1jko: Difference between revisions

Revision as of 21:20, 2 May 2008

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

OverviewOverview

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.

About this StructureAbout this Structure

1JKO is a Single protein structure. Full crystallographic information is available from OCA.

ReferenceReference

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:11847127 Page seeded by OCA on Fri May 2 21:20:19 2008

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OCA

@@ Line 1: / Line 1: @@
 [[Image:1jko.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1jko |SIZE=350|CAPTION= <scene name='initialview01'>1jko</scene>, resolution 2.24&Aring;
+The line below this paragraph, containing "STRUCTURE_1jko", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
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+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1jko|  PDB=1jko  |  SCENE=  }}
-|RELATEDENTRY=[[1hcr|1HCR]], [[1ijw|1IJW]], [[1jj6|1JJ6]], [[1jj8|1JJ8]], [[1jkp|1JKP]], [[1jkq|1JKQ]], [[1jkr|1JKR]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jko OCA], [http://www.ebi.ac.uk/pdbsum/1jko PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jko RCSB]</span>
-}}
 '''Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations'''
@@ Line 19: / Line 16: @@
 ==About this Structure==
-JKO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKO OCA].
+JKO is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKO OCA].
 ==Reference==
@@ Line 28: / Line 25: @@
 [[Category: Johnson, R C.]]
 [[Category: Sohn, C.]]
-[[Category: a10g mutant]]
+[[Category: A10g mutant]]
-[[Category: hin recombinase]]
+[[Category: Hin recombinase]]
-[[Category: protein-dna complex]]
+[[Category: Protein-dna complex]]
-[[Category: water-mediated recognition]]
+[[Category: Water-mediated recognition]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 21:20:19 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:35:01 2008''