74Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

See Also

References

  1. ↑ Rio DC, Laski FA, Rubin GM. Identification and immunochemical analysis of biologically active Drosophila P element transposase. Cell. 1986 Jan 17;44(1):21-32. PMID:2416475
  2. ↑ Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC. THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Nat Struct Mol Biol. 2010 Jan;17(1):117-23. Epub 2009 Dec 13. PMID:20010837 doi:10.1038/nsmb.1742

3kde, resolution 1.74Å

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