2dvy: Difference between revisions

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[[Image:2dvy.jpg|left|200px]]


{{Structure
==Crystal structure of restriction endonucleases PabI==
|PDB= 2dvy |SIZE=350|CAPTION= <scene name='initialview01'>2dvy</scene>, resolution 3.000&Aring;
<StructureSection load='2dvy' size='340' side='right'caption='[[2dvy]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[2dvy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DVY FirstGlance]. <br>
|ACTIVITY=  
</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&#8491;</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvy OCA], [https://pdbe.org/2dvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dvy RCSB], [https://www.ebi.ac.uk/pdbsum/2dvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvy ProSAT]</span></td></tr>
}}
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9V2B6_PYRAB Q9V2B6_PYRAB]


'''Crystal structure of restriction endonucleases PabI'''
==See Also==
 
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Although structures of many DNA-binding proteins have been solved, they fall into a limited number of folds. Here, we describe an approach that led to the finding of a novel DNA-binding fold. Based on the behavior of Type II restriction-modification gene complexes as mobile elements, our earlier work identified a restriction enzyme, R.PabI, and its cognate modification enzyme in Pyrococcus abyssi through comparison of closely related genomes. While the modification methyltransferase was easily recognized, R.PabI was predicted to have a novel 3D structure. We expressed cytotoxic R.PabI in a wheat-germ-based cell-free translation system and determined its crystal structure. R.PabI turned out to adopt a novel protein fold. Homodimeric R.PabI has a curved anti-parallel beta-sheet that forms a 'half pipe'. Mutational and in silico DNA-binding analyses have assigned it as the double-strand DNA-binding site. Unlike most restriction enzymes analyzed, R.PabI is able to cleave DNA in the absence of Mg(2+). These results demonstrate the value of genome comparison and the wheat-germ-based system in finding a novel DNA-binding motif in mobile DNases and, in general, a novel protein fold in horizontally transferred genes.
[[Category: Large Structures]]
 
==About this Structure==
2DVY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVY OCA].
 
==Reference==
Novel protein fold discovered in the PabI family of restriction enzymes., Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I, Nucleic Acids Res. 2007;35(6):1908-18. Epub 2007 Mar 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17332011 17332011]
[[Category: Pyrococcus abyssi]]
[[Category: Pyrococcus abyssi]]
[[Category: Single protein]]
[[Category: Endo Y]]
[[Category: Endo, Y.]]
[[Category: Kamo M]]
[[Category: Kamo, M.]]
[[Category: Kobayashi I]]
[[Category: Kobayashi, I.]]
[[Category: Miyazono K]]
[[Category: Miyazono, K.]]
[[Category: Nagata K]]
[[Category: Nagata, K.]]
[[Category: Sawasaki T]]
[[Category: Sawasaki, T.]]
[[Category: Tanokura M]]
[[Category: Tanokura, M.]]
[[Category: Watanabe M]]
[[Category: Watanabe, M.]]
[[Category: restriction endonuclease]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:32:15 2008''

Latest revision as of 13:48, 13 March 2024

Crystal structure of restriction endonucleases PabI

2dvy, resolution 3.00Å

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