3ecp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:00, 30 August 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3ecp.png|left|200px]]
 
-
<!--
+
==Crystal Structure Of Tn5 Transposase Complexed With 5' Phosphorylated Transposon End DNA==
-
The line below this paragraph, containing "STRUCTURE_3ecp", creates the "Structure Box" on the page.
+
<StructureSection load='3ecp' size='340' side='right'caption='[[3ecp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3ecp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ECP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ECP FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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></td></tr>
-
{{STRUCTURE_3ecp| PDB=3ecp | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ecp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ecp OCA], [https://pdbe.org/3ecp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ecp RCSB], [https://www.ebi.ac.uk/pdbsum/3ecp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ecp ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/TN5P_ECOLX TN5P_ECOLX] Mediates transposition of transposon Tn5 by a 'cut and paste' mechanism. First, the monomeric transposase binds the 19 bp inverted DNA repeats flanking the transposon. Then, dimerization of the DNA-bound transposase creates a synaptic DNA complex. After nicking of the first DNA strand, excision of the transposon proceeds through a series of intermediates. The transposase then mediates the insertion of the transposon at a new site by strand transfer. The activity of the wild-type transposase is very low, and is further inhibited by dimerization with the transposase inhibitor (inh).<ref>PMID:6260374</ref> <ref>PMID:6291786</ref> <ref>PMID:6303899</ref> <ref>PMID:1310499</ref> <ref>PMID:8226636</ref> <ref>PMID:8871560</ref> <ref>PMID:11877443</ref> <ref>PMID:12367522</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ec/3ecp_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=3ecp ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Bacterial DNA transposition is an important model system for studying DNA recombination events such as HIV-1 DNA integration and RAG-1-mediated V(D)J recombination. This communication focuses on the role of protein-phosphate contacts in manipulating DNA structure as a requirement for transposition catalysis. In particular, the participation of the nontransferred strand (NTS) 5' phosphate in Tn5 transposition strand transfer is analyzed. The 5' phosphate plays no direct catalytic role, nonetheless its presence stimulates strand transfer approximately 30-fold. X-ray crystallography indicates that transposase-DNA complexes formed with NTS 5' phosphorylated DNA have two properties that contrast with structures formed with complexes lacking the 5' phosphate or complexes generated from in-crystal hairpin cleavage. Transposase residues R210, Y319 and R322 of the (R)YREK motif coordinate the 5' phosphate rather than the subterminal NTS phosphate, and the 5' NTS end is moved away from the 3' transferred strand end. Mutation R210A impairs the 5' phosphate stimulation. It is posited that DNA phosphate coordination by R210, Y319 and R322 results in movement of the 5' NTS DNA away from the 3'-end thus allowing efficient target DNA binding. It is likely that this role for the newly identified RYR triad is utilized by other transposase-related proteins.
-
===Crystal Structure Of Tn5 Transposase Complexed With 5' Phosphorylated Transposon End DNA===
+
Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif.,Klenchin VA, Czyz A, Goryshin IY, Gradman R, Lovell S, Rayment I, Reznikoff WS Nucleic Acids Res. 2008 Oct;36(18):5855-62. Epub 2008 Sep 12. PMID:18790806<ref>PMID:18790806</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3ecp" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18790806}}, adds the Publication Abstract to the page
+
*[[Transposase|Transposase]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18790806 is the PubMed ID number.
+
*[[Transposase 3D structures|Transposase 3D structures]]
-
-->
+
== References ==
-
{{ABSTRACT_PUBMED_18790806}}
+
<references/>
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
3ECP is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ECP OCA].
+
-
 
+
-
==Reference==
+
-
Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif., Klenchin VA, Czyz A, Goryshin IY, Gradman R, Lovell S, Rayment I, Reznikoff WS, Nucleic Acids Res. 2008 Oct;36(18):5855-62. Epub 2008 Sep 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18790806 18790806]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Klenchin, V A.]]
+
[[Category: Large Structures]]
-
[[Category: Dna recombination/dna complex]]
+
[[Category: Klenchin VA]]
-
[[Category: Protein-dna complex]]
+
-
[[Category: Ribonuclease h-like motif]]
+
-
[[Category: Synaptic complex]]
+
-
[[Category: Transposase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 24 11:00:19 2008''
+

Current revision

Crystal Structure Of Tn5 Transposase Complexed With 5' Phosphorylated Transposon End DNA

PDB ID 3ecp

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ecp"
Personal tools