We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

2nra

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2nra" size="450" color="white" frame="true" align="right" spinBox="true" caption="2nra, resolution 3.10&Aring;" /> '''Crystal structure of...)
Current revision (00:10, 28 December 2023) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2nra.gif|left|200px]]<br /><applet load="2nra" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2nra, resolution 3.10&Aring;" />
 
-
'''Crystal structure of Pi initiator protein in complex with iteron DNA'''<br />
 
-
==Overview==
+
==Crystal structure of Pi initiator protein in complex with iteron DNA==
-
We have determined the crystal structure of a monomeric biologically, active form of the pi initiator protein of plasmid R6K as a complex with a, single copy of its cognate DNA-binding site (iteron) at 3.1-A resolution., The initiator belongs to the family of winged helix type of proteins. The, structure reveals that the protein contacts the iteron DNA at two primary, recognition helices, namely the C-terminal alpha4' and the N-terminal, alpha4 helices, that recognize the 5' half and the 3' half of the 22-bp, iteron, respectively. The base-amino acid contacts are all located in, alpha4', whereas the alpha4 helix and its vicinity mainly contact the, phosphate groups of the iteron. Mutational analyses show that the contacts, of both recognition helices with DNA are necessary for iteron binding and, replication initiation. Considerations of a large number of site-directed, mutations reveal that two distinct regions, namely alpha2 and alpha5 and, its vicinity, are required for DNA looping and initiator dimerization, respectively. Further analysis of mutant forms of pi revealed the possible, domain that interacts with the DnaB helicase. Thus, the structure-function, analysis presented illuminates aspects of initiation mechanism of R6K and, its control.
+
<StructureSection load='2nra' size='340' side='right'caption='[[2nra]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2nra]] 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=2NRA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NRA FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</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=2nra FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nra OCA], [https://pdbe.org/2nra PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nra RCSB], [https://www.ebi.ac.uk/pdbsum/2nra PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nra ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PIR_ECOLX PIR_ECOLX] Initiation for plasmid R6K DNA replication.
 +
== 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/nr/2nra_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=2nra ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We have determined the crystal structure of a monomeric biologically active form of the pi initiator protein of plasmid R6K as a complex with a single copy of its cognate DNA-binding site (iteron) at 3.1-A resolution. The initiator belongs to the family of winged helix type of proteins. The structure reveals that the protein contacts the iteron DNA at two primary recognition helices, namely the C-terminal alpha4' and the N-terminal alpha4 helices, that recognize the 5' half and the 3' half of the 22-bp iteron, respectively. The base-amino acid contacts are all located in alpha4', whereas the alpha4 helix and its vicinity mainly contact the phosphate groups of the iteron. Mutational analyses show that the contacts of both recognition helices with DNA are necessary for iteron binding and replication initiation. Considerations of a large number of site-directed mutations reveal that two distinct regions, namely alpha2 and alpha5 and its vicinity, are required for DNA looping and initiator dimerization, respectively. Further analysis of mutant forms of pi revealed the possible domain that interacts with the DnaB helicase. Thus, the structure-function analysis presented illuminates aspects of initiation mechanism of R6K and its control.
-
==About this Structure==
+
Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication.,Swan MK, Bastia D, Davies C Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18481-6. Epub 2006 Nov 21. PMID:17124167<ref>PMID:17124167</ref>
-
2NRA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2NRA OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication., Swan MK, Bastia D, Davies C, Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18481-6. Epub 2006 Nov 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17124167 17124167]
+
</div>
 +
<div class="pdbe-citations 2nra" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Bastia, D.]]
+
[[Category: Bastia D]]
-
[[Category: Davies, C.]]
+
[[Category: Davies C]]
-
[[Category: Swan, M.K.]]
+
[[Category: Swan MK]]
-
[[Category: dna replication]]
+
-
[[Category: protein-dna complex]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:51:40 2007''
+

Current revision

Crystal structure of Pi initiator protein in complex with iteron DNA

PDB ID 2nra

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/2nra"
Personal tools