2a0i

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[[Image:2a0i.gif|left|200px]]
[[Image:2a0i.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 2a0i |SIZE=350|CAPTION= <scene name='initialview01'>2a0i</scene>, resolution 2.72&Aring;
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The line below this paragraph, containing "STRUCTURE_2a0i", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY=
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or leave the SCENE parameter empty for the default display.
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|GENE= traI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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-->
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|DOMAIN=
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{{STRUCTURE_2a0i| PDB=2a0i | SCENE= }}
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|RELATEDENTRY=[[1p4d|1P4D]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a0i OCA], [http://www.ebi.ac.uk/pdbsum/2a0i PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2a0i RCSB]</span>
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}}
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'''F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA'''
'''F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA'''
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[[Category: Schildbach, J F.]]
[[Category: Schildbach, J F.]]
[[Category: 5-strand antiparallel beta sheet]]
[[Category: 5-strand antiparallel beta sheet]]
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[[Category: protein-dna complex]]
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[[Category: Protein-dna complex]]
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[[Category: single-stranded dna]]
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[[Category: Single-stranded dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:27:16 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:46:14 2008''
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Revision as of 15:27, 3 May 2008

Image:2a0i.gif

Template:STRUCTURE 2a0i

F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA


Overview

The TraI protein of conjugative plasmid F factor binds and cleaves a single-stranded region of the plasmid prior to transfer to a recipient. TraI36, an N-terminal TraI fragment, binds ssDNA with a subnanomolar K(D) and remarkable sequence specificity. The structure of the TraI36 Y16F variant bound to ssDNA reveals specificity determinants, including a ssDNA intramolecular 3 base interaction and two pockets within the protein's binding cleft that accommodate bases in a knob-into-hole fashion. Mutagenesis results underscore the intricate design of the binding site, with the greatest effects resulting from substitutions for residues that both contact ssDNA and stabilize protein structure. The active site architecture suggests that the bound divalent cation, which is essential for catalysis, both positions the DNA by liganding two oxygens of the scissile phosphate and increases the partial positive charge on the phosphorus to enhance nucleophilic attack.

About this Structure

2A0I is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase., Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF, Structure. 2005 Oct;13(10):1533-44. PMID:16216584 Page seeded by OCA on Sat May 3 18:27:16 2008

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