This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1jj8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:39, 7 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1jj8.gif|left|200px]]
 
-
<!--
+
==Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations==
-
The line below this paragraph, containing "STRUCTURE_1jj8", creates the "Structure Box" on the page.
+
<StructureSection load='1jj8' size='340' side='right'caption='[[1jj8]], [[Resolution|resolution]] 2.75&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'>[[1jj8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JJ8 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]] 2.75&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></td></tr>
-
{{STRUCTURE_1jj8| PDB=1jj8 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jj8 OCA], [https://pdbe.org/1jj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jj8 RCSB], [https://www.ebi.ac.uk/pdbsum/1jj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jj8 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/HIN_SALTY HIN_SALTY] A DNA fragment of approximately 900 base pairs, adjacent to the fljB (H2) gene, which specifies the synthesis of phase-2 flagellin, can exist in either orientation with respect to fljB. The orientation of the inversion region controls expression of fljB. The hin gene occupies about two-thirds of the inversion region; it is required for the inversion of the fljB controlling region.
 +
== 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/jj/1jj8_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=1jj8 ConSurf].
 +
<div style="clear:both"></div>
-
'''Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations'''
+
==See Also==
-
 
+
*[[Resolvase 3D structures|Resolvase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The Hin recombinase specifically recognizes its DNA-binding site by means of both major and minor groove interactions. A previous X-ray structure, together with new structures of the Hin DNA-binding domain bound to a recombination half-site that were solved as part of the present study, have revealed that two ordered water molecules are present within the major groove interface. In this report, we test the importance of these waters directly by X-ray crystal structure analysis of complexes with four mutant DNA sequences. These structures, combined with their Hin-binding properties, provide strong support for the critical importance of one of the intermediate waters. A lesser but demonstrable role is ascribed to the second water molecule. The mutant structures also illustrate the prominent roles of thymine methyls both in stabilizing intermediate waters and in interfering with water or amino acid side chain interactions with DNA.
+
[[Category: Large Structures]]
-
 
+
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-
==About this Structure==
+
[[Category: Chiu TK]]
-
1JJ8 is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JJ8 OCA].
+
[[Category: Dickerson RE]]
-
 
+
[[Category: Johnson RC]]
-
==Reference==
+
[[Category: Sohn C]]
-
Testing water-mediated DNA recognition by the Hin recombinase., Chiu TK, Sohn C, Dickerson RE, Johnson RC, EMBO J. 2002 Feb 15;21(4):801-14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11847127 11847127]
+
-
[[Category: Single protein]]
+
-
[[Category: Chiu, T K.]]
+
-
[[Category: Dickerson, R E.]]
+
-
[[Category: Johnson, R C.]]
+
-
[[Category: Sohn, C.]]
+
-
[[Category: Hin recombinase]]
+
-
[[Category: I4 form 2]]
+
-
[[Category: Protein-dna complex]]
+
-
[[Category: Water-mediated recognition]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 21:17:25 2008''
+

Current revision

Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations

PDB ID 1jj8

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/1jj8"
Personal tools