2dvy
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:2dvy.jpg|left|200px]] | + | [[Image:2dvy.jpg|left|200px]] |
| - | + | ||
| - | '''Crystal structure of restriction endonucleases PabI''' | + | {{Structure |
| + | |PDB= 2dvy |SIZE=350|CAPTION= <scene name='initialview01'>2dvy</scene>, resolution 3.000Å | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of restriction endonucleases PabI''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 2DVY is a [ | + | 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== | ==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:// | + | 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: Single protein]] | ||
| Line 23: | Line 32: | ||
[[Category: restriction endonuclease]] | [[Category: restriction endonuclease]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:32:15 2008'' |
Revision as of 14:32, 20 March 2008
| |||||||
| , resolution 3.000Å | |||||||
|---|---|---|---|---|---|---|---|
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of restriction endonucleases PabI
Overview
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.
About this Structure
2DVY is a Single protein structure of sequence from Pyrococcus abyssi. Full crystallographic information is available from 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:17332011
Page seeded by OCA on Thu Mar 20 16:32:15 2008
