2cdm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:03, 6 November 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2cdm.png|left|200px]]
 
-
<!--
+
==The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site==
-
The line below this paragraph, containing "STRUCTURE_2cdm", creates the "Structure Box" on the page.
+
<StructureSection load='2cdm' size='340' side='right'caption='[[2cdm]], [[Resolution|resolution]] 2.70&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'>[[2cdm]] is a 4 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=2CDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CDM 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]] 2.7&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_2cdm| PDB=2cdm | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cdm OCA], [https://pdbe.org/2cdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cdm RCSB], [https://www.ebi.ac.uk/pdbsum/2cdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cdm ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q47673_ECOLX Q47673_ECOLX]
 +
== 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/cd/2cdm_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2cdm ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
TrwC is a DNA strand transferase that catalyzes the initial and final stages of conjugative DNA transfer. We have solved the crystal structure of the N-terminal relaxase domain of TrwC in complex with a 27 base-long DNA oligonucleotide that contains both the recognition hairpin and the scissile phosphate. In addition, a series of ternary structures of protein-DNA complexes with different divalent cations at the active site have been solved. Systematic anomalous difference analysis allowed us to determine unambiguously the nature of the metal bound. Zn2+, Ni2+ and Cu2+ were found to bind the histidine-triad metal binding site. Comparison of the structures of the different complexes suggests two pathways for the DNA to exit the active pocket. They are probably used at different steps of the conjugative DNA-processing reaction. The structural information allows us to propose (i) an enzyme mechanism where the scissile phosphate is polarized by the metal ion facilitating the nucleophilic attack of the catalytic tyrosine, and (ii) a probable sequence of events during conjugative DNA processing that explains the biological function of the relaxase.
-
===THE STRUCTURE OF TRWC COMPLEXED WITH A 27-MER DNA COMPRISING THE RECOGNITION HAIRPIN AND THE CLEAVAGE SITE===
+
Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site.,Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, de la Cruz F J Mol Biol. 2006 May 5;358(3):857-69. Epub 2006 Feb 28. PMID:16540117<ref>PMID:16540117</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_16540117}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2cdm" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 16540117 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_16540117}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2CDM is a 4 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=2CDM OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:16540117</ref><ref group="xtra">PMID:14625590</ref><references group="xtra"/>
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Blanco, A G.]]
+
[[Category: Large Structures]]
-
[[Category: Boer, R.]]
+
[[Category: Blanco AG]]
-
[[Category: Coll, M.]]
+
[[Category: Boer R]]
-
[[Category: Cruz, F De La.]]
+
[[Category: Coll M]]
-
[[Category: Guasch, A.]]
+
[[Category: Guasch A]]
-
[[Category: Lucas, M.]]
+
[[Category: Lucas M]]
-
[[Category: Perez-Luque, R.]]
+
[[Category: Perez-Luque R]]
-
[[Category: Russi, S.]]
+
[[Category: Russi S]]
-
[[Category: Bacterial conjugation]]
+
[[Category: De la Cruz F]]
-
[[Category: Dna transfer]]
+
-
[[Category: Dna-protein complex]]
+
-
[[Category: Relaxase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:23:30 2009''
+

Current revision

The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site

PDB ID 2cdm

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/2cdm"
Personal tools