1dq3
From Proteopedia
(New page: 200px<br /><applet load="1dq3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dq3, resolution 2.10Å" /> '''CRYSTAL STRUCTURE OF...) |
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| - | [[Image:1dq3.gif|left|200px]]<br /><applet load="1dq3" size=" | + | [[Image:1dq3.gif|left|200px]]<br /><applet load="1dq3" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1dq3, resolution 2.10Å" /> | caption="1dq3, resolution 2.10Å" /> | ||
'''CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI'''<br /> | '''CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Inteins possess two different enzymatic activities, self-catalyzed protein | + | Inteins possess two different enzymatic activities, self-catalyzed protein splicing and site-specific DNA cleavage. These endonucleases, which are classified as part of the homing endonuclease family, initiate the mobility of their genetic elements into homologous alleles. They recognize long asymmetric nucleotide sequences and cleave both DNA strands in a monomer form. We present here the 2.1 A crystal structure of the archaeal PI-PfuI intein from Pyroccocus furiosus. The structure reveals a unique domain, designated here as the Stirrup domain, which is inserted between the Hint domain and an endonuclease domain. The horseshoe-shaped Hint domain contains a catalytic center for protein splicing, which involves both N and C-terminal residues. The endonuclease domain, which is inserted into the Hint domain, consists of two copies of substructure related by an internal pseudo 2-fold axis. In contrast with the I-CreI homing endonuclease, PI-PfuI possibly has two asymmetric catalytic sites at the center of a putative DNA-binding cleft formed by a pair of four-stranded beta-sheets. DNase I footprinting experiments showed that PI-PfuI covers more than 30 bp of the substrate asymmetrically across the cleavage site. A docking model of the DNA-enzyme complex suggests that the endonuclease domain covers the 20 bp DNA duplex encompassing the cleavage site, whereas the Stirrup domain could make an additional contact with another upstream 10 bp region. For the double-strand break, the two strands in the DNA duplex were cleaved by PI-PfuI with different efficiencies. We suggest that the cleavage of each strand is catalyzed by each of the two non-equivalent active sites. |
==About this Structure== | ==About this Structure== | ||
| - | 1DQ3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1DQ3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQ3 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: pi-pfui]] | [[Category: pi-pfui]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:19:17 2008'' |
Revision as of 10:19, 21 February 2008
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CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI
Overview
Inteins possess two different enzymatic activities, self-catalyzed protein splicing and site-specific DNA cleavage. These endonucleases, which are classified as part of the homing endonuclease family, initiate the mobility of their genetic elements into homologous alleles. They recognize long asymmetric nucleotide sequences and cleave both DNA strands in a monomer form. We present here the 2.1 A crystal structure of the archaeal PI-PfuI intein from Pyroccocus furiosus. The structure reveals a unique domain, designated here as the Stirrup domain, which is inserted between the Hint domain and an endonuclease domain. The horseshoe-shaped Hint domain contains a catalytic center for protein splicing, which involves both N and C-terminal residues. The endonuclease domain, which is inserted into the Hint domain, consists of two copies of substructure related by an internal pseudo 2-fold axis. In contrast with the I-CreI homing endonuclease, PI-PfuI possibly has two asymmetric catalytic sites at the center of a putative DNA-binding cleft formed by a pair of four-stranded beta-sheets. DNase I footprinting experiments showed that PI-PfuI covers more than 30 bp of the substrate asymmetrically across the cleavage site. A docking model of the DNA-enzyme complex suggests that the endonuclease domain covers the 20 bp DNA duplex encompassing the cleavage site, whereas the Stirrup domain could make an additional contact with another upstream 10 bp region. For the double-strand break, the two strands in the DNA duplex were cleaved by PI-PfuI with different efficiencies. We suggest that the cleavage of each strand is catalyzed by each of the two non-equivalent active sites.
About this Structure
1DQ3 is a Single protein structure of sequence from Pyrococcus furiosus with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI., Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K, J Mol Biol. 2000 Jul 21;300(4):889-901. PMID:10891276
Page seeded by OCA on Thu Feb 21 12:19:17 2008
